Optical properties of some freshwater phytoplanktonic algae

Measurements of absorption and scattering of light by pure cultures of some New Zealand freshwater phytoplankters have been made with a spectrophotometer. An integrating sphere accessory was used to capture most of the light scattered by an algal cell suspension and thus give an indication of the true absorption coefficient, with only a small correction required for residual scattering. The purpose of this study was to investigate the factors affecting the relationships of chlorophyll-a concentration to absorption and scattering by a diverse selection of algae. Qualitative differences in absorption spectra of the different phytoplankton studied here can be related to differences in pigment composition. Quantitative differences in the specific absorption coefficients (absorption coefficient divided by Chl-a concentration) at the Chl-a red peak (676 nm in vivo) are explained in terms of different extents of packaging of pigment in cells or cell aggregates in the different cultures. Qualitative differences in scattering spectra are explained in terms of optical size of the particulates comprising the pure cultures. The green and diatom cultures displayed a complex-shaped but non-trending scattering spectrum with minima (troughs) in scattering associated with maxima (peaks) in absorption. The blue-green cultures behaved as optically small particles and displayed a pattern of decreasing scattering with increasing wavelength. Quantitative differences in specific scattering coefficients (scattering coefficient divided by Chl-a concentration) were related mainly to differences in the effective ratio of surface areas to Chl-a content of scattering centres in the different cultures. Overall, however, the specific absorption and scattering coefficients at any given wavelength were less variable between cultures than expected suggesting that the common assumption that absorption and scattering by the algal component of a lake water depends only on the Chl-a concentration may be a justifiable first approximation in field studies.     

Interactions of photosynthetic pigments in monolayers at a water-air interface

Summary The compression of mixtures of photosynthetic pigments and phosphatidylcholine in monolayers at a water-air interface shows that (i) the phosphatidylcholine disperses the isolated pigment molecules; (ii) chlorophyllsa andb, chlorophylla and -carotene, and chlorophyllb and -carotene form associations which cannot be undone by the phospholipids; and (iii) when the two chlorophylls and -carotene are mixed all together with or without phosphatidylcholine, the three types of associations are ideally mixed and they can be dispersed by phosphatidylcholine.     

Predicting the summer chlorophylla concentration in a reservoir based on the environmental conditions of the preceding spring

From a monthly survey over a ten-year period (1983–1992) of the Ishitegawa Reservoir, Japan, two multiple regression equations describing the mean chlorophylla (Chl-a) concentration at 0.5 m depth during July, August and September (C _S ) and the maximum Chl-a concentration in the photic zone, including its subsurface maximum during this period (C _M ), were obtained. The conductivity at 0.5 m depth in May and the mean air temperature during May or during May and June were used as independent variables. These equations were calculated using seven years of data (1983–1988 and 1992). From 1989 to 1991 two impermeable plastic-coated sheet fences were installed across the upper end of the reservoir along the top 5 m of water column. The equations were used to determine the effectiveness of this flow regulation on the summer Chl-a concentration. In 1989 and 1991, when the fences were in place from June to August, no effects were found on the observed C _S and C _M values. In 1990, when the fences had been in place since October 1989, the observed values were lower than the predicted values.     

Influence of suspended particulate matter on nutrient biogeochemistry of a tropical shallow lagoon,Chilika, India

