Contacts of the strand formed by residues 122 - 127 (chain A) in PDB entry 2ERY


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 MET 122 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PHE*     3.1    24.0    -      -       +      +
     91A  LEU*     3.8    25.6    -      -       +      -
    108A  GLN*     3.9    17.3    -      -       +      -
    111A  ILE*     3.4    39.3    -      -       +      -
    112A  LEU*     3.8    26.0    -      -       +      -
    120A  PHE*     3.1    15.6    +      -       +      +
    121A  PRO*     1.3    80.2    -      -       -      +
    123A  ILE*     1.3    71.9    +      -       -      +
    151A  VAL*     3.9    28.4    -      -       +      +
    152A  THR      4.5     2.3    +      -       -      -
    171A  LEU*     4.1     1.9    -      -       -      +
    174A  VAL*     4.2     8.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PHE      2.9     7.7    +      -       -      -
     90A  LEU*     3.6    11.5    -      -       +      -
     91A  LEU*     2.9    30.2    +      -       -      +
    122A  MET*     1.3    81.7    -      -       -      +
    124A  LEU*     1.3    67.2    +      -       -      +
    125A  ILE*     3.8    13.5    +      -       +      +
    151A  VAL*     4.7     0.7    -      -       -      -
    152A  THR*     3.2    33.9    -      -       +      +
    154A  MET*     4.6     6.1    -      -       +      +
    167A  ALA*     3.8     5.6    -      -       -      +
    170A  GLU*     3.4    24.2    -      -       +      +
    171A  LEU*     3.1    45.5    -      -       +      +
    174A  VAL*     4.3     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  LEU*     3.4    21.1    -      -       +      +
     93A  PHE*     3.7    21.8    -      -       +      -
    104A  ILE*     3.7    27.6    -      -       +      -
    123A  ILE*     1.3    70.9    -      -       -      +
    125A  ILE*     1.3    61.0    +      -       -      +
    142A  GLY      3.6    23.1    -      -       -      +
    145A  LEU*     4.0    15.7    -      -       +      -
    146A  ALA*     3.8    16.4    -      -       +      +
    149A  LEU*     5.1     0.9    -      -       +      -
    151A  VAL*     3.9    14.8    -      -       +      +
    152A  THR      2.9    15.0    +      -       -      +
    153A  TYR*     3.3    17.9    -      -       +      -
    154A  MET      2.9    26.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  LEU*     4.2    18.6    -      -       +      -
     90A  LEU*     4.1    28.7    -      -       +      -
     91A  LEU      2.9    12.8    +      -       -      +
     92A  VAL*     3.4     7.0    -      -       +      -
     93A  PHE*     3.0    33.2    +      -       -      +
    123A  ILE*     4.0    14.8    -      -       +      +
    124A  LEU*     1.3    80.8    -      -       -      +
    126A  GLY*     1.3    63.1    +      -       -      +
    127A  ASN*     4.2     1.8    -      -       +      +
    154A  MET*     3.2    23.1    -      -       +      +
    156A  ALA*     3.9    26.5    -      -       +      -
    167A  ALA*     3.8    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  PHE*     3.6    26.5    -      -       -      -
     95A  VAL*     3.8     8.7    -      -       -      +
    125A  ILE*     1.3    69.4    -      -       -      +
    127A  ASN*     1.3    63.2    +      -       -      -
    129A  ALA*     4.4     0.9    -      -       -      +
    153A  TYR*     3.7    14.2    -      -       -      -
    154A  MET      3.0    11.1    +      -       -      -
    155A  GLU*     3.4     8.0    -      -       -      +
    156A  ALA      3.0    24.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  GDP      3.1    25.7    +      -       -      -
     25A  VAL      2.9    24.7    +      -       -      +
     26A  GLY*     3.6     7.5    -      -       -      -
     30A  LEU*     3.6    20.3    -      -       +      +
     92A  VAL*     4.0    10.8    -      -       +      -
     93A  PHE      2.8    17.1    +      -       -      +
     94A  SER*     3.6     0.2    -      -       -      -
     95A  VAL*     2.9    27.9    +      -       -      +
    125A  ILE*     3.5     3.3    +      -       +      -
    126A  GLY*     1.3    73.1    -      -       -      +
    128A  LYS*     1.3    77.5    +      -       -      +
    129A  ALA      3.3     1.3    -      -       -      -
    156A  ALA      3.4     5.7    -      -       -      +
    157A  SER*     3.4     5.4    -      -       -      -
    158A  ALA      3.3    20.6    +      -       -      -
----------------------------------------------------------
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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