Contacts of the strand formed by residues 89 - 93 (chain A) in PDB entry 1CMO


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 89 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  CYS*     4.1    26.2    -      -       +      -
     74A  VAL*     3.4    33.9    -      -       +      +
     76A  PRO*     5.5    14.6    -      -       +      -
     79A  TRP*     6.5     0.9    -      +       -      -
     87A  ILE*     5.1     4.9    -      -       +      -
     88A  ALA*     1.3    76.9    -      -       -      +
     90A  LYS*     1.3    72.2    +      -       -      +
     91A  VAL*     3.8    14.1    -      -       +      -
    105A  VAL*     4.7    15.0    -      -       +      -
    117A  LEU*     6.5     0.7    -      -       +      -
    130A  ARG*     3.9     3.8    -      -       -      +
    131A  PHE*     2.8    64.3    +      +       -      -
    134A  LEU*     4.8    11.0    -      -       +      -
    148A  LEU*     6.5     0.4    -      -       +      -
    150A  ILE*     4.4    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  SER*     3.1    56.3    +      -       -      +
     74A  VAL*     4.6     2.5    -      -       +      +
     89A  PHE*     1.3    82.0    -      -       -      +
     91A  VAL*     1.3    62.2    +      -       -      +
     92A  VAL*     5.0     4.3    -      -       -      -
    128A  VAL*     4.0    15.3    -      -       +      -
    129A  ALA      3.2    18.8    -      -       -      +
    130A  ARG*     4.6    12.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  PHE*     3.7    36.8    -      -       +      -
     71A  LEU      3.7    12.1    -      -       -      +
     72A  CYS*     4.5     6.1    -      -       -      +
     89A  PHE*     3.8    13.2    -      -       +      -
     90A  LYS*     1.3    77.1    -      -       -      +
     92A  VAL*     1.3    65.2    +      -       -      +
    103A  VAL*     4.6    12.3    -      -       +      -
    124A  MET*     4.5     4.0    -      -       +      +
    127A  GLN      3.6     1.2    -      -       -      +
    128A  VAL*     3.2    27.3    -      -       -      +
    129A  ALA*     3.4    14.6    +      -       +      +
    131A  PHE*     3.7    27.4    -      -       +      -
    150A  ILE*     5.0     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  LEU*     5.3     9.4    -      -       +      -
     69A  ASN      3.6     0.9    -      -       -      +
     70A  PHE*     3.6     0.9    -      -       -      -
     71A  LEU*     2.6    52.6    +      -       +      +
     73A  SER*     3.3    24.7    -      -       -      +
     90A  LYS*     5.0     4.5    -      -       -      -
     91A  VAL*     1.3    78.1    -      -       -      +
     93A  ALA*     1.3    63.7    +      -       -      +
     94A  LEU*     4.3    20.6    -      -       +      -
    127A  GLN*     3.8     2.7    -      -       +      -
    128A  VAL*     4.5    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ASN      3.2     4.5    -      -       -      -
     70A  PHE*     3.2    38.6    -      -       +      -
     92A  VAL*     1.3    75.5    -      -       -      +
     94A  LEU*     1.3    63.7    +      -       -      +
     95A  GLY      3.2     4.3    +      -       -      +
     97A  VAL*     4.1    15.5    -      -       +      -
    124A  MET*     4.6     2.7    -      -       +      -
    127A  GLN*     2.9    43.2    +      -       -      +
----------------------------------------------------------
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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