The behaviour of suspended particulate matter (SPM), salinity profile, dissolved nutrients, total (T.Chl-a) and size fractionated chlorophyll-a (F.Chl-a) were studied seasonally at Chilika Lagoon, east coast of India, during 2008–2009. The study showed large spatio-temporal variations among these parameters. The concentration of dissolved inorganic nitrogen and inorganic phosphate were found to be maximum during the monsoon, followed by post- and pre-monsoon, although the mean N:P ratios, which indicate the relative availability of N with respect to P, were 9.13 ± 3.09, 16.57 ± 11.53 and 5.47 ± 3.13, respectively. It was evident from the results that during pre-monsoon and postmonsoon, the lagoon exhibits nitrogen limitation. Mean T.Chl-a biomass in the lagoon showed distinct seasonality with maximum values during the pre-monsoon (23.12 ± 9.75 mg m^?3) followed by monsoon and post-monsoon. Irrespective of seasons, maximum T.Chl-a was found in the northern part of the lagoon. SPM concentrations during the monsoon were relatively higher in the freshwater dominated zones compared to seawater dominated areas, indicating its riverine sources. The correlation between SPM and various dissolved nutrients (p < 0.05) suggests its influence on the physico-chemical conditions at varying levels. It is summarized that seasonal variation of SPM and nutrients contributed by rivers, wind induced re-suspension events and in situ  regeneration processes play a crucial role in the lagoon biogeochemical cycle.     

H2 production from maltose derived from starch using the visible light, photosensitization of Mg chlorophyll-a from Spirulina

A photoinduced H₂ production system, coupling d-maltose degradation by glucoamylase and glucose dehydrogenase (GDH) and H₂ production with colloidal platinum as a catalyst using the visible light-induced photosensitization of Mg chlorophyll-a (Mg Chl-a), has been developed. H₂ production was continuous when the reaction mixture containing d-maltose, glucoamylase, GDH, NAD⁺, Mg Chl-a, Methyl Viologen (MV²⁺, an electron relay reagent) and colloidal platinum was irradiated by visible light. The amount of H₂ production was estimated to be 5 ± 0.5 mol after 4 h irradiation. The yield of the conversion of d-maltose to H₂ in this system was ca. 1.8 %.     

Deposition behavior and photoelectrochemical characteristics of chlorophylla Langmuir-Blodgett films

The deposition behavior and photoelectric response characteristics of chlorophylla (Chla) monolayers and multilayers were investigated under various film fabrication conditions. Chla LB films were deposited onto quartz and pretreated ITO glass substrates under several fabrication conditions, including surface pressure and number of layers. The absorption spectra of Chla in a solution state and solid-like state (LB films) were fairly consistent with each other, and two absorption peaks were found at 678 and 438 nm, respectively. The prepared Chla LB films were set into an electrochemistry cell equipped with a Pt plate as the counter electrode, and the photoelectric response characteristics were obtained and analyzed relative to the light illumination. By considering the resulting photocurrents, the optimal fabrication conditions for Chla LB films were determined as 20 mN/m of surface pressure and 20 layers. The action spectrum of the Chla LB films was obtained in the visible region, and was found to be in good agreement with the absorption spectrum. The possible application of the proposed system as a constituent of an artificial color recognition device was suggested based on combining with the photoelectric conversion property of another lightsensitive biological pigment.     

Simultaneous photoreduction and photooxidation of cytochrome b-559 in Photosystem II treated with carbonylcyanide-m-chlorophenylhydrazone

The possibility of a Photosystem II (PS II) cyclic electron flow via Cyt b-559 catalyzed by carbonylcyanide m-chlorophenylhydrazone (CCCP) was further examined by studying the effects of the PS II electron acceptor 2,6-dichloro-p-benzoquinone (DCBQ) on the light-induced changes of the redox states of Cyt b-559. Addition to barley thylakoids of micromolar concentrations of DCBQ completely inhibited the changes of the absorbance difference corresponding to the photoreduction of Cyt b-559 observed either in the presence of 10 M ferricyanide or after Cyt b-559 photooxidation in the presence of 2 M CCCP. In CCCP-treated thylakoids, the concentration of photooxidized Cyt b-559 decreased as the irradiance of actinic light increased from 2 to 80 W m^-2 but remained close to the maximal concentration (0.53 photooxidized Cyt b-559 per photoactive Photosystem II) in the presence of 50 M DCBQ. The stimulation of Cyt b-559 photooxidation in parallel with the inhibition of its photoreduction caused by DCBQ demonstrate that the extent of the light-induced changes of the redox state of Cyt b-559 in the presence of CCCP is determined by the difference between the rates of photooxidation and photoreduction of Cyt b-559 occuring simultaneously in a cyclic electron flow around PS II.We also observed that the Photosystem I electron acceptor methyl viologen (MV) at a concentration of 1 mM barely affected the rate and extent of the light-induced redox changes of Cyt b-559 in the presence of either FeCN or CCCP. Under similar experimental conditions, MV strongly quenched Chl-a fluorescence, suggesting that Cyt b-559 is reduced directly on the reducing side of Photosystem II.Abbreviations ADRY acceleration of the deactivation reactions of the water-splitting system Y - ANT-2p 2-(3-chloro-4-trifluoromethyl)anilino-3,5-dinitrothiophene - CCCP carbonylcyanide-m-chlorophenylhydrazone - DCBQ 2,6-dichloro-p-benzoquinone - FeCN ferricyanide - MV methyl viologen - P₆₈₀ Photosystem II reaction center Chl-a dimer CIW-DPB publication No. 1118.     

