Contacts of the strand formed by residues 81 - 87 (chain A) in PDB entry 2XNP


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 THR 81 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  GLU*     3.4    35.4    +      -       +      +
     39A  LEU      3.3    10.8    +      -       -      +
     40A  ASP*     4.4     6.9    -      -       -      +
     41A  TYR*     3.7     4.3    -      -       -      -
     74A  ILE      3.9     0.7    -      -       -      +
     75A  ILE*     3.8     0.9    -      -       -      -
     76A  ASP*     2.7    42.1    +      -       -      +
     79A  ASN*     3.1    21.0    +      -       -      +
     80A  THR*     1.3    77.3    +      -       -      +
     82A  LEU*     1.3    63.4    +      -       -      +
     83A  TYR*     3.6    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LYS      3.3     2.8    -      -       -      +
     38A  GLU*     3.7     0.3    -      -       -      -
     39A  LEU*     2.7    53.2    +      -       +      +
     41A  TYR*     3.8    14.9    -      -       +      -
     52A  LEU*     3.4    37.2    -      -       +      -
     56A  VAL*     4.6     5.6    -      -       +      -
     73A  ARG*     4.5     7.4    -      -       +      -
     74A  ILE      3.4    22.0    -      -       -      +
     75A  ILE*     4.2    14.8    -      -       +      +
     81A  THR*     1.3    74.3    -      -       -      +
     83A  TYR*     1.3    62.8    +      -       -      +
     84A  ILE*     3.9    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ALA*     4.5    12.1    -      -       +      +
     36A  TRP*     3.3    63.3    -      +       +      -
     37A  LYS      3.2     4.0    -      -       -      +
     38A  GLU*     3.4    38.3    +      -       +      -
     73A  ARG*     3.3     5.4    -      -       -      -
     74A  ILE*     2.8    62.5    +      -       +      +
     76A  ASP*     4.0    25.9    +      -       +      -
     79A  ASN*     5.9     1.0    -      -       -      +
     81A  THR*     3.6    21.3    -      -       +      +
     82A  LEU*     1.3    74.3    -      -       -      +
     84A  ILE*     1.3    65.3    +      -       -      +
     85A  VAL*     3.9     1.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  TRP*     3.0     3.8    -      -       -      -
     37A  LYS*     2.8    51.6    +      -       +      +
     39A  LEU*     4.3    20.9    -      -       +      -
     56A  VAL*     3.9    26.5    -      -       +      -
     59A  LEU*     3.7    29.6    -      -       +      -
     70A  TYR*     3.8    11.7    -      -       +      -
     72A  ASP      3.8     1.1    -      -       -      -
     73A  ARG*     4.0    11.4    -      -       +      -
     82A  LEU*     3.9    20.4    -      -       +      -
     83A  TYR*     1.3    81.3    -      -       -      +
     85A  VAL*     1.3    64.7    +      -       -      +
     86A  MET*     3.8    12.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TYR*     4.4    10.3    -      -       +      +
     25A  ILE*     4.3     4.5    -      -       +      -
     34A  LEU*     3.9    26.0    -      -       +      -
     35A  VAL      3.4    10.1    -      -       -      +
     36A  TRP*     4.1    16.6    -      -       +      -
     70A  TYR*     3.8     5.5    -      -       -      -
     71A  TYR*     2.8    38.6    +      -       +      -
     72A  ASP*     2.9    33.9    +      -       +      +
     74A  ILE*     4.2    22.7    -      -       +      -
     83A  TYR      4.6     1.6    -      -       -      +
     84A  ILE*     1.3    73.8    -      -       -      +
     86A  MET*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  CYS*     5.4     0.2    -      -       -      -
     34A  LEU*     3.5     7.4    -      -       -      +
     35A  VAL*     2.8    56.8    +      -       +      +
     36A  TRP*     4.9     0.2    -      -       -      -
     37A  LYS*     4.0    33.0    -      -       +      -
     59A  LEU*     5.0     9.0    -      -       +      -
     68A  VAL*     4.3     8.3    -      -       +      -
     69A  ARG      3.3    15.0    -      -       -      +
     70A  TYR*     4.8     1.8    -      -       -      -
     71A  TYR*     3.7     7.4    -      -       -      -
     84A  ILE*     4.3    15.0    -      -       +      +
     85A  VAL*     1.3    75.8    -      -       -      +
     87A  GLU*     1.3    61.6    +      -       -      +
    159A  ASP*     4.0    11.4    -      -       -      +
   1280A  WCX      3.8    38.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU*     4.2     3.8    -      -       +      -
     35A  VAL*     3.8     2.1    -      -       -      +
     67A  ILE      3.5     2.6    -      -       -      +
     68A  VAL*     3.4    17.1    -      -       +      +
     69A  ARG*     2.6    43.3    +      -       -      +
     71A  TYR*     3.7    22.8    -      -       +      +
     86A  MET*     1.3    80.3    -      -       -      +
     88A  TYR*     1.3    61.6    +      -       -      +
     89A  CYS*     4.0     9.3    -      -       -      -
    150A  ASP*     5.1     2.9    -      -       -      +
    156A  LYS*     2.9    37.8    +      -       -      +
   1280A  WCX      3.3    19.9    -      -       -      -
----------------------------------------------------------
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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