Contacts of the strand formed by residues 3290 - 3293 (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 TRP3290 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3285D  GLU      3.7     0.2    -      -       -      +
   3286D  LYS*     3.4     3.0    -      -       -      -
   3287D  ALA*     2.8    44.9    +      -       +      +
   3289D  ALA*     1.3    78.8    -      -       +      +
   3291D  TYR*     1.3    63.0    +      -       -      +
   3292D  SER*     3.9     2.9    +      -       -      +
   3297D  LYS*     3.7    59.2    -      -       +      +
   3299D  GLY*     3.5    32.5    -      -       -      -
   3300D  GLN*     3.7    39.4    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR3291 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1233A  GLU*     5.1     4.5    +      -       -      -
   3275D  VAL*     3.7    18.1    -      -       +      +
   3276D  ASP*     5.1     1.6    +      -       -      -
   3279D  VAL*     3.6    27.6    -      -       +      -
   3284D  ILE*     4.2     4.9    -      -       +      -
   3285D  GLU      3.2     6.1    -      -       -      +
   3286D  LYS*     3.6    30.9    -      -       +      +
   3288D  GLY      5.6     0.2    -      -       -      -
   3289D  ALA*     3.5    16.2    -      -       -      -
   3290D  TRP*     1.3    73.1    -      -       -      +
   3292D  SER*     1.3    60.7    +      -       -      +
   3297D  LYS*     3.7     4.0    -      -       -      +
   3298D  ILE*     2.8    32.7    +      -       +      +
   3299D  GLY      2.9    20.0    +      -       -      +
   3301D  GLY*     3.5     9.6    -      -       -      -
   3302D  LYS*     3.3    43.7    +      -       +      +
   3305D  ALA*     3.8    16.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER3292 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3284D  ILE*     3.3     7.9    -      -       -      +
   3285D  GLU*     2.7    53.8    +      -       -      +
   3287D  ALA*     5.6     3.6    -      -       -      +
   3290D  TRP*     4.4     4.7    +      -       -      +
   3291D  TYR*     1.3    76.9    +      -       -      +
   3293D  TYR*     1.3    60.4    +      -       -      +
   3294D  LYS      4.2     0.2    -      -       -      -
   3295D  GLY*     4.6    12.5    +      -       -      -
   3296D  GLU      3.4    13.7    -      -       -      -
   3297D  LYS*     3.9    22.9    -      -       -      +
   3298D  ILE*     4.6     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR3293 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3283D  LEU*     3.2    30.7    -      -       +      -
   3284D  ILE*     4.3     4.0    -      -       +      -
   3292D  SER*     1.3    74.1    -      -       -      +
   3294D  LYS*     1.3   101.5    +      -       +      +
   3295D  GLY      3.3     0.7    -      -       -      -
   3296D  GLU*     2.7    28.5    +      -       -      +
   3298D  ILE*     3.8    23.8    -      -       +      +
   3308D  TRP*     4.7     7.2    -      +       +      -
   3315D  THR*     3.4    30.3    -      -       +      -
   3318D  GLU*     2.7    28.6    +      -       -      +
   3319D  ILE*     3.8    32.1    -      -       +      +
   3322D  LYS*     4.5     6.9    +      -       -      +
----------------------------------------------------------
 Back to top of page


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