Some properties of chlorophylla at hydrocarbon-water interfaces and in black lipid membranes

Summary Chlorophylla is very surface active in the system 2,2,4-trimethylpentanewater. The standard free energy of adsorption may be as high as 10.6 kcal/mole. However, chlorophyll adsorption at this interface is unable to stabilize black membranes. Black films formed from solutions of glyceryl monooleate and chlorophylla exhibit a weak fluorescence which indicates that a small amount of pigment, ca. 1 to 2% by area, may be contained in the membranes. Calculations based on adsorption data show that inclusion of somewhat more chlorophylla than this might be expected. However, interfacial tension data for mixed solutions do not support this expectation.Whether or not they are illuminated, black lipid membranes formed from mixed solutions of chlorophylla and glyceryl monooleate have electrical properties indistinguishable from those of films made in the absence of pigment.     

Isolation of membrane bound light-harvesting-complexes from the dinoflagellates Heterocapsa pygmaea and Prorocentrum minimum

We have isolated Chl a-Chl c-carotenoid binding proteins from the dinoflagellates Prorocentrum minimum and Heterocapsa pygmaea grown under high (500 mol m^–2 s^–1, HL) and low (35 mol m^–2 s^–1, LL) light conditions. We compared various isolation procedures of membrane bound light harvesting complexes (LHCs) and assayed the functionality of the solubilized proteins by determining the energy transfer efficiency from the accessory pigments to Chl a by means of fluorescence excitation spectra. The identity of the newly isolated protein-complexes were confirmed by immunological cross-reactions with antibodies raised against the previously described membrane bound Chl a-c proteins (Boczar et al. (1980) FEBS Lett 120: 243–247). Spectroscopic analysis demonstrated the relatedness of these proteins with the recently described Chl-a-c ₂-peridinin (ACP) binding protein (Hiller et al. (1993) Photochem Photobiol 57: 125–131; Iglesias Prieto et al. (1993) Phil Trans R Soc London B 338: 381–392). The water-soluble peridinin-Chl a binding-protein (PCP) was not detectable in P. minimum. Two functional forms of ACP with different pigmentation were isolated. A variant of ACP which was isolated from high-light grown cells, that specifically binds increased amounts of diadinoxanthin was compared to the previously described ACPs that bind proportionately more peridinin.Abbreviations ACP Chl a-Chl c-peridinin binding protein - AEBSF 4-(2-aminoethyl)-benzenesulfonyl fluoride hydrochloride - DDM dodecyl -d maltoside - Deriphat 160 N-lauryl-beta-iminopropionic acid - HEPES (N-2-hydroxyethylpiparizine-N-2-ethanesulphonic acid) - HL high light (500 mol m^–2 s^–1) - LL low light (35 mol m^–2 s^–1) - ₇₃₀ fluorescence yield (emission at 730 nm) - PCP peridinin-Chl a-binding protein - PMSF phenyl-methyl-sulfonyl-fluoride - PS I Photosystem I - PS II Photosystem II     

Mating reaction in Saccharomyces cerevisiae

Summary Haploid Saccharomyces yeasts showed sexual agglutination when a and type cells were mixed. Two types of a type strains were found; one constitutive and the other inducible concerning agglutinability. In type strains, no such differentiation was observed. Agglutination was inhibited by protease treatment. Secretion from type cells induced agglutinability in inducible a type cells. The activity of the secreted principle was heat-stable. The secretion is thought to induce de novo synthesis of proteinous sex-specific substances or to uncover preexisting sex substances.     

