Contacts of the strand formed by residues 311 - 319 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310C  LYS*     1.3    84.0    -      -       -      +
    312C  ILE*     1.3    60.3    +      -       -      -
    313C  TYR*     3.8     6.7    -      -       -      -
    597C  VAL      3.6     2.1    -      -       -      +
    599C  THR*     3.4    31.1    +      -       -      -
    664C  ILE*     3.5    23.5    -      -       -      +
    665C  PRO*     5.4     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 312 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311C  GLY*     1.3    72.6    -      -       -      -
    313C  TYR*     1.3    65.9    +      -       -      +
    596C  SER*     3.0    28.7    -      -       -      +
    597C  VAL      3.3     4.7    -      -       -      +
    598C  ILE*     3.6    28.9    -      -       +      -
    611C  LEU*     4.1    15.9    -      -       +      -
    613C  GLN*     5.9     1.6    -      -       -      +
    664C  ILE*     3.6     1.7    -      -       +      +
    665C  PRO*     3.3    35.0    -      -       +      +
    666C  ILE*     4.3     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 313 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299C  THR*     5.3     6.1    -      -       -      -
    302C  THR*     5.9     1.3    -      -       -      +
    303C  LEU*     3.8    30.1    -      -       +      -
    308C  VAL*     4.6     9.0    -      -       +      -
    309C  GLU*     2.8    48.2    +      -       -      +
    310C  LYS      3.1    16.0    +      -       -      -
    311C  GLY      3.8    13.2    -      -       -      -
    312C  ILE*     1.3    79.8    -      -       -      +
    314C  GLN*     1.3    59.9    +      -       -      +
    315C  THR*     3.7     7.9    +      -       +      -
    596C  SER*     2.6    19.0    +      -       -      -
    597C  VAL*     2.9    40.0    +      -       +      +
    599C  THR*     4.4     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 314 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    735A  SER*     3.6    20.7    +      -       -      -
    736A  VAL      5.3     3.0    +      -       -      -
    737A  ASP*     5.6     7.3    +      -       -      +
    764A  ASN*     3.5    33.3    +      -       -      +
    768A  THR*     4.8     8.3    +      -       +      +
    861A  LEU*     5.8     1.6    -      -       -      +
    302C  THR*     4.6     4.3    +      -       -      -
    313C  TYR*     1.3    72.9    -      -       -      +
    315C  THR*     1.3    62.1    +      -       -      +
    316C  SER*     4.4    15.0    +      -       -      +
    317C  ASN*     6.1     1.4    -      -       -      +
    594C  GLY*     5.6     4.3    -      -       -      -
    595C  VAL      3.9    11.7    -      -       -      +
    596C  SER*     3.4     9.3    +      -       -      +
    613C  GLN*     4.4    21.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 315 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298C  GLU*     4.0    22.3    +      -       -      +
    299C  THR*     3.5    40.6    -      -       +      -
    302C  THR*     3.3    33.1    -      -       -      +
    313C  TYR*     3.7    13.4    +      -       +      +
    314C  GLN*     1.3    78.2    -      -       -      +
    316C  SER*     1.3    65.7    +      -       -      +
    595C  VAL*     3.4    14.8    +      -       -      +
    597C  VAL*     4.1    10.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 316 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298C  GLU*     4.4    12.3    -      -       -      -
    314C  GLN*     3.8    12.7    +      -       -      +
    315C  THR*     1.3    86.9    +      -       -      +
    317C  ASN*     1.3    80.3    +      -       -      +
    594C  GLY*     3.9     2.6    -      -       -      -
    595C  VAL*     3.2    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 317 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    737A  ASP*     3.4    41.0    +      -       -      +
    739A  THR*     5.8     1.8    -      -       +      -
    740A  MET*     5.3     1.3    -      -       -      -
    857A  GLY*     5.7     0.8    -      -       -      -
    314C  GLN*     6.1     1.2    -      -       -      +
    316C  SER*     1.3    93.5    +      -       -      +
    318C  PHE*     1.3    80.0    +      -       -      +
    319C  ARG*     4.7    11.0    +      -       -      +
    592C  PHE*     3.7    13.8    -      -       -      -
    593C  GLY*     2.8    39.6    +      -       -      +
    594C  GLY*     3.6     4.6    -      -       -      +
    595C  VAL*     4.1     3.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 318 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317C  ASN*     1.3    90.0    +      -       -      +
    319C  ARG*     1.3    74.2    +      -       -      +
    591C  SER      4.7     4.3    -      -       -      -
    592C  PHE*     3.1    22.0    -      -       -      +
    593C  GLY*     2.8    47.9    +      -       -      -
    594C  GLY      3.5    12.8    -      -       -      -
    595C  VAL*     3.9    20.2    -      -       +      -
    612C  TYR*     4.0    26.9    -      +       +      -
    615C  VAL*     3.5    33.4    -      -       +      -
    619C  GLU*     5.5    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 319 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    737A  ASP*     5.1     1.8    +      -       -      -
    739A  THR*     6.1     1.6    -      -       -      +
    740A  MET*     4.3    28.1    -      -       -      +
    744A  GLY*     4.9     0.2    -      -       -      -
    745A  ASP*     4.0    39.0    +      -       -      +
    317C  ASN*     4.7     9.7    +      -       -      +
    318C  PHE*     1.3    89.0    -      -       -      +
    320C  VAL*     1.3    67.1    +      -       -      +
    321C  GLN*     3.9    32.0    +      -       -      +
    322C  PRO*     6.0     1.3    -      -       -      -
    590C  CYS*     5.4     5.4    -      -       -      +
    591C  SER      3.9     8.5    -      -       -      +
    592C  PHE*     3.8    12.7    -      -       +      +
----------------------------------------------------------
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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