Contacts of the strand formed by residues 135 - 140 (chain B) in PDB entry 5CYO


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 CYS 135 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     4.6    10.5    -      -       +      -
     25B  ASN      3.4     3.0    +      -       -      +
     26B  ILE*     3.4    10.9    -      -       +      +
     27B  MET      3.0    23.7    +      -       -      -
    133B  VAL*     3.5     6.7    -      -       -      +
    134B  HIS*     1.3    83.3    -      -       -      +
    136B  CYS*     1.3    66.6    +      -       -      +
    137B  LEU*     4.2     6.5    -      -       -      -
    162B  VAL*     4.6     0.9    -      -       -      -
    163B  ASN*     3.6    11.0    -      -       +      -
    165B  VAL*     3.5    35.2    -      -       -      -
    198B  TYR*     5.7     0.2    -      -       -      -
    265B  LEU*     4.1    15.5    -      -       +      -
    273B  ILE*     4.0    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  MET*     3.3    15.7    -      -       +      +
     29B  VAL*     3.4    39.0    -      -       -      -
    133B  VAL*     4.9     0.9    -      -       +      -
    135B  CYS*     1.3    75.9    -      -       -      +
    137B  LEU*     1.3    66.2    +      -       -      +
    138B  TYR*     3.4     2.2    +      -       -      -
    158B  LEU*     4.1     8.1    -      -       -      -
    162B  VAL*     3.9    12.6    -      -       +      -
    163B  ASN      2.7    16.0    +      -       -      +
    164B  ILE*     3.5    22.5    -      -       +      +
    165B  VAL      2.9    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  ILE*     4.0    21.1    -      -       +      -
     27B  MET      2.7    11.9    +      -       -      +
     28B  VAL*     3.5    11.5    -      -       +      -
     29B  VAL      2.9    27.9    +      -       -      +
     39B  LEU*     4.7    13.9    -      -       +      -
     43B  LEU*     5.8     6.3    -      -       +      -
    135B  CYS*     4.4     3.1    -      -       -      -
    136B  CYS*     1.3    70.2    -      -       -      +
    138B  TYR*     1.3    61.0    +      -       -      +
    139B  PHE*     3.5    14.6    -      -       +      -
    165B  VAL*     3.3    32.8    -      -       +      +
    167B  VAL*     4.6     5.2    -      -       +      -
    261B  LEU*     4.2    22.7    -      -       +      -
    265B  LEU*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  VAL*     3.5    31.9    -      -       +      -
     30B  GLY*     4.8     5.5    -      -       -      -
     91B  PHE*     4.5     2.8    -      -       -      -
    136B  CYS*     3.4     2.5    +      -       -      +
    137B  LEU*     1.3    71.7    -      -       -      +
    139B  PHE*     1.3    71.4    +      -       -      +
    140B  ILE*     3.6     6.3    +      -       +      +
    150B  LEU      4.4     0.2    +      -       -      -
    151B  ASP*     2.5    49.3    +      -       +      -
    154B  PHE*     3.4    25.5    -      +       +      +
    155B  MET*     3.4    40.8    -      -       +      -
    158B  LEU*     3.8    13.7    -      -       +      -
    164B  ILE*     4.3    16.6    -      -       +      -
    165B  VAL      3.1     7.5    +      -       -      -
    166B  PRO*     3.4     5.6    -      -       +      +
    167B  VAL*     2.8    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  VAL*     3.8    25.8    -      -       +      -
     29B  VAL      2.8    16.8    +      -       -      +
     30B  GLY*     4.1     4.7    -      -       -      -
     34B  LEU*     3.5    39.5    -      -       +      +
     35B  GLY      4.1     6.7    -      -       -      -
     36B  LYS*     3.6    38.1    -      -       +      -
     39B  LEU*     3.5    34.5    -      -       +      -
    137B  LEU*     3.5    21.5    -      -       +      -
    138B  TYR*     1.3    84.6    -      -       -      +
    140B  ILE*     1.3    60.9    +      -       -      +
    141B  PRO*     4.0     2.4    -      -       -      +
    151B  ASP*     4.7     1.4    -      -       -      +
    167B  VAL*     3.5    18.8    -      -       +      -
    169B  ALA*     4.0     9.0    -      -       +      -
    170B  LYS      6.0     0.2    -      -       -      -
    224B  VAL*     4.5     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  TYR*     4.0    15.5    -      -       +      +
    139B  PHE*     1.3    75.1    -      -       -      +
    141B  PRO*     1.3    83.9    -      -       +      +
    142B  ALA*     3.4     0.5    +      -       -      -
    147B  LEU*     4.0    32.3    -      -       +      -
    151B  ASP*     5.0     1.6    -      -       -      +
    155B  MET*     4.6     4.0    -      -       -      -
    166B  PRO*     3.8    28.0    -      -       +      -
    167B  VAL      2.7    18.0    +      -       -      +
    168B  ILE*     3.7     4.6    -      -       +      +
    169B  ALA*     2.8    29.0    +      -       -      +
    182B  PHE*     4.0    19.1    -      -       +      -
    186B  ILE*     4.0    17.7    -      -       +      -
    221B  PRO*     4.3     5.8    -      -       +      -
----------------------------------------------------------
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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