Contacts of the strand formed by residues 311 - 319 (chain B) in PDB entry 6VSB


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 GLY 311 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310B  LYS*     1.3    79.6    -      -       -      +
    312B  ILE*     1.3    59.0    +      -       -      -
    313B  TYR*     3.8     5.3    -      -       -      -
    597B  VAL      3.8     1.4    -      -       -      +
    599B  THR*     2.9    37.0    +      -       -      +
    664B  ILE*     3.5    25.6    -      -       -      -
    665B  PRO*     5.7     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311B  GLY*     1.3    73.4    -      -       -      -
    313B  TYR*     1.3    69.9    +      -       -      +
    596B  SER*     4.0    21.5    -      -       -      +
    597B  VAL      3.2    12.3    -      -       -      +
    598B  ILE*     3.6    25.1    -      -       +      -
    611B  LEU*     4.6     3.4    -      -       +      -
    664B  ILE*     3.5     8.3    -      -       +      +
    665B  PRO*     3.1    40.2    -      -       +      +
    666B  ILE*     4.3    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299B  THR*     5.5     4.3    -      -       -      -
    303B  LEU*     3.5    39.1    -      -       +      +
    308B  VAL*     4.5     7.2    -      -       +      -
    309B  GLU*     2.8    44.3    +      -       -      +
    310B  LYS      3.1    12.0    +      -       -      -
    311B  GLY*     3.8    16.6    -      -       -      -
    312B  ILE*     1.3    80.1    -      -       -      +
    314B  GLN*     1.3    63.7    +      -       -      +
    315B  THR*     4.5     6.1    -      -       +      -
    596B  SER*     3.2     7.2    -      -       -      -
    597B  VAL*     2.8    49.9    +      -       +      +
    599B  THR*     4.4     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302B  THR*     4.7     5.5    +      -       -      -
    303B  LEU*     6.1     1.2    -      -       -      +
    313B  TYR*     1.3    75.6    -      -       -      +
    315B  THR*     1.3    65.0    +      -       -      +
    316B  SER      4.4     9.3    +      -       -      +
    317B  ASN*     4.4    17.8    +      -       -      +
    594B  GLY*     4.8     5.9    -      -       -      -
    595B  VAL      3.9    12.3    -      -       -      +
    596B  SER*     3.8    12.0    +      -       -      +
    613B  GLN*     5.0    10.0    +      -       -      +
    735C  SER*     4.7    12.2    +      -       -      -
    764C  ASN*     4.1    22.7    +      -       -      +
    768C  THR*     4.5    16.3    +      -       +      +
    861C  LEU*     6.0     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298B  GLU*     3.4    23.5    +      -       -      +
    299B  THR*     3.6    38.8    -      -       +      -
    302B  THR*     3.4    26.7    -      -       -      +
    313B  TYR*     4.0     5.6    +      -       +      +
    314B  GLN*     1.3    78.7    -      -       -      +
    316B  SER*     1.3    68.6    +      -       -      +
    595B  VAL*     3.4    15.5    +      -       -      +
    597B  VAL*     4.0    20.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298B  GLU*     4.3    15.5    +      -       -      -
    314B  GLN*     4.0     7.0    -      -       -      +
    315B  THR*     1.3    83.7    +      -       -      +
    317B  ASN*     1.3    76.4    +      -       -      +
    594B  GLY*     3.7     2.6    -      -       -      -
    595B  VAL*     2.7    44.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314B  GLN*     4.4    11.1    +      -       -      +
    316B  SER*     1.3    92.8    +      -       -      +
    318B  PHE*     1.3    66.9    +      -       -      +
    319B  ARG*     6.2     0.7    -      -       +      -
    592B  PHE*     6.5     0.9    -      -       +      -
    593B  GLY*     3.3     9.8    -      -       -      +
    594B  GLY*     3.3    19.9    +      -       -      -
    595B  VAL*     4.2     4.7    -      -       -      +
    737C  ASP*     2.6    42.0    +      -       -      +
    739C  THR*     5.1     1.4    +      -       -      -
    764C  ASN*     5.5     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317B  ASN*     1.3    78.5    -      -       -      +
    319B  ARG*     1.3    81.5    +      -       -      +
    320B  VAL*     5.3     4.0    -      -       +      -
    591B  SER*     4.3     7.0    -      -       -      -
    592B  PHE*     3.4    25.7    -      -       -      +
    593B  GLY*     2.8    49.2    +      -       -      +
    594B  GLY      3.5    17.0    -      -       -      -
    595B  VAL*     4.5     9.6    -      -       +      -
    612B  TYR*     4.4    15.9    -      +       +      -
    613B  GLN      4.1     9.2    -      -       -      -
    615B  VAL*     3.6    37.0    -      -       +      -
    619B  GLU*     5.9     1.3    -      -       +      -
    620B  VAL      5.0    14.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317B  ASN*     6.2     0.7    -      -       +      -
    318B  PHE*     1.3    93.1    -      -       -      +
    320B  VAL*     1.3    65.9    +      -       -      +
    321B  GLN*     3.3    39.4    +      -       -      +
    322B  PRO*     5.2     2.0    -      -       -      +
    590B  CYS*     5.5     6.9    -      -       -      +
    591B  SER      4.2     4.7    -      -       -      +
    592B  PHE*     3.5    18.6    -      -       +      -
    740C  MET*     4.9    19.3    -      -       -      +
    744C  GLY      6.3     0.2    -      -       -      -
    745C  ASP*     2.3    55.1    +      -       -      +
----------------------------------------------------------
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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