Contacts of the strand formed by residues 24 - 31 (chain B) in PDB entry 4CYM


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 HIS 24 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  GLU*     1.3    83.3    +      -       -      +
     25B  LEU*     1.3    57.6    +      -       -      +
     26B  PHE*     3.6    28.1    -      +       +      -
     73B  THR*     3.9    23.3    -      -       +      +
     74B  LEU      2.9    10.4    +      -       -      +
     75B  VAL*     4.4     4.7    -      -       +      -
     76B  ARG*     2.7    38.7    +      -       -      +
    193B  LEU*     3.5    29.3    -      -       +      +
    196B  HIS*     3.8    36.4    +      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  HIS*     1.3    74.6    -      -       -      +
     26B  PHE*     1.3    71.1    +      -       -      +
     27B  LYS      4.3     0.7    +      -       -      -
     64B  LEU*     4.9     3.1    -      -       +      -
     76B  ARG*     3.4    35.0    -      -       +      -
     78B  GLN*     3.9    28.9    -      -       +      +
    100B  VAL*     5.8     0.9    -      -       -      +
    553E  VAL*     3.3    41.6    -      -       +      +
    554E  GLU*     3.6    41.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  HIS*     3.6    28.3    -      +       +      -
     25B  LEU*     1.3    79.5    -      -       -      +
     27B  LYS*     1.3    60.4    +      -       -      +
     28B  VAL*     3.5     5.8    +      -       +      +
     75B  VAL*     3.4    33.0    -      -       +      -
     76B  ARG      2.9     9.5    +      -       -      -
     77B  LEU*     3.8    17.4    -      -       +      -
     78B  GLN*     2.8    33.0    +      -       -      +
    100B  VAL*     3.7    20.2    -      -       +      -
    189B  VAL*     4.3     6.5    -      -       +      -
    192B  ILE*     3.5    34.5    -      -       +      -
    193B  LEU*     4.0    22.7    -      -       +      -
    196B  HIS*     4.4    19.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  LEU*     4.3     1.4    +      -       -      +
     26B  PHE*     1.3    69.3    -      -       -      +
     28B  VAL*     1.3    62.1    +      -       -      +
     29B  LEU*     4.7     1.3    -      -       +      -
     78B  GLN*     3.7    15.2    -      -       -      +
     80B  TRP*     3.2    54.0    -      -       +      +
     94B  VAL      4.3     2.8    +      -       -      -
     95B  TYR      2.8    25.6    +      -       -      -
     97B  LYS*     2.4    38.0    +      -       -      +
     98B  GLU*     3.4    25.9    +      -       +      +
     99B  ALA*     3.6    18.6    -      -       +      +
    100B  VAL*     3.0    31.4    +      -       -      +
    101B  GLY      3.7     1.0    +      -       -      -
    551E  TYR*     5.6     0.2    -      -       -      -
    553E  VAL*     5.2    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  PHE*     4.1    11.4    -      -       +      +
     27B  LYS*     1.3    79.6    -      -       -      +
     29B  LEU*     1.3    76.5    +      -       -      +
     77B  LEU*     4.1    21.3    -      -       +      -
     78B  GLN      2.8    13.3    +      -       -      +
     79B  LEU*     3.5    20.2    -      -       +      +
     80B  TRP*     2.8    26.5    +      -       -      -
    101B  GLY      3.2    15.9    -      -       -      +
    103B  PHE*     4.3     5.6    -      -       +      -
    188B  LEU*     3.8    18.4    -      -       +      -
    192B  ILE*     4.2    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  LYS*     4.7     2.0    -      -       -      -
     28B  VAL*     1.3    74.8    -      -       -      +
     30B  VAL*     1.3    64.9    +      -       -      +
     31B  ILE*     4.2    10.3    -      -       +      -
     80B  TRP*     3.7    21.8    -      -       +      -
     82B  ILE*     3.8    14.1    -      -       +      -
     95B  TYR      3.7    22.2    -      -       -      +
     96B  TYR*     3.4    27.1    -      -       +      -
     99B  ALA*     3.8    25.6    -      -       +      -
    101B  GLY      3.0     7.4    +      -       -      +
    102B  ALA*     3.4     8.0    -      -       +      -
    103B  PHE      2.8    27.0    +      -       -      -
    124B  LEU*     3.5    23.1    -      -       +      -
    136B  ILE*     4.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  VAL      4.6     0.7    -      -       -      +
     29B  LEU*     1.3    78.4    -      -       -      +
     31B  ILE*     1.3    64.0    +      -       -      +
     38B  LYS*     3.7    33.4    -      -       +      +
     41B  ILE*     5.7     4.5    -      -       +      -
     42B  ILE*     3.7    30.3    -      -       +      -
     79B  LEU*     4.4    12.8    -      -       +      -
     80B  TRP      2.9    13.7    +      -       -      +
     81B  ASP*     4.1     1.3    -      -       -      -
     82B  ILE*     3.1    26.0    +      -       -      +
    103B  PHE*     3.4    22.4    -      -       +      -
    105B  VAL*     4.1    14.8    -      -       +      -
    141B  LEU*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  LEU*     4.2     7.2    -      -       +      -
     30B  VAL*     1.3    84.4    -      -       -      +
     32B  GLY*     1.3    59.5    +      -       -      +
     38B  LYS*     3.3    11.9    -      -       -      +
     82B  ILE*     3.9    28.5    -      -       +      -
     96B  TYR*     4.2    14.1    -      -       +      +
    102B  ALA*     5.2     2.0    -      -       +      -
    103B  PHE      2.9    16.7    +      -       -      +
    104B  VAL*     3.4    22.8    -      -       +      -
    105B  VAL*     2.9    25.8    +      -       -      +
    120B  TRP*     3.9    40.6    -      -       +      +
    124B  LEU*     4.5    20.0    -      -       +      -
----------------------------------------------------------
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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