Contacts of the strand formed by residues 1120 - 1125 (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 THR1120 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1088C  HIS*     3.8    22.9    +      -       -      +
   1089C  PHE      3.2    13.5    -      -       -      -
   1090C  PRO*     4.0     4.5    -      -       +      -
   1091C  ARG*     4.0     7.0    +      -       -      +
   1095C  PHE*     3.4    33.9    -      -       +      -
   1104C  VAL*     4.3     3.4    -      -       +      -
   1115C  ILE*     4.2     5.6    -      -       +      -
   1116C  THR      3.1    13.1    +      -       -      +
   1117C  THR*     3.0    17.0    +      -       -      +
   1118C  ASP      3.6     0.6    -      -       -      -
   1119C  ASN*     1.3    98.2    -      -       -      +
   1121C  PHE*     1.3    61.5    +      -       -      +
   1122C  VAL*     4.1     0.3    +      -       -      +
   1137C  VAL*     4.6     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1121 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    912A  THR*     4.8     5.6    -      -       +      -
    913A  GLN*     4.7    11.0    -      -       +      -
    914A  ASN*     3.1    42.6    -      -       +      -
   1111A  GLU*     5.6     0.4    -      -       -      -
   1113A  GLN*     6.1     2.9    -      -       -      -
   1088C  HIS*     3.5     2.8    -      -       -      -
   1089C  PHE*     2.7    64.8    +      +       +      +
   1090C  PRO      3.3    23.6    -      -       -      -
   1091C  ARG*     3.6    34.0    -      -       +      +
   1120C  THR*     1.3    75.7    -      -       -      +
   1122C  VAL*     1.3    66.9    +      -       -      +
   1123C  SER*     4.1     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1122 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1113A  GLN*     5.0     7.6    +      -       -      -
   1086C  LYS*     3.6    34.5    -      -       +      -
   1087C  ALA      3.2    18.8    -      -       -      +
   1088C  HIS*     4.1    17.3    -      -       +      +
   1120C  THR      5.8     0.2    -      -       -      +
   1121C  PHE*     1.3    77.8    -      -       -      +
   1123C  SER*     1.3    66.7    +      -       -      +
   1124C  GLY      4.8     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1123 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    914A  ASN*     3.1    34.4    +      -       -      +
    918A  GLU*     3.7     7.0    +      -       -      +
   1111A  GLU*     4.0    18.8    -      -       -      -
   1113A  GLN*     5.5     3.6    -      -       -      -
   1087C  ALA*     3.3     5.6    +      -       -      +
   1089C  PHE*     3.4    20.8    -      -       -      -
   1121C  PHE*     4.4     5.8    +      -       -      -
   1122C  VAL*     1.3    82.2    -      -       -      +
   1124C  GLY*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1124 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    918A  GLU*     3.9    12.5    +      -       -      -
   1086C  LYS*     4.0     6.9    -      -       -      +
   1087C  ALA      3.3    16.3    +      -       -      +
   1122C  VAL*     4.8     0.9    -      -       -      +
   1123C  SER*     1.3    76.5    +      -       -      +
   1125C  ASN*     1.3    63.6    +      -       -      -
   1128C  VAL*     5.3     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN1125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1085C  GLY      3.5    15.7    -      -       -      +
   1086C  LYS*     4.5     0.4    -      -       -      +
   1087C  ALA*     3.5    12.0    -      -       -      +
   1124C  GLY*     1.3    77.6    -      -       -      -
   1126C  CYS*     1.3    61.6    +      -       -      +
   1127C  ASP*     2.6    43.5    +      -       -      +
   1128C  VAL*     3.2    26.7    +      -       -      +
   1129C  VAL*     4.8     1.0    -      -       -      +
----------------------------------------------------------
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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