Contacts of the strand formed by residues 1192 - 1198 (chain A) in PDB entry 6FF7


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 PHE1192 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1188A  ASN*     5.2     0.4    -      -       -      +
   1189A  MET*     2.9    25.1    +      -       -      +
   1190A  CYS      3.6     1.2    +      -       -      -
   1191A  GLY*     1.3    80.5    -      -       -      +
   1193A  GLU*     1.3    61.7    +      -       -      +
   1194A  CYS*     4.2     1.2    +      -       -      +
   1230A  LEU*     6.5     0.4    -      -       +      -
   1231A  ARG      3.7    11.7    -      -       -      +
   1232A  VAL*     4.2     9.2    -      -       +      -
   1233A  ASP*     4.0     4.9    -      -       -      +
   1274A  PHE*     6.2     2.5    -      -       +      -
   1277A  ALA*     4.9    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1187A  PHE      3.6    14.1    -      -       -      +
   1188A  ASN*     3.7    20.2    -      -       +      +
   1192A  PHE*     1.3    73.9    -      -       -      +
   1194A  CYS*     1.3    63.7    +      -       -      +
   1230A  LEU*     3.5     2.6    -      -       -      +
   1231A  ARG*     2.8    38.3    +      -       +      +
   1232A  VAL      5.5     0.2    -      -       -      -
   1233A  ASP*     4.3    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS1194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1186A  LEU*     3.7     1.4    -      -       -      +
   1187A  PHE      2.9    32.1    +      -       -      +
   1192A  PHE      4.2     1.7    +      -       -      +
   1193A  GLU*     1.3    76.5    -      -       -      +
   1195A  ARG*     1.3    65.7    +      -       -      +
   1228A  CYS*     5.4     6.7    -      -       +      -
   1229A  PHE      3.1    15.5    -      -       -      +
   1230A  LEU*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1184A  ASN*     5.8     3.8    -      -       +      -
   1185A  LEU      3.1    16.2    -      -       -      +
   1186A  LEU*     3.7    13.7    -      -       +      -
   1194A  CYS*     1.3    79.9    -      -       -      +
   1196A  ILE*     1.3    62.1    +      -       -      +
   1197A  LEU*     4.0     1.1    +      -       -      +
   1227A  GLN      3.5     1.0    -      -       -      +
   1228A  CYS*     3.2     7.0    -      -       -      -
   1229A  PHE*     2.9    38.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    956A  CYS*     6.5     1.3    -      -       +      -
   1183A  PRO      4.7     0.2    -      -       -      +
   1184A  ASN*     3.8     4.2    -      -       -      +
   1185A  LEU*     2.8    46.1    +      -       +      +
   1195A  ARG*     1.3    73.7    -      -       -      +
   1197A  LEU*     1.3    60.3    +      -       -      +
   1198A  PRO      4.1     0.6    -      -       -      -
   1226A  ALA*     5.2     9.4    -      -       +      -
   1227A  GLN      3.3     7.4    -      -       -      +
   1228A  CYS*     4.7     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1183A  PRO      4.7     9.6    -      -       -      +
   1184A  ASN*     5.3     3.6    -      -       +      +
   1195A  ARG      4.0     1.0    +      -       -      +
   1196A  ILE*     1.3    71.7    -      -       -      +
   1198A  PRO*     1.3    66.2    -      -       -      +
   1226A  ALA*     4.4     1.6    -      -       -      -
   1227A  GLN*     2.9    40.3    +      -       +      +
   1229A  PHE*     6.5     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO1198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1183A  PRO      5.0     5.2    -      -       -      +
   1196A  ILE*     4.1     1.6    -      -       -      -
   1197A  LEU*     1.3    76.9    -      -       -      +
   1199A  LYS*     1.3    62.7    +      -       -      +
   1200A  CYS*     3.3    11.1    +      -       +      +
   1201A  ARG*     3.9    19.7    +      -       +      +
   1202A  THR*     4.4     5.0    +      -       -      -
   1225A  THR      4.9     1.6    -      -       -      +
   1226A  ALA*     4.0    12.8    -      -       +      -
----------------------------------------------------------
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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