Factors affecting the accuracy of chlorophylla andb determination by means of their paper chromatographic separation and colorimetric measurement in eluates

Quantitative determination of chlorophyll a and β can be made by paper chromatography of acetone extracts of plant material with colorimetric measurement of the eluates from the separated zones. From the suitable solvent systems which give adequate separation of the pigments at a distance of 20 cm. from the start,Hager's mixture (1955) separates the chlorophylls better than the toluene-isopropanol (400: 1 v/v.) mixture, which, however, is better for the separation of carotenoids. Twice the amount of chlorophyll is separated on Whatman 31 ET paper, equally well and with the same time of development, as on Whatman No. 3 paper, on which it is possible to separate a maximum of about 15 μg of chlorophyll pigments per 1 em. start length. Losses on elution are, however, higher on using Whatman 31 ET paper. In plants with a high chlorophyllase activity, the error of determining chlorophyll a andb is greatly reduced if the leaves are placed for 1 min. in boiling water before extraction. For elution of chlorophylla andb from paper it is better to use anhydrous acetone, for chlorophyllides 80% acetone. A comparison of the procedure investigated with the method of two-wave length spectrophotometric measurement of crude acetone extracts showed that in view of the average 10% loss, the chromatographic method is hardly suitable for determining the absolute amounts of chlorophylla andb, although the relation (a/b) can be determined with similar precision by both methods. Moreover, in view of the greater amount of work involved the chromatographic method can only be recommended for confirming the results of spectrophotometrie determination. Quantitative determination of chlorophylls from the area of the spot or from the "R_F" value can only be of an informative character.     

Folded chromosomes of mating-factor arrested yeast cells: comparison with G0 arrest

Folded chromosomes of haploid a or diploid aa cells arrested by -factor are characterized by a heterogeneous sedimentation distribution, distinguishable from the corresponding g ₀and g ₁ structures. The extent of heterogeneity appears to depend in part on the extent of the characteristic schmoe morphology. Under conditions where a and mating-type cells are mixed together without conjugation, folded chromosomes characteristic of -factor arrested a and aa cells appear in both cell types in a synchronous manner. Attempts to order G₀ and -factor arrest suggest that these two arrest stages represent two different branch pathways out of the cell cycle. These two branch pathways may have a common branch point, or they may be characterized by two different branch points.     

Reduction of vinyl groups in naturally occurring chlorophylls-a

3,8-Divinyl-chlorophyll(Chl)-a possessing a phytyl ester was hydrogenated in acetone by rhodium catalyst on alumina to afford 3-vinyl-8-ethyl-, 3-ethyl-8-vinyl- and 3,8-diethyl-Chls. The ratio of produced 3-ethyl-8-vinyl- over 3-vinyl-8-ethyl-Chls was determined to be 1.2, indicating that the reactivity of the 3-vinyl group was slightly higher than that of the 8-vinyl group. Catalytic hydrogenation of divinyl-protochlorophyll-a possessing a porphyrin ??-skeleton (C17C18) instead of the above chlorin moiety (C17H-C18H) gave an equal amount of mono-reduced regioisomers. The slight (or no) selectivity is different from that in the enzymatic reduction of divinyl-(proto)chlorophyllides-a lacking a phytyl ester in the biosynthetic pathway of Chl-a where the sole 8-vinyl group is transformed to the ethyl group.     

