Contacts of the strand formed by residues 161 - 168 (chain A) in PDB entry 2EA3


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 161 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  CYS*     4.7     4.9    -      -       -      -
    156A  GLY*     3.5     5.0    -      -       -      -
    157A  ASN      2.9    28.9    +      -       -      +
    158A  CYS*     4.3     1.9    -      -       -      -
    159A  ARG      3.6     1.6    -      -       -      +
    160A  THR*     1.3    84.9    +      -       -      +
    162A  GLY*     1.3    58.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  THR*     3.5    25.1    +      -       -      +
    130A  VAL      4.1     4.7    -      -       -      -
    131A  CYS*     4.3     8.1    -      -       -      +
    155A  SER*     3.2    15.5    -      -       -      -
    156A  GLY*     4.0     2.2    -      -       -      -
    157A  ASN      3.8     2.3    +      -       -      -
    161A  GLY*     1.3    75.0    -      -       -      -
    163A  THR*     1.3    64.5    +      -       -      -
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Residues in contact with THR 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ARG*     3.7    42.4    +      -       +      +
    128A  THR      3.4    17.9    +      -       -      +
    129A  THR*     5.6     0.3    -      -       -      -
    154A  GLY*     3.2     3.9    -      -       -      -
    155A  SER*     2.9    44.5    +      -       -      +
    162A  GLY*     1.3    73.8    +      -       -      -
    164A  THR*     1.3    64.8    +      -       -      +
    165A  PHE*     3.8    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  THR*     2.9    37.7    +      -       -      -
    130A  VAL      2.6    24.8    +      -       -      -
    131A  CYS*     3.4     0.7    -      -       -      -
    132A  ALA*     3.3    27.4    +      -       +      +
    151A  THR*     3.8    17.7    -      -       +      -
    153A  GLY      3.4    12.7    -      -       -      +
    154A  GLY*     5.3     0.3    -      -       -      -
    155A  SER      5.1     0.9    +      -       -      -
    163A  THR*     1.3    74.9    +      -       -      +
    165A  PHE*     1.3    71.3    +      -       -      +
    166A  PHE*     3.6    31.0    -      -       +      -
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Residues in contact with PHE 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  SER*     3.8    20.0    -      -       -      -
    114A  SER      4.7     2.2    -      -       -      -
    115A  VAL*     3.5    33.2    -      -       +      -
    117A  TYR*     4.7     2.9    -      -       -      +
    125A  LEU*     3.8    20.0    -      -       +      -
    126A  ILE      3.1     5.4    -      -       -      +
    127A  ARG*     3.4    55.9    -      -       +      -
    152A  SER*     2.9    24.0    +      -       -      -
    153A  GLY      2.7    24.7    +      -       -      +
    154A  GLY*     4.0    13.0    -      -       -      -
    155A  SER*     5.5     0.9    -      -       -      -
    163A  THR*     3.8    14.4    -      -       +      -
    164A  THR*     1.3    76.0    -      -       -      +
    166A  PHE*     1.3    66.4    -      -       -      +
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Residues in contact with PHE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ARG*     3.9    15.7    -      -       +      -
    125A  LEU*     3.4     9.2    -      -       -      -
    126A  ILE*     2.7    45.4    +      -       +      +
    128A  THR*     3.3    42.6    -      -       +      -
    130A  VAL*     4.4     3.6    -      -       +      -
    141A  LEU*     3.6    48.0    -      -       +      -
    149A  GLY*     4.5     0.2    -      -       -      -
    150A  VAL      3.3    11.9    -      -       -      +
    151A  THR*     3.1    44.6    -      -       -      -
    152A  SER      4.1     0.4    -      -       -      +
    164A  THR*     3.6    23.8    -      -       +      -
    165A  PHE*     1.3    75.5    -      -       -      +
    167A  GLN*     1.3    61.6    +      -       -      +
    168A  PRO*     3.4     1.2    -      -       -      +
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Residues in contact with GLN 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ASN*     3.7     9.6    +      -       -      +
     56A  ASP*     2.9    51.2    +      -       +      +
     57A  TYR*     3.7    20.9    -      -       +      -
    123A  ARG      5.0     2.7    -      -       -      +
    124A  GLY      5.6     0.2    -      -       -      -
    125A  LEU*     3.7    13.5    -      -       +      +
    149A  GLY*     3.0     1.1    -      -       -      -
    150A  VAL*     2.9    37.6    +      -       +      +
    152A  SER*     4.3     2.3    -      -       -      -
    166A  PHE*     1.3    70.1    -      -       -      +
    168A  PRO*     1.3   100.9    +      -       -      +
    171A  PRO*     4.1    14.5    -      -       -      +
    172A  ILE*     3.8    15.2    -      -       +      +
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Residues in contact with PRO 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  GLY      3.2    28.3    -      -       -      +
    126A  ILE*     4.0    17.3    -      -       +      -
    148A  GLN      3.4    11.2    -      -       -      +
    166A  PHE      3.4     7.8    -      -       -      +
    167A  GLN*     1.3   112.1    +      -       -      +
    169A  VAL*     1.3    63.9    +      -       -      +
    170A  ASN*     4.5     1.1    -      -       +      +
    171A  PRO*     3.5    20.3    -      -       +      +
    172A  ILE*     3.5     5.9    -      -       -      +
----------------------------------------------------------
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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