Contacts of the strand formed by residues 1147 - 1154 (chain A) in PDB entry 2NVX


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 THR1147 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1143A  LEU*     2.5    39.0    +      -       -      +
   1144A  LYS      3.6     7.7    +      -       -      +
   1146A  VAL*     1.3    78.0    -      -       -      +
   1148A  ILE*     1.3    65.2    +      -       -      +
   1149A  ALA      3.8    15.3    -      -       -      +
   1150A  SER*     4.2     1.8    -      -       -      +
   1195A  LEU*     3.7    29.8    -      -       +      +
   1196A  GLU      3.7     9.9    -      -       -      +
   1197A  LEU*     4.0     1.8    -      -       -      +
   1268A  LEU*     3.6    15.2    -      -       +      +
     48I  LEU*     3.8    21.5    -      -       +      +
     49I  ILE*     4.2     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1146A  VAL      3.6     1.6    +      -       -      -
   1147A  THR*     1.3    72.7    -      -       -      +
   1149A  ALA*     1.3    62.6    +      -       +      +
   1196A  GLU*     3.4    44.1    +      -       +      +
   1197A  LEU      3.9     0.4    -      -       -      -
   1198A  ASP*     3.8    45.1    -      -       +      +
     45I  ARG*     5.0     4.7    -      -       -      +
     47I  GLU*     3.4     4.0    -      -       +      -
     48I  LEU      2.8    30.1    +      -       -      -
     49I  ILE*     3.4    35.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA1149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1147A  THR*     3.5     5.3    -      -       -      +
   1148A  ILE*     1.3    85.9    -      -       +      +
   1150A  SER*     1.3    61.3    +      -       -      +
   1151A  GLU*     3.8     9.2    +      -       -      +
   1194A  ARG      4.0     0.3    -      -       -      +
   1195A  LEU*     3.7     5.4    -      -       -      +
   1196A  GLU*     3.3    29.5    +      -       +      +
     45I  ARG*     3.7    35.4    -      -       +      +
     47I  GLU*     3.7    14.8    -      -       -      +
     48I  LEU      4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1147A  THR*     4.2     5.5    -      -       -      +
   1149A  ALA*     1.3    71.7    -      -       -      +
   1151A  GLU*     1.4    57.4    +      -       -      +
   1193A  LEU*     4.3     8.0    -      -       -      +
   1195A  LEU*     3.5    21.2    -      -       -      +
   1264A  GLU*     2.7    35.3    +      -       -      +
   1268A  LEU*     4.8     6.5    -      -       -      -
     44I  TYR*     3.7     5.4    -      -       -      -
     45I  ARG*     3.7     1.6    -      -       -      -
     46I  HIS*     2.9    37.0    +      -       -      +
     47I  GLU      3.9     6.1    -      -       -      +
     48I  LEU*     5.3     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1149A  ALA*     3.8    10.3    +      -       +      +
   1150A  SER*     1.4    72.7    +      -       -      +
   1152A  ILE*     1.3    63.2    +      -       -      +
   1153A  TYR*     3.1    38.3    +      -       +      -
   1193A  LEU*     3.1     9.5    -      -       -      +
   1194A  ARG*     3.0    67.9    +      -       +      +
   1196A  GLU*     5.5     2.8    +      -       -      +
     42I  LEU*     3.8     4.2    -      -       -      +
     44I  TYR      3.1     5.6    -      -       -      +
     45I  ARG*     2.9    51.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1150A  SER*     5.1     0.2    -      -       -      +
   1151A  GLU*     1.3    73.7    -      -       -      +
   1153A  TYR*     1.3    73.5    +      -       -      +
   1191A  TRP*     4.2    14.1    -      -       +      -
   1192A  LEU      3.5     2.5    -      -       -      -
   1193A  LEU*     3.9    13.5    -      -       +      -
   1257A  ASP*     4.9     5.8    -      -       -      +
   1260A  LEU*     3.6    39.0    -      -       +      +
   1261A  LYS*     3.9    22.2    -      -       +      -
   1264A  GLU*     5.0     5.2    -      -       +      +
     43I  VAL*     3.1    32.6    +      -       +      +
     44I  TYR*     2.8    48.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1151A  GLU*     3.1    34.2    +      -       +      -
   1152A  ILE*     1.3    89.6    -      -       -      +
   1154A  TYR*     1.3    63.5    -      -       -      +
   1155A  ASP*     3.9     1.8    -      -       +      -
   1163A  ILE*     3.4    38.6    -      -       +      -
   1191A  TRP*     3.7     4.0    -      -       -      -
   1192A  LEU*     3.2    42.7    +      -       +      +
   1194A  ARG*     4.5    18.8    +      -       +      +
     41I  PRO*     3.8    10.1    -      -       +      -
     42I  LEU*     2.6    57.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR1154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1153A  TYR*     1.3    75.6    -      -       -      +
   1155A  ASP*     1.3    59.0    +      -       -      +
   1156A  PRO*     3.8    17.0    -      -       +      +
   1162A  VAL*     5.4     3.3    -      -       -      +
   1190A  PRO*     3.6    27.1    -      -       +      -
   1191A  TRP*     3.6    30.3    -      +       +      -
     18I  GLU*     3.4    38.5    +      -       +      +
     23I  ASN*     3.1    35.2    +      -       -      -
     24I  ARG*     3.5     4.1    +      -       -      -
     25I  LEU*     3.7    49.4    -      -       +      -
     41I  PRO*     3.3    22.6    +      -       +      +
----------------------------------------------------------
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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