Contacts of the strand formed by residues 319 - 324 (chain B) in PDB entry 6G4O


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 ILE 319 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  ILE*     3.5    31.6    -      -       +      -
    222B  ALA*     3.4    13.2    -      -       +      +
    224B  LEU*     4.0    10.5    -      -       +      -
    317B  THR*     4.1     0.8    +      -       -      -
    318B  GLN*     1.3    78.3    -      -       -      +
    320B  LEU*     1.3    58.2    +      -       -      +
    321B  LEU*     4.1    10.1    -      -       +      -
    407B  PHE*     4.0    18.2    -      -       +      -
    408B  VAL*     5.2     2.5    -      -       -      -
    411B  TYR*     3.3    42.2    -      -       +      +
    417B  GLY      3.1     3.1    +      -       -      +
    418B  THR*     3.4    26.8    -      -       +      +
    419B  TYR      3.1    20.3    +      -       -      -
    476B  PHE*     3.6     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222B  ALA      3.2     5.9    +      -       -      -
    223B  ILE*     3.1    38.9    -      -       +      +
    224B  LEU*     3.1     2.6    +      -       -      +
    319B  ILE*     1.3    72.9    -      -       -      +
    321B  LEU*     1.3    65.5    +      -       -      +
    419B  TYR*     3.3     9.2    -      -       +      +
    421B  TYR*     4.0    10.3    -      -       +      -
    472B  TYR      4.1     4.5    -      -       -      +
    473B  TRP*     3.8    36.6    -      -       +      +
    476B  PHE*     3.4    35.8    -      -       +      -
    482B  PRO*     4.0    19.3    -      -       +      -
    492B  TRP*     3.7    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 321 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224B  LEU*     3.1    28.3    -      -       +      +
    319B  ILE*     4.1     7.9    -      -       +      -
    320B  LEU*     1.3    78.0    -      -       -      +
    322B  GLY*     1.3    60.3    +      -       -      +
    404B  LEU*     3.9    22.0    -      -       +      -
    407B  PHE*     3.9    33.4    -      -       +      -
    408B  VAL*     4.1     7.9    -      -       +      -
    418B  THR*     3.6    31.2    -      -       +      -
    419B  TYR      2.9    11.2    +      -       -      +
    420B  LEU*     3.1    24.6    -      -       +      -
    421B  TYR*     3.0    30.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224B  LEU      3.1     4.5    +      -       -      +
    225B  GLN      3.6     0.3    -      -       -      -
    226B  SER      2.7    31.2    +      -       -      -
    321B  LEU*     1.3    79.5    -      -       -      +
    323B  VAL*     1.3    61.6    +      -       -      +
    404B  LEU*     3.8     3.6    -      -       -      +
    420B  LEU*     4.2     9.2    -      -       -      -
    421B  TYR*     3.1    30.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226B  SER*     3.7     5.2    -      -       -      -
    322B  GLY*     1.3    80.3    -      -       -      +
    324B  ASN*     1.3    66.3    -      -       -      +
    327B  GLU*     3.6     8.7    -      -       -      +
    400B  VAL*     3.8    26.7    -      -       +      +
    401B  ILE*     3.4    31.2    -      -       +      -
    404B  LEU*     3.9    24.0    -      -       +      -
    421B  TYR*     3.2     5.1    +      -       -      +
    422B  PHE*     3.6    15.9    -      -       +      -
    423B  PHE*     2.8    25.1    +      -       -      +
    516B  LEU*     4.5    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226B  SER*     3.9     2.8    +      -       -      -
    323B  VAL*     1.3    76.9    -      -       -      +
    325B  LYS*     1.3    69.5    +      -       -      +
    327B  GLU*     2.5    29.8    +      -       -      +
    401B  ILE*     3.8     9.0    -      -       -      +
    421B  TYR*     4.6     1.9    +      -       -      -
    422B  PHE*     4.3     3.1    -      -       -      -
    423B  PHE*     3.1    41.3    -      -       -      +
    438B  VAL*     3.8    16.4    -      -       +      +
    439B  ILE      3.7    15.0    +      -       -      -
    440B  HIS*     3.7     8.2    -      -       -      +
    443B  GLU*     2.2    42.6    +      -       -      +
----------------------------------------------------------
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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