Contacts of the strand formed by residues 1303 - 1308 (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 GLU1303 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1119A  TYR*     3.6    13.3    -      -       -      -
   1120A  LEU      5.9     1.3    +      -       -      -
   1125A  ALA*     4.7    19.0    -      -       +      +
   1126A  ALA*     4.9     3.4    -      -       +      +
   1286A  LYS*     3.3     5.2    -      -       -      +
   1287A  TYR*     2.7    47.9    +      -       +      +
   1288A  ASP      5.2     0.2    -      -       -      +
   1289A  ARG*     3.6    26.7    +      -       +      +
   1301A  GLU*     4.9     3.6    -      -       +      +
   1302A  PRO*     1.3    75.5    -      -       -      +
   1304A  TRP*     1.3    64.4    +      -       -      +
   1305A  VAL*     3.5    13.1    +      -       +      +
   1326A  ARG*     2.8    43.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP1304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1120A  LEU*     4.2    24.5    +      -       +      +
   1125A  ALA      3.7    10.9    +      -       -      +
   1126A  ALA*     3.2    31.0    +      -       -      -
   1127A  ASP      4.4     0.4    -      -       -      -
   1128A  GLN*     3.3    44.4    -      -       +      +
   1131A  ALA*     4.1    18.2    -      -       +      -
   1284A  MET*     3.6    45.1    -      -       +      -
   1285A  MET      4.0     7.0    -      -       -      -
   1286A  LYS*     4.0    46.1    -      -       +      +
   1303A  GLU*     1.3    74.1    -      -       -      +
   1305A  VAL*     1.3    64.2    +      -       -      +
   1306A  LEU*     4.2     1.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1117A  THR*     4.8     3.4    -      -       -      -
   1118A  VAL      3.3    17.3    -      -       -      +
   1119A  TYR*     3.8    26.2    -      -       +      -
   1283A  VAL      3.5     1.7    -      -       -      +
   1284A  MET*     3.7     0.9    -      -       -      -
   1285A  MET*     2.8    44.5    +      -       -      +
   1287A  TYR*     3.5    50.6    -      -       +      +
   1303A  GLU*     3.8    14.6    -      -       +      -
   1304A  TRP*     1.3    79.5    -      -       -      +
   1306A  LEU*     1.3    70.8    +      -       -      +
   1307A  GLU*     3.9     1.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1306 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1116A  LEU      3.7     1.0    -      -       -      +
   1117A  THR*     3.4     3.1    -      -       -      -
   1118A  VAL*     2.7    55.8    +      -       +      +
   1120A  LEU*     4.8    11.9    -      -       +      -
   1131A  ALA*     4.2     7.4    -      -       +      +
   1134A  ILE*     3.7    33.0    -      -       +      -
   1135A  ARG*     3.8    31.0    -      -       +      +
   1138A  ILE*     4.3     5.4    -      -       +      -
   1282A  VAL*     4.0    10.3    -      -       +      -
   1283A  VAL      3.3     6.7    -      -       -      +
   1284A  MET*     3.5    32.5    -      -       +      -
   1304A  TRP      4.2     0.8    +      -       -      -
   1305A  VAL*     1.3    73.5    -      -       -      +
   1307A  GLU*     1.3    59.4    +      -       -      +
   1308A  THR*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU1307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1115A  SER*     4.1     7.9    +      -       -      +
   1116A  LEU      3.5     2.0    -      -       -      +
   1117A  THR*     3.4    24.8    -      -       +      +
   1281A  ARG      3.5     0.2    -      -       -      +
   1282A  VAL*     3.4     3.5    -      -       -      +
   1283A  VAL*     2.7    56.7    +      -       +      +
   1285A  MET*     3.4    24.2    -      -       -      +
   1287A  TYR*     2.8    31.4    +      -       -      -
   1305A  VAL*     3.9     1.5    +      -       -      +
   1306A  LEU*     1.3    74.1    -      -       -      +
   1308A  THR*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR1308 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1115A  SER*     3.1    21.0    +      -       -      -
   1116A  LEU*     2.8    39.0    +      -       +      +
   1118A  VAL*     5.3     4.1    -      -       -      +
   1138A  ILE*     5.4     0.5    -      -       -      +
   1279A  ILE*     3.8    12.8    -      -       +      +
   1281A  ARG      3.2     4.0    -      -       -      -
   1282A  VAL*     3.3    23.4    -      -       -      +
   1306A  LEU      5.6     0.2    -      -       -      -
   1307A  GLU*     1.3    75.6    -      -       -      +
   1309A  ASP*     1.3    75.0    +      -       -      +
   1310A  GLY      2.8    31.6    -      -       -      +
----------------------------------------------------------
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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