Contacts of the strand formed by residues 272 - 277 (chain B) in PDB entry 2XH1


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 272 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  VAL*     3.4     8.7    -      -       -      +
    114B  THR*     2.7    41.6    +      -       -      +
    116B  GLY      3.6    12.2    -      -       -      +
    117B  SER      4.0     1.1    -      -       -      -
    259B  ASP      3.7     9.9    -      -       -      -
    260B  SER*     4.5     4.3    -      -       -      -
    271B  ILE*     1.3    74.1    -      -       -      +
    273B  PHE*     1.3    67.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 273 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  LEU*     3.9    40.2    -      -       +      -
     90B  LEU*     4.1    14.1    -      -       +      -
     91B  GLN*     3.9    18.6    -      -       +      -
    111B  LEU*     4.1     9.4    -      -       +      -
    112B  CYS      3.4    11.7    -      -       -      +
    113B  VAL*     4.4     1.1    -      -       -      -
    114B  THR*     3.7     4.8    +      -       -      -
    117B  SER*     5.1     1.1    -      -       -      -
    235B  PHE*     5.3     5.4    -      +       -      -
    257B  ARG      4.0     0.3    -      -       -      +
    258B  ALA*     3.6     3.1    -      -       -      +
    259B  ASP*     2.9    74.2    +      -       +      +
    260B  SER      4.7     3.1    -      -       -      -
    261B  PHE*     3.9    33.4    -      +       -      -
    272B  GLY*     1.3    80.2    -      -       -      +
    274B  LEU*     1.3    60.7    +      -       -      +
    275B  THR*     4.2    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 274 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  LEU*     3.1     5.2    -      -       -      +
    112B  CYS*     2.9    41.8    +      -       -      +
    114B  THR*     4.2     7.1    -      -       +      +
    120B  GLY*     4.1    17.9    -      -       -      +
    121B  LEU*     4.6     2.7    -      -       +      +
    124B  VAL*     3.7    26.7    -      -       +      -
    256B  ILE*     3.8    16.8    -      -       +      -
    257B  ARG      3.5    11.7    -      -       -      +
    258B  ALA*     4.1    17.7    -      -       +      +
    273B  PHE*     1.3    74.4    -      -       -      +
    275B  THR*     1.3    62.2    +      -       -      +
    281B  ILE*     4.0    17.9    -      -       +      +
    284B  VAL*     3.8    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 275 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  GLN*     2.9    29.7    +      -       +      +
    109B  MET*     3.8    28.7    -      -       +      -
    110B  ASP      3.4    12.3    -      -       -      +
    111B  LEU*     3.8    13.4    -      -       +      +
    247B  LEU*     4.0    20.7    -      -       +      +
    255B  VAL      4.2     0.5    -      -       -      +
    256B  ILE*     3.6     2.9    -      -       -      +
    257B  ARG*     2.8    45.1    +      -       -      +
    259B  ASP*     4.7     0.5    +      -       -      -
    273B  PHE*     4.2     4.5    -      -       -      -
    274B  LEU*     1.3    76.3    +      -       -      +
    276B  GLY*     1.3    62.1    +      -       -      +
    281B  ILE*     4.0     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 276 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  GLY      4.7     0.4    -      -       -      -
    108B  GLN      3.7     0.4    -      -       -      +
    109B  MET*     4.6     5.4    -      -       -      -
    110B  ASP      2.9    33.3    +      -       -      +
    247B  LEU*     5.5     3.8    -      -       -      -
    255B  VAL      3.7     6.7    -      -       -      -
    256B  ILE*     4.5     1.3    -      -       -      -
    275B  THR*     1.3    78.6    -      -       -      +
    277B  PRO*     1.4    77.8    -      -       -      +
    281B  ILE*     3.4     9.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 277 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  TYR*     3.7    23.3    -      -       +      +
    107B  GLY*     3.5    16.6    -      -       -      +
    250B  ASP*     5.6     0.4    -      -       -      +
    253B  GLY*     3.4    26.7    -      -       -      +
    254B  ARG*     5.2     0.9    -      -       -      -
    255B  VAL      3.3    15.9    -      -       -      +
    256B  ILE*     4.1    13.5    -      -       +      -
    276B  GLY*     1.4    81.8    -      -       -      +
    278B  LYS*     1.3    66.1    +      -       -      +
    279B  PRO*     4.1     6.3    -      -       +      -
    280B  LEU*     3.0    31.7    +      -       +      +
    281B  ILE*     3.0    11.0    +      -       +      -
----------------------------------------------------------
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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