Contacts of the strand formed by residues 152 - 157 (chain B) in PDB entry 4U7B


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 ILE 152 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  PHE*     3.6    17.6    +      -       +      +
    149B  LEU*     3.1    17.7    +      -       +      +
    150B  HIS      3.4     1.6    -      -       -      +
    151B  ARG*     1.3    77.9    -      -       -      +
    153B  VAL*     1.3    68.1    +      -       -      +
    154B  THR*     5.0     1.3    -      -       -      +
    198B  ASP*     3.5    20.1    -      -       -      +
    199B  GLN      4.5     1.0    +      -       -      -
    245B  ILE*     3.6    27.6    -      -       +      +
    247B  LEU*     3.5    41.1    -      -       +      -
    271B  LEU*     4.6     4.3    -      -       +      -
    326B  ILE*     3.5    41.3    -      -       +      -
    329B  LEU*     5.3     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 153 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  ARG      4.6     1.6    -      -       -      +
    152B  ILE*     1.3    76.5    -      -       -      +
    154B  THR*     1.3    67.8    +      -       -      +
    196B  TRP*     4.8     6.3    -      -       +      -
    197B  TRP      3.5    20.6    -      -       -      +
    198B  ASP*     4.4     5.2    -      -       +      -
    203B  ILE*     4.4    14.4    -      -       +      -
    226B  LEU*     5.4     2.9    -      -       +      -
    230B  LEU*     4.7    16.6    -      -       +      -
    244B  VAL*     3.5    26.7    -      -       +      -
    245B  ILE      2.8    17.7    +      -       -      +
    246B  PHE*     3.4    17.7    -      -       +      -
    247B  LEU      3.1    21.1    +      -       -      -
    268B  TRP*     5.8     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152B  ILE*     5.0     2.5    -      -       -      -
    153B  VAL*     1.3    76.2    -      -       -      +
    155B  GLY*     1.3    60.4    +      -       -      +
    196B  TRP*     3.0     8.6    -      -       -      +
    197B  TRP*     2.7    76.5    +      -       +      +
    246B  PHE*     5.0     1.1    -      -       -      -
    247B  LEU*     2.6    41.8    +      -       -      +
    248B  HIS*     4.8     0.2    -      -       -      -
    281B  ALA*     6.0     0.2    -      -       -      -
    282B  PRO*     4.2    11.9    -      -       +      +
    283B  SER*     3.4     9.6    +      -       -      +
    326B  ILE*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  THR*     1.3    81.2    +      -       -      +
    156B  ASP*     1.3    65.7    +      -       -      +
    195B  VAL      2.8    15.9    -      -       -      -
    196B  TRP*     3.6    17.4    -      -       -      -
    197B  TRP*     4.5     0.2    -      -       -      -
    246B  PHE*     5.1     0.4    -      -       -      -
    247B  LEU      3.5    11.1    +      -       -      +
    248B  HIS*     4.0    14.5    -      -       -      +
    249B  ALA      4.8     0.7    +      -       -      -
    283B  SER*     3.7     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 156 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  GLY*     1.3    76.7    -      -       -      +
    157B  GLU*     1.3    96.9    +      -       -      +
    194B  CYS*     3.8     0.9    -      -       -      +
    195B  VAL      3.0    26.6    +      -       -      +
    196B  TRP*     4.9     3.9    -      -       -      +
    249B  ALA*     4.4    22.0    -      -       -      +
    254B  HIS*     5.7     5.0    +      -       -      -
    281B  ALA*     5.0     3.7    -      -       +      +
    283B  SER*     3.8    10.8    +      -       -      -
    284B  ASP*     3.1    26.0    -      -       -      +
    288B  PHE*     3.7    23.8    -      -       +      -
     57D    T      4.2    11.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  ASP*     1.3   100.7    +      -       -      +
    158B  LYS*     1.3    62.3    +      -       -      +
    192B  MET*     3.5    28.9    -      -       +      +
    193B  LEU      3.3    11.2    -      -       -      +
    194B  CYS*     3.9    15.5    -      -       -      +
    196B  TRP*     5.7     2.3    -      -       -      -
    214B  VAL*     3.6    27.1    -      -       -      +
    219B  TYR*     4.6     6.1    -      -       -      -
    222B  GLN*     5.6     0.3    -      -       -      +
    253B  SER*     5.1     0.5    +      -       -      -
    254B  HIS*     3.2    32.3    +      -       +      -
    284B  ASP*     5.5     0.2    -      -       -      +
    288B  PHE*     4.1     3.2    -      -       -      -
     56D    A      4.7     1.9    +      -       -      -
     57D    T      4.2    10.7    +      -       -      +
----------------------------------------------------------
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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