Contacts of the strand formed by residues 3090 - 3093 (chain A) in PDB entry 3CMT


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 CYS3090 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3080A  ILE*     3.8    37.7    -      -       +      -
   3083A  ALA*     3.9    14.6    -      -       -      -
   3084A  GLN*     4.0    14.1    -      -       -      +
   3088A  LYS      3.9     2.9    +      -       -      -
   3089A  THR*     1.3    79.4    -      -       -      +
   3091A  ALA*     1.3    60.3    +      -       -      +
   3113A  ASN      4.1     4.0    +      -       -      +
   3114A  LEU*     3.3     9.3    -      -       +      +
   3115A  LEU*     3.0    27.7    +      -       -      +
   3138A  VAL*     4.1     2.2    -      -       -      -
   3140A  VAL*     3.1    34.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA3091 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3080A  ILE*     4.7     0.7    -      -       -      +
   3090A  CYS*     1.3    76.1    -      -       -      +
   3092A  PHE*     1.3    60.1    +      -       -      +
   3093A  ILE*     4.2     3.6    -      -       +      -
   3114A  LEU*     4.2     2.0    -      -       -      -
   3115A  LEU*     3.2    17.7    -      -       +      +
   3132A  LEU*     3.7    30.7    -      -       +      -
   3138A  VAL*     3.9    10.3    -      -       +      +
   3140A  VAL      2.9     7.4    +      -       -      +
   3141A  ILE*     3.4     9.5    -      -       +      -
   3142A  VAL*     3.0    29.0    +      -       -      +
   4026A  ILE*     5.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE3092 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3073A  THR*     4.1     9.2    -      -       +      -
   3076A  THR*     3.5    25.4    -      -       +      -
   3077A  LEU*     4.0    14.1    -      -       +      -
   3080A  ILE*     3.9    15.7    -      -       +      -
   3091A  ALA*     1.3    74.0    -      -       -      +
   3093A  ILE*     1.3    64.6    +      -       -      +
   3094A  ASP*     3.6    34.1    +      -       +      -
   3099A  LEU*     3.6    26.5    -      -       +      -
   3114A  LEU*     3.8    22.9    -      -       +      -
   3115A  LEU      2.7     8.3    +      -       -      +
   3116A  CYS*     3.3     3.7    -      -       -      -
   3117A  SER      3.0    24.4    +      -       -      -
   3142A  VAL*     3.6    15.5    -      -       +      -
   3144A  ASP*     3.5    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE3093 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3091A  ALA*     4.9     1.1    -      -       +      -
   3092A  PHE*     1.3    79.2    -      -       -      +
   3094A  ASP*     1.3    58.3    +      -       -      +
   3095A  ALA*     3.1     5.7    +      -       +      +
   3117A  SER*     3.6    12.3    -      -       -      +
   3119A  PRO*     3.8    30.1    -      -       +      -
   3125A  ALA*     4.0    17.9    -      -       +      +
   3128A  ILE*     3.9    27.1    -      -       +      -
   3129A  CYS*     4.1    13.9    -      -       -      -
   3132A  LEU*     4.7     7.0    -      -       +      -
   3141A  ILE*     4.0    21.8    -      -       +      -
   3142A  VAL      2.7    18.4    +      -       -      +
   3143A  VAL*     3.6    12.5    -      -       +      +
   3144A  ASP      2.9    28.1    +      -       -      -
   4026A  ILE*     5.5     0.9    -      -       +      -
----------------------------------------------------------
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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