Contacts of the strand formed by residues 306 - 312 (chain C) in PDB entry 6VSU


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 306 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153C  ARG*     2.8    26.1    +      -       -      -
    265C  VAL      3.2    15.5    -      -       -      +
    267C  ILE*     3.7    33.7    -      -       +      -
    304C  ALA*     3.4    23.3    +      -       +      +
    305C  ASP*     1.3    68.6    +      -       -      +
    307C  VAL*     1.3    55.5    +      -       -      +
    308C  GLY      3.9    15.0    -      -       -      +
    339C  LYS*     4.2    22.0    +      -       +      +
    340C  ILE*     3.7    39.6    -      -       +      +
    342C  LYS*     4.8     3.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 307 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147C  MET*     5.4     2.4    -      -       +      +
    153C  ARG*     3.4    33.3    -      -       -      +
    154C  PRO*     3.6    20.8    -      -       -      +
    171C  VAL*     3.6    27.1    -      -       +      +
    175C  LEU*     3.6    24.5    -      -       +      -
    179C  VAL*     4.2     5.2    -      -       +      -
    263C  LYS      3.8     5.6    -      -       -      +
    264C  GLY*     3.8    14.4    -      -       -      -
    265C  VAL      3.1    23.6    +      -       -      +
    266C  TYR*     4.7     1.8    -      -       -      +
    305C  ASP*     3.8    13.9    -      -       -      +
    306C  VAL*     1.3    73.1    -      -       -      +
    308C  GLY*     1.3    59.4    +      -       -      +
    340C  ILE*     5.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 308 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154C  PRO*     3.4    15.7    -      -       -      -
    171C  VAL*     5.0     1.6    -      -       -      -
    266C  TYR*     3.1    26.9    -      -       -      -
    267C  ILE      3.1    21.1    +      -       -      -
    306C  VAL*     3.7     7.1    -      -       -      +
    307C  VAL*     1.3    82.6    -      -       -      +
    309C  ALA*     1.3    62.0    -      -       -      +
    340C  ILE*     5.0     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 309 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154C  PRO      3.2     5.8    +      -       -      +
    155C  LEU*     3.1     8.8    -      -       +      -
    156C  VAL*     2.8    31.5    +      -       -      +
    167C  VAL*     5.7     0.2    -      -       -      +
    266C  TYR*     3.8     6.7    +      -       -      -
    267C  ILE*     3.0    21.1    -      -       +      +
    306C  VAL*     4.7     1.3    -      -       +      -
    308C  GLY*     1.3    73.9    -      -       -      +
    310C  ASP*     1.3    55.1    +      -       -      +
    336C  LEU*     4.0    21.5    -      -       +      -
    340C  ILE*     3.6    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 310 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155C  LEU*     4.8     0.2    -      -       -      -
    156C  VAL*     3.1    21.5    -      -       +      +
    163C  ILE*     5.0     1.6    -      -       +      -
    164C  SER*     3.1    24.6    +      -       -      -
    266C  TYR*     2.5    35.1    +      -       -      +
    267C  ILE      3.0     7.8    +      -       -      +
    268C  SER*     2.5    27.8    +      -       -      -
    269C  ILE*     3.0    26.0    +      -       -      +
    309C  ALA*     1.3    72.7    -      -       -      +
    311C  VAL*     1.3    65.5    +      -       -      +
    312C  VAL*     3.4    20.3    -      -       +      +
    336C  LEU*     4.1     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 311 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89C  ILE*     4.9     6.3    -      -       +      +
    155C  LEU*     4.3     3.4    -      -       +      -
    156C  VAL      3.1     6.3    +      -       -      +
    157C  LEU*     3.7     4.1    -      -       +      -
    158C  GLY*     2.8    24.4    +      -       -      +
    269C  ILE*     3.4     9.4    -      -       +      +
    271C  VAL*     4.1    21.5    -      -       +      -
    310C  ASP*     1.3    69.4    -      -       -      +
    312C  VAL*     1.3    61.4    +      -       -      +
    314C  PHE*     5.8     0.8    -      -       +      +
    329C  ALA*     4.3    23.6    -      -       +      +
    332C  LEU*     4.5    10.8    -      -       +      -
    333C  VAL*     3.8    28.5    -      -       +      +
    336C  LEU*     3.6    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 312 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158C  GLY*     4.2     1.1    -      -       -      -
    159C  GLY      3.3    11.2    -      -       -      +
    160C  ASP      4.4     2.5    -      -       -      +
    161C  HIS*     3.6    41.3    -      -       +      +
    163C  ILE*     3.8    27.1    -      -       +      -
    164C  SER*     4.5     2.2    -      -       -      +
    269C  ILE      3.0     8.7    +      -       -      +
    270C  ASP*     3.7     9.0    -      -       -      +
    271C  VAL*     3.1    26.9    +      -       -      +
    310C  ASP*     3.4    26.2    -      -       +      +
    311C  VAL*     1.3    79.5    -      -       -      +
    313C  GLU*     1.3    62.3    +      -       +      +
    314C  PHE*     3.1    10.2    +      -       -      -
----------------------------------------------------------
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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