Contacts of the strand formed by residues 338 - 343 (chain C) in PDB entry 6GR2


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 VAL 338 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332C  ALA*     3.5    26.7    -      -       +      +
    333C  LEU*     4.7     8.1    -      -       +      +
    335C  VAL*     3.4    29.4    +      -       +      +
    336C  PRO      3.3     1.2    -      -       -      -
    337C  GLY*     1.3    78.2    +      -       -      +
    339C  TYR*     1.3    64.9    +      -       -      +
    340C  GLY*     3.6    15.7    -      -       -      +
    341C  SER*     4.8     0.2    -      -       -      -
    354C  THR*     3.5    29.4    -      -       +      -
    355C  LEU      3.6     2.5    -      -       -      -
    356C  LEU*     3.7    16.2    -      -       +      -
    360C  ALA*     5.6     0.7    -      -       +      -
    364C  ALA*     4.6     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 339 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217C  LYS      5.4     2.4    +      -       -      -
    218C  LEU*     3.8    17.7    -      -       +      -
    300C  TYR*     3.3    61.0    -      +       +      +
    301C  ARG*     3.6    28.6    -      -       +      +
    304C  GLY*     3.0    21.8    -      -       -      +
    305C  ARG*     3.8     3.5    +      -       -      +
    308C  VAL*     4.7     1.6    -      -       -      +
    333C  LEU*     5.3     1.0    -      -       -      +
    337C  GLY      4.2     2.0    -      -       -      -
    338C  VAL*     1.3    75.6    -      -       -      +
    340C  GLY*     1.3    55.9    +      -       -      +
    355C  LEU*     2.6    31.9    +      -       +      +
    356C  LEU*     3.9    12.3    -      -       -      -
    357C  GLU*     3.9    24.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 340 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304C  GLY*     3.5    19.2    -      -       -      -
    307C  MET*     4.0     7.0    -      -       -      -
    308C  VAL*     3.9     6.7    -      -       -      -
    333C  LEU*     4.1     6.1    -      -       -      -
    338C  VAL*     3.5     4.8    -      -       -      -
    339C  TYR*     1.3    82.6    -      -       -      +
    341C  SER*     1.3    63.7    +      -       -      -
    354C  THR*     3.3     5.2    -      -       -      +
    355C  LEU*     3.0    24.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 341 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307C  MET*     4.1     8.2    -      -       -      +
    308C  VAL*     4.0    11.7    -      -       -      +
    311C  HIS*     4.2     0.3    -      -       -      +
    329C  VAL*     3.3    22.6    -      -       -      +
    332C  ALA*     3.8    19.9    -      -       -      +
    333C  LEU*     3.9     9.7    -      -       -      +
    340C  GLY*     1.3    74.3    -      -       -      -
    342C  ARG*     1.3    65.4    +      -       -      +
    352C  THR*     2.9    21.8    -      -       -      +
    353C  VAL      3.3     6.5    -      -       -      -
    354C  THR*     2.5    27.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 342 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  ASN*     3.4    12.6    +      -       -      +
     40C  LEU      2.9    16.8    +      -       -      -
     41C  ILE*     3.1    29.9    -      -       -      +
     42C  GLY      3.8     1.6    -      -       -      +
     43C  GLU*     2.9    24.5    +      -       -      +
    307C  MET*     3.2    38.6    -      -       +      +
    310C  SER*     3.2    13.6    +      -       -      -
    311C  HIS*     3.4    14.8    -      -       +      -
    314C  LEU*     3.1    26.7    -      -       -      +
    329C  VAL*     3.8    13.9    -      -       -      -
    341C  SER*     1.3    81.5    +      -       -      +
    343C  MET*     1.3    85.6    +      -       -      +
    352C  THR*     3.4     2.9    -      -       -      -
    353C  VAL*     3.0    35.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 343 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  GLU*     4.4     1.6    -      -       +      -
    311C  HIS*     3.2    25.2    +      -       +      +
    314C  LEU*     3.8    31.8    -      -       +      +
    320C  VAL*     4.1     9.6    -      -       +      -
    321C  SER*     3.4    34.8    -      -       -      -
    325C  LEU*     3.7    22.9    -      -       +      -
    329C  VAL*     4.0     0.4    -      -       -      +
    342C  ARG*     1.3   106.5    +      -       -      +
    344C  THR*     1.3    58.4    +      -       -      +
    345C  GLY      3.6    18.4    -      -       -      +
    347C  GLY*     3.6    25.4    -      -       -      +
    351C  CYS      3.7     6.3    -      -       -      +
    352C  THR*     4.3     3.1    -      -       -      -
----------------------------------------------------------
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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