Tuning Energy Transfer in the Peridinin–chlorophyll Complex by Reconstitution with Different Chlorophylls

In vitro studies of the carotenoid peridinin, which is the primary pigment from the peridinin chlorophyll-a protein (PCP) light harvesting complex, showed a strong dependence on the lifetime of the peridinin lowest singlet excited state on solvent polarity. This dependence was attributed to the presence of an intramolecular charge transfer (ICT) state in the peridinin excited state manifold. The ICT state was also suggested to be a crucial factor in efficient peridinin to Chl-a energy transfer in the PCP complex. Here we extend our studies of peridinin dynamics to reconstituted PCP complexes, in which Chl-a was replaced by different chlorophyll species (Chl-b, acetyl Chl-a, Chl-d and BChl-a). Reconstitution of PCP with different Chl species maintains the energy transfer pathways within the complex, but the efficiency depends on the chlorophyll species. In the native PCP complex, the peridinin S₁/ICT state has a lifetime of 2.7 ps, whereas in reconstituted PCP complexes it is 5.9 ps (Chl-b) 2.9 ps (Chl-a), 2.2 ps (acetyl Chl-a), 1.9 ps (Chl-d), and 0.45 ps (BChl-a). Calculation of energy transfer rates using the Förster equation explains the differences in energy transfer efficiency in terms of changing spectral overlap between the peridinin emission and the absorption spectrum of the acceptor. It is proposed that the lowest excited state of peridinin is a strongly coupled S₁/ICT state, which is the energy donor for the major energy transfer channel. The significant ICT character of the S₁/ICT state in PCP enhances the transition dipole moment of the S₁/ICT state, facilitating energy transfer to chlorophyll via the Förster mechanism. In addition to energy transfer via the S₁/ICT, there is also energy transfer via the S₂ and hot S₁/ICT states to chlorophyll in all reconstituted PCP complexes.     

Spectroscopic Characterization of the Excitation Energy Transfer in the Fucoxanthin–Chlorophyll Protein of Diatoms

We characterized the energy transfer pathways in the fucoxanthin–chlorophyll protein (FCP) complex of the diatom Cyclotella meneghiniana by conducting ultrafast transient absorption measurements. This light harvesting antenna has a distinct pigment composition and binds chlorophyll a (Chl-a), fucoxanthin and chlorophyll c (Chl-c) molecules in a 4:4:1 ratio. We find that upon excitation of fucoxanthin to its S₂ state, a significant amount of excitation energy is transferred rapidly to Chl-a. The ensuing dynamics illustrate the presence of a complex energy transfer network that also involves energy transfer from the unrelaxed or ‘hot’ intermediates. Chl-c to Chl-a energy transfer occurs on a timescale of a 100 fs. We observe no significant spectral evolution in the Chl-a region of the spectrum. We have applied global and target analysis to model the measured excited state dynamics and estimate the spectra of the states involved; the energy transfer network is discussed in relation to the pigment organization of the FCP complex.     

Chemical modification ofPseudomonas fluorescens malonyl-CoA synthetase by diethylpyrocarbonate: Kinetic evidence for an essential histidyl residue on alpha subunit

Malonyl-CoA synthetase fromPseudomonas fluorescens was inactivated by diethylpyrocarbonate (DEP) with the second-order rate constant of 775 M^–1 min^–1 atpH 7.0, 25°C, showing a concomitant increase in absorbance at 242 nm due to the formation of N-carbethoxyhistidyl derivatives. The inactivated enzyme at low concentration of DEP (<0.2 mM) could be completely reactivated by hydroxylamine but not completely reactivated at high concentration (>0.5 mM), indicating that there may be another functional group modified by DEP. Complete inactivation of malonyl-CoA synthetase required the modification of seven residues per molecule of enzyme; however, only one is calculated to be essential for enzyme activity by a statistical analysis of the residual enzyme activity.pH dependence of inactivation indicated the involvement of a residue with apK _a of 6.7, which is closely related to that of histidyl residue of proteins. Whena subunit treated with DEP was mixed with subunits complex, the enzyme activity completely disappeared, whereas when subunit complex treated with the reagent was mixed witha subunit, the activity remained. Inactivation of the enzyme by the reagent was protected by the presence of malonate and ATP. These results indicate that a catalytically essential histidyl residue is located at or near the malonate and ATP binding region ona subunit of the enzyme.     

