Contacts of the strand formed by residues 758 - 762 (chain A) in PDB entry 6S1M


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with SER 758 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600A  THR*     4.4    13.5    -      -       -      -
    601A  LEU      3.5     6.1    -      -       -      -
    602A  ASP*     3.7    15.5    -      -       -      -
    728A  ILE*     4.1     4.0    -      -       -      +
    754A  GLY*     3.3    20.8    -      -       -      -
    755A  ASP*     3.4    15.1    +      -       -      +
    757A  ASP*     1.3    89.8    +      -       -      +
    759A  VAL*     1.3    69.4    +      -       -      +
    760A  MET*     5.0    10.4    -      -       -      +
     25P  DOC      5.0     6.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 759 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    587A  ILE*     5.2     4.7    -      -       +      -
    599A  ALA      3.6     2.1    -      -       -      +
    600A  THR*     3.4     3.2    -      -       -      -
    601A  LEU*     2.9    43.0    +      -       +      +
    603A  PHE*     6.3     0.9    -      -       +      -
    728A  ILE*     4.6    13.7    -      -       +      +
    731A  THR*     3.7    33.7    -      -       +      -
    732A  LYS*     5.0     5.2    -      -       +      +
    735A  VAL*     5.1     7.9    -      -       +      -
    751A  VAL*     4.3    19.3    -      -       +      -
    753A  TYR      3.8     6.3    -      -       -      +
    754A  GLY*     5.0     2.2    -      -       -      -
    758A  SER*     1.3    80.6    -      -       -      +
    760A  MET*     1.3    63.4    +      -       -      +
    761A  CYS*     4.2    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 760 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  ILE*     3.6    13.2    -      -       +      -
    599A  ALA      3.6     5.8    -      -       -      -
    600A  THR*     4.1    25.1    -      -       +      +
    751A  VAL*     4.6     0.2    -      -       -      -
    752A  VAL*     3.3    31.0    +      -       +      +
    753A  TYR*     2.9    35.0    +      -       +      +
    754A  GLY*     5.8     0.4    -      -       -      -
    758A  SER*     5.0    10.1    -      -       -      +
    759A  VAL*     1.3    76.3    -      -       -      +
    761A  CYS*     1.3    60.9    +      -       -      +
    798A  TYR*     4.5     9.6    -      -       +      -
    801A  TYR*     2.8    32.1    -      -       -      -
    809A  TYR*     3.4    37.7    -      -       +      +
     25P  DOC      5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 761 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  ILE*     3.4     1.7    -      -       -      +
    599A  ALA*     2.9    35.6    +      -       -      +
    601A  LEU*     5.5     4.3    -      -       +      -
    735A  VAL*     3.7    29.4    -      -       +      -
    736A  GLU*     6.0     0.2    -      -       -      -
    749A  ALA*     3.7    27.6    -      -       -      -
    750A  LYS      4.6     3.8    -      -       -      -
    751A  VAL*     4.4    15.9    -      -       +      +
    759A  VAL*     3.7     6.8    -      -       +      -
    760A  MET*     1.3    72.5    -      -       -      +
    762A  ARG*     1.3    65.6    +      -       -      +
    763A  PHE*     3.9    22.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 762 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    590A  LEU*     6.0     2.2    -      -       -      +
    594A  TYR*     3.4    40.6    +      -       -      -
    596A  VAL*     3.8    21.6    -      -       +      +
    597A  PRO      4.1     7.2    -      -       -      +
    598A  ILE*     3.7    23.6    -      -       +      -
    748A  SER      5.8     1.8    +      -       -      -
    749A  ALA*     3.4     3.8    -      -       -      +
    750A  LYS*     3.3    51.0    +      -       -      +
    752A  VAL*     3.9     9.0    -      -       +      +
    760A  MET      3.8     0.8    +      -       -      -
    761A  CYS*     1.3    73.0    -      -       -      +
    763A  PHE*     1.3    64.9    +      -       -      +
    764A  GLY*     4.7     8.1    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il