Contacts of the strand formed by residues 21 - 27 (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 ARG 21 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  THR*     3.9    14.2    +      -       +      -
     15A  GLY      3.3    13.2    -      -       -      +
     16A  THR*     4.0    12.6    -      -       +      +
     19A  TYR*     3.8     7.5    -      -       -      -
     20A  GLY*     1.3    76.0    -      -       -      +
     22A  CYS*     1.3    59.9    +      -       -      +
     23A  GLN*     3.5    36.4    +      -       +      +
     36A  TRP      3.7     0.9    -      -       -      +
     37A  LYS*     3.6     1.1    -      -       -      -
     38A  GLU*     2.6    74.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  THR*     3.6     0.7    -      -       -      +
     14A  ILE*     2.7    42.2    +      -       +      -
     15A  GLY      2.9    10.2    +      -       -      +
     19A  TYR*     4.3     2.9    -      -       +      +
     21A  ARG*     1.3    72.5    -      -       -      +
     23A  GLN*     1.3    60.9    +      -       -      +
     35A  VAL*     4.2    15.9    -      -       -      -
     36A  TRP      3.3    12.3    -      -       -      -
     37A  LYS*     4.5     8.5    -      -       +      +
   1280A  WCX      3.0    57.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  VAL*     3.5    33.7    -      -       +      +
     12A  TYR      3.5     9.2    -      -       -      +
     13A  THR*     3.1    25.0    +      -       -      +
     14A  ILE*     4.1     2.2    -      -       -      +
     21A  ARG*     3.5    41.2    +      -       +      +
     22A  CYS*     1.3    80.3    -      -       -      +
     24A  LYS*     1.3    62.6    +      -       -      +
     25A  ILE*     3.7     1.9    -      -       +      +
     35A  VAL*     3.1     7.8    -      -       -      -
     36A  TRP*     2.9    64.8    +      -       +      +
     38A  GLU*     4.5     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  VAL*     3.9     1.0    -      -       -      +
     11A  LEU*     2.8    43.1    +      -       +      +
     12A  TYR*     2.8    52.1    +      -       +      +
     14A  ILE*     4.1    17.1    -      -       +      +
     23A  GLN*     1.3    71.8    -      -       -      +
     25A  ILE*     1.3    63.9    +      -       -      +
     33A  ILE*     3.7    21.8    -      -       +      -
     34A  LEU      3.6    10.8    -      -       -      +
     35A  VAL*     4.2     3.6    -      -       +      -
     88A  TYR*     3.4    38.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TYR*     3.5    31.6    -      -       +      -
      9A  GLU      3.3    10.3    -      -       -      +
     10A  VAL*     4.1    12.3    -      -       +      -
     11A  LEU*     4.1     4.7    -      -       -      +
     23A  GLN      3.7    10.3    -      -       -      +
     24A  LYS*     1.3    80.8    -      -       -      +
     26A  ARG*     1.3    63.7    +      -       -      +
     33A  ILE*     3.5     8.1    -      -       -      +
     34A  LEU*     2.9    50.5    +      -       +      +
     35A  VAL      4.1    13.9    -      -       -      +
     36A  TRP*     3.8    46.7    -      -       +      +
     85A  VAL*     4.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TYR*     3.4     4.0    -      -       -      -
      9A  GLU*     2.8    59.3    +      -       +      +
     11A  LEU*     4.2    27.2    -      -       +      +
     25A  ILE*     1.3    76.6    -      -       -      +
     27A  ARG*     1.3    69.9    +      -       -      +
     28A  LYS*     3.3     4.6    +      -       -      +
     31A  GLY*     3.6    31.1    +      -       -      +
     32A  LYS      3.5     2.5    -      -       -      -
     33A  ILE*     4.0    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ASP*     4.2     5.8    -      -       +      +
      8A  TYR*     3.8    38.5    +      -       +      -
     25A  ILE      4.3     0.2    -      -       -      -
     26A  ARG*     1.3    72.8    -      -       -      +
     28A  LYS*     1.3    61.6    +      -       -      +
     29A  SER*     3.8    16.9    +      -       -      +
     30A  ASP*     2.8    37.4    +      -       -      +
     31A  GLY*     2.8    31.5    +      -       -      -
     32A  LYS*     2.8    44.3    +      -       +      +
     34A  LEU*     4.3     8.1    -      -       +      +
     71A  TYR*     4.5    21.0    -      -       -      -
----------------------------------------------------------
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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