Synthesis and antimicrobial activity of some new N-glycosides of 2-thioxo-4-thiazolidinone derivatives

5-Arylidene-2-thioxo-4-thiazolidinones 3a-f react with each of 2,3,4,6-tetra-O-acetyl-α-d-glucopyranosyl and α-d-galactopyranosyl bromides 4a,b in acetone in the presence of aqueous potassium hydroxide at room temperature to afford N-(2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl) or N-(2,3,4,6-tetra-O-acetyl-β-d-galactopyranosyl) 2-thioxo-4-thiazolidinone derivatives 5a-f. Similarly, the reaction of 5-cycloalkylidene-2-thioxo-4-thiazolidinones 7a,b with 4a gave the corresponding N-glucosides 8a,b. Also, 5-pyrazolidene rhodanines 10a-e react with 4a to afford the new N-glucosides 11a-e. Treatment of compounds 15 and 16 with 4a in the presence of few drops of triethylamine or in KOH solution accomplished the mono- and bis-nucleosides 17 and 18, respectively. Some selected products were tested for their antimicrobial activities.     

Deep chlorophyll-<Emphasis Type="Italic">a</Emphasis> maxima (DCMs) in Antarctic waters

The US Antarctic Marine Living Resources (AMLR) program has, since 1990, conducted annual surveys from early January through mid-March in a large sampling grid around Elephant Island, Antarctica. Approximately 100 hydrographic stations were occupied twice during each field season, with physical, chemical, optical, and biological data acquired from the surface to 750 m depth or to within 10 m of the bottom at shallower stations. During these 14 years, most of the stations in pelagic waters to the northwest of Elephant Island had very low chlorophyll-a (Chl-a) concentrations (<0.2 mg m^–3) in the upper mixed layer (UML) of ~45 m, but a deep chlorophyll-a maximum (DCM) existed between 50 and 100 m, with a peak at approximately 75 m. This was in contrast to adjacent stations which had higher Chl-a concentrations (approximately 1.0 mg m^–3) in the UML and no DCM. We provide evidence that the higher Chl-a concentrations that occur at depths of 50–100 m result from increased photosynthetic activity and not from a passive sinking of cells from the UML or by the intrusion of Chl-a rich coastal waters. Data to support this conclusion include (1) elevated dissolved oxygen concentrations between 50 and 100 m, (2) evidence of active photosynthesis at the depth of the DCM as indicated by increased natural upwelling radiation at 683 nm, and (3) water samples obtained from the DCM at 75 m and incubated under simulated conditions of temperature and light had assimilation numbers of approximately 1.0–1.5 mg carbon fixed per milligram Chl-a per hour. DCMs occur in the same depth range as the temperature minimum layer (TML) (the winter remnant of Antarctic surface water, AASW), which is known to have elevated concentrations of inorganic nutrients essential for growth of phytoplankton. Our data indicate that a DCM develops as a result of (1) depletion of iron (Fe) in the UML with the onset of the summer season, and (2) growth of phytoplankton in the TML where both Fe concentrations and solar irradiance levels are high enough to permit an increase of phytoplankton biomass.     

Chromosomal loci of genes controlling site-specific restriction endonucleases of Bacillus subtilis

Summary In Saccharomyces cerevisiae, diploid strains which are respiratory deficient (e.g., rho^–) or are homozygous for the mating-type locus (i.e., either a/a or /) are unable to sporulate. In order to induce sporulation in these nonsporulating strains, the technique of protoplast fusion mediated by polyethylene glycol was adopted. In this study, the products of protoplast fusion were induced to sporulate without reversion to normal cells.Protoplasts from a respiratory-deficient diploid strain were mixed with those from a respiratory-competent haploid one carrying mitochondrial drug resistance markers, treated with 30% polyethylene glycol-4000 and 25 mM CaCl₂, and incubated in 0.1 M potassium acetate containing 0.8 M sorbitol as an osmotic stabilizer. After two days' incubation, asci with three to eight spores were formed at a frequency of 1×10^–3 to 2×10^–4. Sporulation was also observed in products of fusion between an a/a diploid and haploid strains and between an / diploid and a haploid strains. The analysis of the genotypes of spores revealed that when fusion products were cultured under conditions for sporulation, karyogamy did not take place, diploid nuclei underwent meiosis, and both diploid and haploid nuclei were able to develop into spores.     

