Contacts of the strand formed by residues 152 - 155 (chain B) in PDB entry 1A7A


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 152 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  MSE      3.5    16.6    -      -       -      +
    128B  ILE      3.1    24.6    +      -       -      +
    150B  ILE*     3.7     2.8    -      -       -      +
    151B  ARG*     1.3    81.7    -      -       -      +
    153B  ILE*     1.3    63.8    +      -       -      -
    154B  SER*     5.8     0.2    -      -       -      -
    175B  VAL*     3.5     7.3    -      -       -      +
    176B  PRO      3.1    11.2    -      -       -      -
    369B  GLN*     5.3     1.0    +      -       -      -
    372B  LEU*     4.0    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 153 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  ILE*     3.5    16.4    -      -       +      +
    130B  ASP*     5.0     0.2    -      -       +      -
    136B  THR*     3.2    45.8    -      -       +      -
    140B  HIS*     4.2    10.3    -      -       +      -
    152B  GLY*     1.3    74.3    -      -       -      -
    154B  SER*     1.3    73.0    +      -       -      +
    155B  GLU*     4.2     3.8    -      -       +      +
    164B  LEU*     4.5    10.3    -      -       +      -
    173B  LEU*     4.4    12.8    -      -       +      -
    175B  VAL*     3.3    30.7    -      -       +      -
    176B  PRO      2.6     9.3    +      -       -      +
    177B  ALA*     2.9    18.8    -      -       +      -
    178B  ILE      2.8    24.4    +      -       -      -
    372B  LEU*     4.2     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  ILE      2.8     7.2    +      -       -      -
    130B  ASP      2.9    27.7    +      -       -      +
    153B  ILE*     1.3    77.5    -      -       -      +
    155B  GLU*     1.3    58.8    +      -       -      +
    178B  ILE*     3.9     5.2    -      -       -      +
    180B  VAL*     3.7     2.8    -      -       -      +
    365B  GLN*     2.4    27.8    +      -       -      -
    368B  ALA*     3.2    25.7    -      -       -      +
    369B  GLN*     3.0    29.3    +      -       -      -
    372B  LEU*     5.1     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  ASP*     3.1     7.3    -      -       +      +
    131B  ASP*     3.1    10.2    +      -       -      -
    132B  GLY      2.5    28.8    +      -       -      -
    133B  GLY*     3.0    12.1    +      -       -      +
    136B  THR*     5.5     0.4    -      -       -      +
    153B  ILE*     4.1     3.9    -      -       +      +
    154B  SER*     1.3    73.2    -      -       -      +
    156B  GLU*     1.3    77.1    +      -       -      +
    157B  THR      2.7    25.6    +      -       -      +
    160B  GLY*     3.6    17.6    -      -       -      +
    161B  VAL*     3.9     7.1    -      -       +      +
    164B  LEU*     3.4    35.7    -      -       +      -
    178B  ILE      3.2     7.7    +      -       -      +
    179B  ASN      4.1     0.3    -      -       -      -
    180B  VAL*     3.0    30.8    +      -       -      +
    181B  ASN      3.6     1.4    +      -       -      -
    365B  GLN*     4.3     0.4    -      -       -      -
----------------------------------------------------------
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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