Contacts of the strand formed by residues 22 - 29 (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 PHE 22 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  GLY*     1.3    74.7    -      -       -      +
     23B  GLU*     1.3    56.3    +      -       -      +
     80B  ARG      3.9    18.3    +      -       -      +
     81B  MET*     3.3    10.3    -      -       +      +
     82B  LYS      2.4    34.2    +      -       -      +
    270B  MET*     5.8     8.7    -      -       +      -
    274B  LYS*     5.3     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  GLY      3.4    14.7    -      -       -      +
     22B  PHE*     1.3    74.4    -      -       -      +
     24B  PHE*     1.3    62.3    +      -       -      +
     25B  ASN*     4.9     2.9    -      -       -      +
     82B  LYS*     3.5    15.5    -      -       +      +
    128B  ILE      4.2     5.5    -      -       -      +
    129B  PRO*     4.0     9.2    -      -       -      +
    130B  ASP*     3.2    53.6    +      -       +      +
    131B  THR*     5.9     0.5    -      -       -      +
    134B  HIS*     3.8     3.1    -      -       -      -
    270B  MET*     5.2     0.6    -      -       -      +
    274B  LYS*     2.7    38.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  PHE      4.0     0.2    +      -       -      -
     23B  GLU*     1.3    75.3    -      -       -      +
     25B  ASN*     1.3    62.1    +      -       -      +
     26B  ILE*     3.5    34.3    -      -       +      -
     81B  MET*     4.0    24.0    -      -       +      -
     82B  LYS      3.0     8.2    +      -       -      +
     83B  LEU*     3.5    14.3    -      -       +      +
     84B  THR      2.9    25.3    +      -       -      +
    134B  HIS*     3.6    24.2    -      -       +      -
    135B  CYS*     4.6     4.9    -      -       +      -
    265B  LEU*     3.3    27.4    -      -       +      -
    266B  ILE*     5.0     2.5    -      -       +      -
    270B  MET*     3.7    33.7    -      -       +      -
    273B  ILE*     3.9    21.8    -      -       +      -
    274B  LYS*     3.7    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  GLU*     4.9     2.3    -      -       -      +
     24B  PHE*     1.3    79.1    +      -       -      +
     26B  ILE*     1.3    63.7    +      -       -      +
     82B  LYS      4.9     0.5    -      -       -      +
     84B  THR*     3.3    30.6    +      -       -      +
     86B  ILE*     4.6    10.5    -      -       +      -
    130B  ASP      3.0    27.7    +      -       -      +
    131B  THR*     3.3    12.0    -      -       -      -
    132B  ARG      2.7    29.8    +      -       -      +
    133B  VAL*     4.0     4.1    -      -       -      -
    134B  HIS*     3.0    39.5    +      -       -      +
    135B  CYS      3.4     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     3.5    34.5    -      -       +      -
     25B  ASN*     1.3    73.9    -      -       -      +
     27B  MET*     1.3    65.6    +      -       -      +
     28B  VAL*     5.2     0.4    -      -       +      -
     43B  LEU*     4.0    25.6    -      -       +      -
     83B  LEU*     4.0    13.0    -      -       +      -
     84B  THR      2.7    11.5    +      -       -      +
     85B  VAL*     3.1    14.8    -      -       +      +
     86B  ILE*     2.6    37.1    +      -       -      +
    135B  CYS*     3.4    14.1    -      -       +      +
    137B  LEU*     4.0    25.6    -      -       +      -
    265B  LEU*     4.4    16.6    -      -       +      -
    266B  ILE*     5.1     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  ILE*     1.3    76.1    -      -       -      +
     28B  VAL*     1.3    61.7    +      -       -      +
     29B  VAL*     3.6    28.0    -      -       +      -
     67B  ILE*     5.2     0.7    -      -       +      -
     86B  ILE*     3.5    25.4    -      -       +      +
     88B  THR*     3.9     9.9    -      -       +      -
    104B  ILE*     3.8    21.1    -      -       +      -
    107B  PHE*     3.6    35.0    -      -       +      -
    108B  ILE*     4.3    14.1    -      -       +      -
    133B  VAL*     3.7    23.0    -      -       +      +
    135B  CYS      3.0     7.2    +      -       -      +
    136B  CYS*     3.3     7.6    -      -       -      -
    137B  LEU*     2.7    33.6    +      -       -      +
----------------------------------------------------------
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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  ILE*     5.2     0.7    -      -       +      -
     27B  MET*     1.3    77.1    -      -       -      +
     29B  VAL*     1.3    57.1    +      -       -      +
     36B  LYS*     3.9    16.6    -      -       +      +
     39B  LEU*     5.8     1.3    -      -       +      -
     40B  ILE*     3.7    27.4    -      -       +      +
     85B  VAL*     4.3     8.3    -      -       +      -
     86B  ILE      3.0    14.5    +      -       -      +
     87B  ASP*     3.6    23.8    -      -       -      +
     88B  THR*     2.5    31.1    +      -       -      +
    137B  LEU*     3.5    16.6    -      -       +      -
    139B  PHE*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  MET*     3.6    20.0    -      -       -      -
     28B  VAL*     1.3    80.3    -      -       -      +
     30B  GLY*     1.3    61.2    +      -       -      +
     36B  LYS*     3.5     5.2    -      -       -      -
     88B  THR*     3.7     9.0    -      -       -      +
    104B  ILE*     4.1    13.2    -      -       +      -
    136B  CYS*     3.4    28.3    -      -       -      -
    137B  LEU      2.9     6.5    +      -       -      +
    138B  TYR*     3.5    20.5    -      -       +      -
    139B  PHE*     2.8    30.1    +      -       -      +
    154B  PHE*     3.4    31.2    -      -       +      -
    158B  LEU*     3.9     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