Contacts of the strand formed by residues 121 - 125 (chain P) in PDB entry 2XTJ


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 GLY 121 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79P  VAL*     6.1     0.2    -      -       -      -
     80P  VAL      2.9    15.0    -      -       -      -
     81P  VAL*     4.3     0.2    -      -       -      -
     82P  LEU*     3.9    13.9    -      -       -      -
     91P  SER*     3.9     8.0    +      -       -      -
    114P  VAL*     3.7     6.1    -      -       -      +
    115P  PHE*     2.9    30.8    +      -       -      +
    119P  LEU*     3.5     4.9    +      -       -      -
    120P  PRO*     1.3    74.2    -      -       -      +
    122P  PHE*     1.3    66.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 122 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78P  TYR      3.8     0.2    -      -       -      +
     79P  VAL*     3.7     5.0    -      -       -      +
     80P  VAL*     2.9    68.0    +      -       +      +
     82P  LEU*     4.7     3.8    -      -       +      -
     91P  SER      4.0     8.7    -      -       -      -
     94P  THR*     3.6    29.6    -      -       +      -
     95P  ALA*     3.7    32.1    -      -       +      -
     98P  LEU*     3.8    23.6    -      -       +      -
    111P  ILE*     4.5     7.0    -      -       +      -
    113P  HIS      3.3    13.0    -      -       -      +
    114P  VAL*     4.1    15.7    -      -       +      -
    115P  PHE*     3.8     8.8    -      -       -      -
    121P  GLY*     1.3    78.9    -      -       -      +
    123P  LEU*     1.3    61.2    +      -       -      +
    124P  VAL*     3.9    13.7    -      -       +      -
    137P  LEU*     4.6     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 123 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  ASN*     6.0     0.2    -      -       -      +
    262A  SER*     3.5    37.0    -      -       -      +
    266A  ILE*     4.1    19.1    -      -       +      -
     77P  THR*     3.7    15.5    -      -       +      -
     78P  TYR      3.6    14.1    -      -       -      +
     79P  VAL*     4.0    12.3    -      -       +      -
    111P  ILE*     3.5     4.9    -      -       -      +
    112P  LEU*     2.8    58.5    +      -       +      -
    113P  HIS*     2.7    20.1    +      -       +      +
    115P  PHE*     4.1    11.2    -      -       +      -
    122P  PHE*     1.3    74.4    -      -       -      +
    124P  VAL*     1.3    59.5    +      -       -      +
    146P  ASP*     4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 124 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77P  THR*     3.4     6.0    -      -       -      +
     78P  TYR*     2.9    46.1    +      -       +      +
     80P  VAL*     3.8    24.0    -      -       +      -
     98P  LEU*     4.0     7.6    -      -       +      -
    109P  THR*     4.0    19.3    -      -       -      -
    110P  LYS      3.2    10.3    -      -       -      +
    111P  ILE*     4.1     5.6    -      -       +      -
    112P  LEU*     5.0     1.1    -      -       -      -
    122P  PHE*     3.9    13.7    -      -       +      -
    123P  LEU*     1.3    75.7    -      -       -      +
    125P  LYS*     1.3    62.7    +      -       -      +
    126P  MET*     3.8    31.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 125 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76P  GLY      3.4    14.1    -      -       -      +
     77P  THR*     4.1    12.1    -      -       -      +
    108P  LEU*     4.1     1.7    -      -       -      +
    109P  THR*     3.5     2.4    -      -       -      -
    110P  LYS*     2.8    72.9    +      -       +      +
    112P  LEU*     4.3    18.1    -      -       +      +
    124P  VAL*     1.3    70.8    -      -       -      +
    126P  MET*     1.3    61.7    -      -       -      +
----------------------------------------------------------
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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