Contacts of the strand formed by residues 3026 - 3028 (chain D) 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 ILE3026 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2091D  ALA*     5.4     1.3    -      -       +      -
   2093D  ILE*     5.4     1.1    -      -       +      -
   2115D  LEU*     4.2    28.9    -      -       +      -
   2116D  CYS      3.6    15.3    -      -       -      +
   2117D  SER*     4.1     8.7    -      -       -      -
   2128D  ILE*     4.4    12.1    -      -       +      -
   2132D  LEU*     4.3    25.4    -      -       +      -
   3014D  LEU*     4.4    18.5    -      -       +      +
   3017D  ILE*     3.7    33.4    -      -       +      -
   3018D  GLU*     2.9    33.1    +      -       +      +
   3024D  GLY      4.3     0.4    -      -       -      -
   3025D  SER*     1.3    78.9    +      -       -      +
   3027D  MET*     1.3    67.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET3027 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2115D  LEU*     4.6     6.3    -      -       -      -
   2116D  CYS*     2.7    42.2    +      -       +      +
   3014D  LEU*     5.9     2.0    -      -       -      -
   3018D  GLU*     5.1     1.3    -      -       -      +
   3024D  GLY*     3.5    31.9    -      -       -      +
   3026D  ILE*     1.3    78.0    -      -       -      +
   3028D  ARG*     1.3    65.8    +      -       -      +
   3031D  GLU*     4.7    12.3    -      -       +      +
   3032D  ASP*     3.4    52.7    -      -       +      +
   3033D  ARG      5.8     0.2    -      -       -      +
   3034D  SER*     5.2     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG3028 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2112D  ASP*     3.2    36.2    +      -       -      +
   2113D  ASN*     4.4    16.3    +      -       -      +
   2114D  LEU      3.6     7.9    -      -       -      +
   2115D  LEU*     4.6    15.3    -      -       +      +
   3010D  LEU*     6.3     1.4    -      -       -      +
   3014D  LEU*     5.4     7.9    -      -       -      +
   3027D  MET*     1.3    77.1    -      -       -      +
   3029D  LEU*     1.3    67.3    +      -       -      +
   3030D  GLY      4.5     1.1    -      -       -      +
   3031D  GLU*     3.1    55.3    +      -       +      +
   3032D  ASP*     3.4     7.1    +      -       -      +
----------------------------------------------------------
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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