Contacts of the strand formed by residues 125 - 131 (chain H) in PDB entry 2Q5E


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 PHE 125 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269B  ARG      6.5     0.7    -      -       -      -
    113H  VAL*     4.8     1.1    -      -       +      -
    123H  ALA*     4.2     2.1    -      -       -      +
    124H  ASP*     1.3    89.0    -      -       +      +
    126H  ILE*     1.3    67.7    +      -       -      +
    127H  VAL*     4.2     4.3    -      -       +      -
    139H  TYR*     3.6     0.2    -      -       -      -
    140H  VAL*     2.7    64.4    +      -       +      +
    142H  LYS*     3.4    39.9    -      -       +      -
    173H  VAL*     4.5     6.1    -      -       +      -
    176H  LEU*     3.8    57.7    -      -       +      -
    177H  LEU*     3.9    20.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 126 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269B  ARG*     5.1    33.6    -      -       +      +
    120H  ILE      5.3     2.7    -      -       -      +
    123H  ALA*     4.6    11.4    -      -       +      +
    125H  PHE*     1.3    79.1    -      -       -      +
    127H  VAL*     1.3    68.5    +      -       -      +
    128H  PRO*     4.3     3.8    -      -       +      +
    137H  GLN*     3.7    39.7    -      -       +      +
    138H  VAL      3.2     6.7    -      -       -      +
    139H  TYR*     3.5    33.4    -      -       +      -
    176H  LEU*     4.8     4.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 127 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125H  PHE*     4.2     8.3    -      -       +      -
    126H  ILE*     1.3    81.9    -      -       -      +
    128H  PRO*     1.3    65.8    -      -       +      +
    129H  ILE*     3.8    24.0    +      -       +      -
    137H  GLN*     4.2     2.5    -      -       -      -
    138H  VAL*     2.7    43.5    +      -       +      +
    140H  VAL*     4.6     3.4    -      -       +      -
    172H  PRO*     4.0    26.7    -      -       +      +
    173H  VAL*     4.3    22.2    -      -       +      -
    176H  LEU*     4.0    23.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 128 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227B  PRO*     6.2     0.4    -      -       +      -
    126H  ILE*     4.3     3.8    -      -       +      +
    127H  VAL*     1.3    86.6    -      -       +      +
    129H  ILE*     1.3    63.4    -      -       -      +
    130H  GLU      4.5     0.2    +      -       -      -
    135H  THR*     4.2    13.2    -      -       -      +
    136H  HIS      3.4     1.8    -      -       -      +
    137H  GLN*     3.2    25.8    -      -       -      +
    172H  PRO*     5.4     4.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 129 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117H  PHE*     4.7     8.7    -      -       +      -
    127H  VAL*     3.9    16.8    -      -       +      -
    128H  PRO*     1.3    79.1    -      -       -      +
    130H  GLU*     1.3    64.5    +      -       -      +
    131H  ILE*     3.7    24.6    +      -       +      +
    134H  THR      3.6     1.2    -      -       -      +
    135H  THR*     3.2     3.0    -      -       -      -
    136H  HIS*     2.7    39.4    +      -       -      +
    138H  VAL*     3.3    28.5    -      -       +      -
    168H  LYS*     4.2    26.2    -      -       +      +
    169H  TYR*     3.8    33.2    -      -       +      -
    172H  PRO*     5.2     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 130 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130D  GLU*     5.1    16.3    -      -       +      +
    168D  LYS*     4.8    17.5    -      -       -      +
    128H  PRO      4.3     0.2    -      -       -      -
    129H  ILE*     1.3    74.1    -      -       -      +
    131H  ILE*     1.3    60.7    +      -       -      +
    132H  GLU*     3.4     6.4    +      -       -      -
    133H  GLY*     2.7    46.3    +      -       -      +
    134H  THR      3.6     3.8    -      -       -      -
    135H  THR*     3.8    17.7    -      -       +      +
    168H  LYS*     3.9    19.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 131 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194C  PHE*     4.8    20.9    -      -       +      -
    199C  TYR*     5.6     4.0    -      -       -      +
    117H  PHE*     4.8    14.6    -      -       +      -
    129H  ILE*     4.1    19.1    -      -       +      +
    130H  GLU*     1.3    76.4    -      -       -      +
    132H  GLU*     1.3    89.3    +      -       +      +
    133H  GLY      2.8     1.3    +      -       -      -
    134H  THR*     2.8    28.4    +      -       -      +
    136H  HIS*     4.0    16.2    -      -       +      +
    168H  LYS*     3.2    35.7    -      -       -      +
----------------------------------------------------------
 Back to top of page


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