Contacts of the strand formed by residues 193 - 198 (chain G) 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 LEU 193 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156G  ASP      3.9     0.9    -      -       -      +
    157G  GLU*     3.1     5.5    -      -       -      -
    158G  LYS*     2.9    39.1    +      -       +      +
    160G  ILE*     3.9    23.1    -      -       +      -
    192G  MET*     1.3    74.4    -      -       -      +
    194G  CYS*     1.3    76.7    +      -       -      +
    195G  VAL*     4.2    19.1    -      -       +      -
    205G  TYR*     3.7    27.1    -      -       +      -
    206G  GLU      3.7     5.2    -      -       -      +
    207G  LEU*     4.1    14.8    -      -       +      -
    288G  PHE*     4.5     7.4    -      -       +      -
    291G  MET*     4.1    14.1    -      -       +      -
    310G  LEU*     4.0    18.2    -      -       +      -
    314G  PHE*     4.7     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 194 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156G  ASP      3.7     6.1    -      -       -      +
    157G  GLU*     4.1     9.6    -      -       +      +
    192G  MET*     4.0    12.6    -      -       -      -
    193G  LEU*     1.3    76.2    -      -       -      +
    195G  VAL*     1.3    61.5    +      -       -      +
    196G  TRP*     3.6    25.5    -      -       +      -
    205G  TYR*     3.2     4.2    -      -       -      +
    206G  GLU*     2.8    40.4    +      -       +      +
    208G  LEU*     3.9    12.1    -      -       -      -
    214G  VAL*     3.9    17.7    -      -       -      -
    222G  GLN*     3.5    24.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 195 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155G  GLY*     3.1    20.1    -      -       -      -
    156G  ASP      3.2     8.5    +      -       -      -
    193G  LEU*     4.2    14.6    -      -       +      -
    194G  CYS*     1.3    74.8    -      -       -      +
    196G  TRP*     1.3    73.3    +      -       -      +
    197G  TRP*     4.3    10.2    +      -       +      -
    202G  VAL*     3.5    29.4    -      -       +      -
    204G  TYR      3.7     4.5    -      -       -      -
    205G  TYR*     3.8     9.9    -      -       +      -
    283G  SER*     6.0     0.4    -      -       -      -
    287G  LEU*     4.5     9.4    -      -       +      -
    288G  PHE*     3.9    33.0    -      -       +      -
    314G  PHE*     4.2    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 196 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153G  VAL*     4.5     4.7    -      -       +      -
    154G  THR      3.2     5.8    -      -       -      +
    155G  GLY*     3.6    22.2    -      -       -      -
    156G  ASP      5.5     3.1    -      -       -      -
    157G  GLU*     5.7     1.3    -      -       -      -
    194G  CYS*     3.6    31.4    -      -       +      -
    195G  VAL*     1.3    79.2    -      -       -      +
    197G  TRP*     1.3    63.1    +      -       -      +
    202G  VAL*     3.7     3.3    -      -       -      +
    203G  ILE*     2.9    23.2    +      -       -      -
    204G  TYR*     3.1    42.7    +      +       -      +
    206G  GLU      4.8     0.7    -      -       -      -
    219G  TYR*     3.8    28.8    +      +       -      -
    222G  GLN*     3.5    37.2    -      -       +      -
    223G  LEU*     5.3     2.2    -      -       +      +
    226G  LEU*     3.9    31.3    -      -       +      +
    246G  PHE*     3.7    36.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with TRP 197 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153G  VAL*     4.5     2.4    -      -       -      +
    154G  THR*     2.8    45.3    +      -       +      +
    195G  VAL*     4.3     6.5    -      -       +      -
    196G  TRP*     1.3    81.3    -      -       -      +
    198G  ASP*     1.3    77.4    +      -       -      +
    201G  GLY      3.2    15.7    -      -       -      +
    202G  VAL*     3.7    10.8    -      -       +      -
    203G  ILE*     3.9     6.7    -      -       -      +
    282G  PRO*     3.4    48.2    -      -       +      -
    283G  SER*     3.2    19.0    +      -       -      -
    286G  HIS*     4.5    10.1    -      -       -      -
    287G  LEU*     3.1    36.5    -      -       +      +
    322G  TYR*     3.7    29.6    -      +       +      -
    325G  GLY      4.5     3.6    -      -       -      -
    326G  ILE*     3.3    28.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 198 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150G  HIS      5.2     6.0    -      -       -      +
    152G  ILE      3.1    24.0    -      -       -      +
    153G  VAL*     4.2     5.6    -      -       +      -
    197G  TRP*     1.3    90.3    -      -       -      +
    199G  GLN*     1.3    67.5    +      -       +      +
    200G  SER*     3.2     7.2    +      -       -      -
    201G  GLY      2.9    18.2    +      -       -      +
    203G  ILE*     3.8    11.6    -      -       +      +
    234G  ARG*     2.8    48.9    +      -       -      +
    322G  TYR*     3.7     1.6    -      -       -      +
    326G  ILE*     4.1     4.0    -      -       -      -
----------------------------------------------------------
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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