Distance-constraint approach to protein folding. I. Statistical analysis of protein conformations in terms of distances between residues

A statistical analysis of protein conformations in terms of the distance between residues, represented by their C atoms, is presented. We consider four factors that contribute to the determination of the distanced _i,i+k between a given pair ofith and(i+k)th residues in the native conformation of a globular protein: (1) the distancek along the chain, (2) the size of the protein, (3) the conformational states of theith to(i+k)th residues, and (4) the amino acid types of the and(i+k)th residues. In order to account for the dependence on the distancek along the chain, the statistics are taken for three ranges, viz., short, medium, and long ranges (k8; 9k20; andk21; respectively). In the statistics of short-range distances, a mean distanceD _k and its standard deviationS _k are calculated for each value ofk, with and without taking into account the conformational states of all residues fromi toi+k (factors 1 and 3). As an Appendix, the relations for converting from the distances between residues into other conformational parameters are discussed. In the statistics of long-range distances, a reduced distanced* _ij (the actual distance divided by the radius of gyration) is used to scale the data so that they become independent of protein size, and then a mean reduced distanceD _l (a, a) and its standard deviation _l (a, a) are calculated for each amino acid pair (a, a) (factors 2 and 4). The effect of the neighboring residues along the chain on the value of the distanced* _ij is explored by a linear regression analysis between the actual reduced distanced* _ij and the mean value over theD _l for all possible pairs of residues in the two segments of the (i–2)th to the (i+2)th and the (j–2)th to the (j+2)th residues. The effect is assessed in terms of the tangentA _l (a, a) of the calculated regression line for each amino acid pair (a, a). In the statistics of medium-range distances, only factors 1 and 4 are considered, to simplify the analysis. The scaled distanced _i,i+k =(d _i,i+k -D _k )/S _k is used to eliminate the dependence onk, the distance along the chain. The propertiesD _m (a, a), _m (a, a) andA _m (a, a) corresponding toD _l (a, a), _l (a, a), andA _l (a, a), and also calculated for each amino acid pair (a, a). The results are interpreted as follows: the smaller values ofD _l (a, a) andD _m (a, a) indicate a preference of the pair (a, a) for a contact (e.g., pairs between hydrophobic amino acids, and pairs of Cys with aromatic amino acids), and the larger values of these quantities indicate a preference for distant mutual location (e.g., pairs between strong hydrophilic amino acids); the smaller values of _l (a, a) and _m (a, a) indicate a strong preference for either contact or noncontact (e.g., pairs between hydrophobic amino acids, and pairs between strong hydrophobic and hydrophilic amino acids, respectively), and the larger values of these quantities indicate the ambivalent/neutral nature of the preference for contact and noncontact (e.g., pairs containing Ser or Thr); the smaller values ofA _l (a, a) andA _m (a, a) indicate that the distance of an (a, a) pair is determined independently of the amino acid character of the neighboring residues along the chain (e.g., some pairs of Cys or Met with other amino acids) and the larger values of these quantities indicare that such amino acid character contributes strongly to the determination of the distance (e.g., pairs containing Ser or Thr, and pairs between amino acids with small side chains). The difference between the statistics for the long- and medium-range distances is also discussed; the former reflect the difference between the hydrophobic and hydrophilic character of the residues, but the latter cannot be easily interpretable only in terms of hydrophobicity and hydrophilicity. The data analyzed here are used in the optimization of an object function to compute protein conformation in a subsequent paper.