Contacts of the strand formed by residues 1192 - 1197 (chain A) in PDB entry 2RFI


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 ARG1192 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1012A  GLN*     5.6     9.1    -      -       -      +
   1013A  ASN*     4.0    16.0    -      -       -      +
   1089A  VAL*     4.9     5.8    +      -       +      -
   1090A  GLN*     5.3     2.8    -      -       -      +
   1123A  GLU*     2.8    43.7    +      -       -      +
   1156A  ILE*     5.5     0.9    -      -       -      -
   1179A  VAL      3.3     3.3    -      -       -      +
   1180A  ARG*     3.4     3.1    -      -       -      -
   1181A  VAL*     2.9    39.1    +      -       +      +
   1182A  PHE*     6.1     0.2    -      -       -      +
   1183A  MET*     3.4    48.6    -      -       +      +
   1184A  ALA*     4.9     7.1    -      -       -      +
   1185A  HIS*     5.1    11.4    -      -       -      +
   1190A  PHE      3.7     5.4    +      -       -      +
   1191A  PRO*     1.3    76.7    -      -       -      +
   1193A  ILE*     1.3    60.7    +      -       -      +
   1194A  ALA      3.7     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1123A  GLU*     3.2    10.2    +      -       -      +
   1124A  TYR*     2.8    50.5    +      -       +      +
   1144A  PHE*     3.8    31.0    -      -       +      -
   1146A  LEU*     3.7    32.5    -      -       +      -
   1156A  ILE*     4.5     6.2    -      -       +      +
   1178A  PRO*     3.7    26.7    -      -       +      -
   1179A  VAL      3.6     2.5    -      -       -      +
   1180A  ARG*     4.1    24.0    -      -       +      +
   1191A  PRO*     4.8     2.2    -      -       +      +
   1192A  ARG*     1.3    76.9    -      -       -      +
   1194A  ALA*     1.3    60.7    +      -       -      +
   1195A  PHE*     4.2     4.9    +      -       +      -
      9P  THR*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1089A  VAL*     3.7    24.0    -      -       +      -
   1120A  PHE*     3.7    20.6    -      -       +      -
   1122A  CYS      3.8     3.8    -      -       -      -
   1123A  GLU*     4.4     0.7    -      -       -      +
   1177A  VAL      3.5     1.6    -      -       -      +
   1178A  PRO*     3.5     0.8    -      -       -      +
   1179A  VAL*     2.8    39.3    +      -       -      +
   1181A  VAL*     3.9    12.6    -      -       +      -
   1192A  ARG      3.7     0.8    +      -       -      -
   1193A  ILE*     1.3    73.6    -      -       -      +
   1195A  PHE*     1.3    61.7    +      -       -      +
   1196A  PHE*     3.7    11.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE1195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1120A  PHE*     3.6     6.1    -      -       -      -
   1121A  VAL*     2.9    26.2    +      -       -      -
   1122A  CYS*     2.8    44.2    +      -       -      +
   1124A  TYR*     3.7    43.3    -      +       +      -
   1144A  PHE*     4.2     5.2    -      +       -      -
   1165A  SER*     3.9     8.5    -      -       -      -
   1168A  ILE*     4.5     3.4    -      -       +      -
   1176A  LEU*     4.0    26.5    -      -       +      -
   1177A  VAL      3.4     3.4    -      -       -      -
   1178A  PRO*     3.9    24.7    -      -       +      -
   1193A  ILE*     4.4     2.5    -      -       +      -
   1194A  ALA*     1.3    70.5    -      -       -      +
   1196A  PHE*     1.3    61.0    +      -       -      +
   1209A  PHE*     3.5    52.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE1196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1053A  TYR*     3.8    38.6    -      +       -      -
   1057A  GLY      4.9     0.9    -      -       -      -
   1059A  LEU*     3.6    27.8    -      -       +      -
   1071A  ILE*     4.5     6.5    -      -       +      -
   1088A  VAL*     4.6     2.0    -      -       +      -
   1089A  VAL*     3.8    13.5    -      -       +      -
   1118A  GLY      3.5    13.0    -      -       -      -
   1119A  THR      3.1     4.5    -      -       -      -
   1120A  PHE*     3.5    33.0    -      +       +      -
   1176A  LEU*     3.3     5.3    -      -       -      -
   1177A  VAL*     2.9    38.9    +      -       +      +
   1179A  VAL*     3.7    27.8    -      -       +      -
   1181A  VAL*     4.8     0.4    -      -       +      -
   1194A  ALA*     3.7    22.2    -      -       +      -
   1195A  PHE*     1.3    78.3    -      -       -      +
   1197A  SER*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER1197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1065A  MET*     3.7     6.6    -      -       -      +
   1115A  ILE*     4.1     8.1    -      -       -      -
   1116A  PRO      2.8    25.5    +      -       -      -
   1117A  PRO*     3.5     0.5    -      -       -      +
   1118A  GLY*     2.8    31.4    +      -       -      -
   1119A  THR*     2.9    13.9    +      -       -      -
   1121A  VAL*     4.4     1.6    -      -       -      -
   1175A  ASN      3.2     7.2    -      -       -      -
   1176A  LEU*     4.0     4.2    -      -       -      +
   1196A  PHE*     1.3    74.0    -      -       -      +
   1198A  THR*     1.3    61.1    +      -       -      +
   1199A  ARG      3.6    13.2    -      -       -      -
   1201A  ILE*     3.7    19.7    -      -       -      -
----------------------------------------------------------
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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