Contacts of the strand formed by residues 193 - 197 (chain B) in PDB entry 1CP3


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 PHE 193 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  THR*     3.9    14.4    -      -       -      -
    143B  PHE*     3.6    18.4    -      -       +      -
    144B  ARG*     3.9    12.3    -      -       +      -
    156B  LYS*     3.5    38.1    -      -       +      -
    158B  PHE*     3.6    32.1    -      +       -      -
    189B  VAL      4.1     5.4    -      -       -      -
    190B  ASP*     3.5    29.6    -      -       -      +
    191B  ALA      3.3    16.1    -      -       -      -
    192B  ASP*     1.3    78.4    -      -       -      +
    194B  LEU*     1.3    60.6    +      -       -      +
    195B  TYR*     3.6    32.3    -      +       +      -
    266B  VAL      4.1     1.1    -      -       -      +
    268B  MET*     2.9    33.3    +      -       +      +
    269B  LEU*     3.7     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  LYS      3.1     7.9    +      -       -      +
    157B  LEU*     3.7    21.0    -      -       +      -
    158B  PHE*     2.9    31.4    +      -       -      +
    159B  ILE*     6.1     0.4    -      -       +      -
    193B  PHE*     1.3    76.0    -      -       -      +
    195B  TYR*     1.3    67.2    +      -       -      +
    196B  ALA*     3.9    16.8    -      -       +      +
    232B  PHE*     3.7    28.3    -      -       +      -
    233B  MET*     3.8    25.6    -      -       -      -
    236B  LEU*     4.1    10.1    -      -       +      -
    265B  ILE*     4.6     2.7    -      -       +      -
    266B  VAL      3.5     7.4    -      -       -      +
    267B  SER*     4.0     9.6    -      -       -      -
    269B  LEU*     3.5    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  PRO*     6.3     0.9    -      -       +      -
    137B  LYS*     4.4    11.4    +      -       -      -
    140B  THR*     3.8    34.3    +      -       +      -
    158B  PHE*     3.5    24.7    -      +       +      -
    160B  ILE*     4.7     5.2    -      -       +      -
    190B  ASP*     4.5     3.6    +      -       -      -
    193B  PHE*     3.6    32.3    -      +       +      -
    194B  LEU*     1.3    72.9    -      -       -      +
    196B  ALA*     1.3    60.5    +      -       -      +
    197B  TYR*     3.3    43.2    +      +       +      -
    264B  CYS      3.4     2.1    -      -       -      +
    266B  VAL*     2.9    47.2    +      -       +      -
    268B  MET*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  PHE      2.9    14.0    +      -       -      +
    159B  ILE*     3.5    18.0    -      -       +      -
    160B  ILE*     2.9    27.8    +      -       -      +
    194B  LEU*     3.9    14.7    -      -       +      +
    195B  TYR*     1.3    68.1    -      -       -      +
    197B  TYR*     1.3    62.4    +      -       -      +
    198B  SER      3.9     0.2    +      -       -      -
    215B  PHE*     3.9    16.3    -      -       +      -
    219B  LEU*     5.4     0.4    -      -       +      -
    232B  PHE*     5.6     1.3    -      -       +      -
    236B  LEU*     4.3    20.0    -      -       +      -
    264B  CYS      4.2     2.0    -      -       -      -
    265B  ILE*     4.9     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  GLU*     5.7     0.2    -      -       -      -
    136B  LEU*     4.8    13.3    -      -       +      +
    160B  ILE*     3.7    37.0    -      -       +      +
    164B  ARG*     3.8    41.3    +      -       +      -
    195B  TYR*     3.5    36.1    -      +       +      -
    196B  ALA*     1.3    74.1    -      -       -      +
    198B  SER*     1.3    59.0    +      -       -      +
    199B  THR      3.7    15.3    -      -       -      +
    215B  PHE*     4.0     3.6    -      -       -      -
    263B  PRO*     3.4     5.9    -      -       -      +
    264B  CYS*     2.8    40.1    +      -       +      +
    266B  VAL*     3.6    28.9    -      -       +      -
----------------------------------------------------------
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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