Contacts of the strand formed by residues 1191 - 1197 (chain A) in PDB entry 2NVT


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 TRP1191 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1152A  ILE*     4.6     3.8    -      -       +      -
   1153A  TYR      3.8    11.7    -      -       -      -
   1154A  TYR*     3.8    28.0    -      +       +      -
   1189A  SER*     3.3     6.8    +      -       -      -
   1190A  PRO*     1.3    87.3    -      -       +      +
   1192A  LEU*     1.3    64.9    +      -       -      +
   1240A  CYS      4.2     3.3    -      -       -      +
   1241A  ARG*     4.3     8.4    -      -       -      -
   1242A  VAL      4.6     0.3    +      -       -      -
   1256A  GLU*     3.6    41.0    -      -       +      +
   1257A  ASP*     3.7    42.2    -      -       +      +
   1260A  LEU*     4.0    22.5    -      -       +      +
     16I  PRO*     4.5    12.1    -      -       +      -
     17I  ARG*     5.0     6.1    -      -       -      -
     18I  GLU*     4.9    15.1    +      -       +      +
     25I  LEU*     3.5    24.0    -      -       +      -
     43I  VAL*     3.9    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1152A  ILE*     3.5    12.8    -      -       -      +
   1153A  TYR*     3.0    36.0    +      -       +      +
   1155A  ASP*     4.3    11.2    -      -       +      +
   1163A  ILE*     4.0    14.1    -      -       +      -
   1190A  PRO      3.3     3.6    +      -       -      -
   1191A  TRP*     1.3    77.0    -      -       -      +
   1193A  LEU*     1.3    72.3    +      -       -      +
   1194A  ARG*     4.0    15.0    -      -       +      -
   1227A  ILE*     5.8     0.2    -      -       +      -
   1239A  ARG*     3.4    59.7    -      -       +      +
   1240A  CYS      3.7     9.9    -      -       -      +
   1241A  ARG*     3.9    18.4    -      -       +      +
   1260A  LEU*     3.3    13.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1150A  SER*     4.5    12.3    -      -       -      +
   1151A  GLU      3.3    24.2    -      -       -      +
   1152A  ILE*     4.3     7.2    -      -       +      +
   1192A  LEU*     1.3    75.9    -      -       -      +
   1194A  ARG*     1.3    67.6    +      -       -      +
   1195A  LEU*     4.7     3.8    -      -       +      +
   1224A  LEU*     6.4     1.3    -      -       +      -
   1238A  ILE      3.8     0.2    -      -       -      +
   1240A  CYS*     2.9    44.9    +      -       +      +
   1260A  LEU*     4.0    25.8    -      -       +      +
   1263A  ILE*     5.0     4.5    -      -       +      -
   1264A  GLU*     3.6    32.3    -      -       +      +
   1267A  MET*     3.8    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1149A  ALA      4.2     0.5    -      -       -      +
   1150A  SER*     3.7     1.6    -      -       -      -
   1151A  GLU*     2.7    69.6    +      -       +      +
   1153A  TYR*     4.6    10.2    +      -       +      -
   1163A  ILE*     4.3    20.4    -      -       -      +
   1165A  GLU*     3.5    30.1    +      -       -      +
   1166A  ASP*     2.6    41.4    +      -       -      +
   1192A  LEU*     4.0    18.7    -      -       +      +
   1193A  LEU*     1.3    73.9    -      -       -      +
   1195A  LEU*     1.3    63.7    +      -       -      +
   1196A  GLU*     4.3     7.0    +      -       -      +
   1237A  ILE*     3.4    41.1    -      -       +      +
   1238A  ILE      3.7     3.1    -      -       -      +
   1239A  ARG*     4.7     3.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1143A  LEU*     5.0    11.0    -      -       +      -
   1147A  THR*     4.1    25.8    -      -       +      +
   1149A  ALA      3.8     4.3    -      -       -      +
   1150A  SER*     3.5    31.9    -      -       -      -
   1193A  LEU*     4.7     4.5    -      -       +      +
   1194A  ARG*     1.3    75.4    -      -       -      +
   1196A  GLU*     1.3    62.3    +      -       -      +
   1197A  LEU*     4.0     2.6    +      -       +      +
   1216A  ILE*     5.0     2.0    -      -       +      -
   1237A  ILE*     3.2    11.5    -      -       -      +
   1238A  ILE*     2.8    64.2    +      -       +      +
   1240A  CYS*     4.9     1.8    -      -       -      -
   1267A  MET*     3.7    31.6    -      -       +      -
   1268A  LEU*     5.2     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1147A  THR*     3.3     6.9    -      -       -      -
   1148A  ILE*     2.7    50.6    +      -       +      +
   1149A  ALA*     3.1    27.3    +      -       +      +
   1151A  GLU*     5.3     5.7    -      -       -      +
   1165A  GLU*     4.7     3.3    -      -       -      +
   1194A  ARG*     4.3     7.2    +      -       -      +
   1195A  LEU*     1.3    73.1    -      -       -      +
   1197A  LEU*     1.3    64.6    +      -       -      +
   1235A  LYS*     4.1    26.5    -      -       +      +
   1236A  LEU      3.6     8.3    -      -       -      +
   1237A  ILE*     4.2    14.0    -      -       +      +
     45I  ARG*     4.6     9.0    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
   1143A  LEU*     4.6     6.7    -      -       +      -
   1146A  VAL*     3.7    11.4    -      -       +      +
   1147A  THR*     3.4    36.6    -      -       +      +
   1148A  ILE*     3.9     8.4    -      -       -      +
   1195A  LEU*     5.0     4.7    -      -       +      +
   1196A  GLU*     1.3    82.2    -      -       -      +
   1198A  ASP*     1.3    62.1    +      -       -      +
   1199A  ARG      4.2     0.7    +      -       -      -
   1202A  MET*     3.9    21.1    -      -       +      -
   1209A  MET*     3.5    27.6    -      -       -      -
   1212A  VAL*     4.3     8.7    -      -       +      -
   1235A  LYS*     6.0     0.2    -      -       -      +
   1236A  LEU*     2.9    36.5    +      -       +      +
   1238A  ILE*     4.0    22.2    -      -       +      -
----------------------------------------------------------
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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