Contacts of the strand formed by residues 4290 - 4293 (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 TRP4290 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4285D  GLU      3.7     0.7    -      -       -      +
   4286D  LYS*     3.4     3.4    -      -       -      -
   4287D  ALA*     2.8    46.3    +      -       +      +
   4289D  ALA*     1.3    79.3    -      -       +      +
   4291D  TYR*     1.3    62.7    +      -       -      +
   4292D  SER*     3.9     2.4    +      -       -      +
   4297D  LYS*     3.7    60.5    -      -       +      +
   4299D  GLY*     3.5    32.3    -      -       -      -
   4300D  GLN*     3.7    40.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR4291 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4275D  VAL*     3.7    16.7    -      -       +      +
   4276D  ASP*     5.2     1.8    +      -       -      -
   4279D  VAL*     3.6    28.7    -      -       +      -
   4284D  ILE*     4.2     5.6    -      -       +      -
   4285D  GLU      3.3     4.3    -      -       -      +
   4286D  LYS*     3.6    31.2    -      -       +      +
   4289D  ALA*     3.5    16.4    -      -       -      -
   4290D  TRP*     1.3    73.4    -      -       -      +
   4292D  SER*     1.3    61.5    +      -       -      +
   4297D  LYS*     3.7     3.8    -      -       -      +
   4298D  ILE*     2.8    33.5    +      -       +      +
   4299D  GLY      2.9    21.1    +      -       -      +
   4301D  GLY*     3.5    10.5    -      -       -      -
   4302D  LYS*     3.3    42.5    +      -       +      +
   4305D  ALA*     3.8    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER4292 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4284D  ILE*     3.3     7.6    -      -       -      +
   4285D  GLU*     2.7    54.1    +      -       -      +
   4287D  ALA*     5.6     3.5    -      -       -      +
   4290D  TRP*     3.9     5.2    +      -       -      +
   4291D  TYR*     1.3    75.8    +      -       -      +
   4293D  TYR*     1.3    60.3    +      -       -      +
   4294D  LYS      4.2     0.2    -      -       -      -
   4295D  GLY*     4.6    11.8    +      -       -      -
   4296D  GLU      3.4    13.9    -      -       -      -
   4297D  LYS*     3.9    23.5    -      -       -      +
   4298D  ILE*     4.6     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR4293 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4283D  LEU*     3.2    31.2    -      -       +      -
   4284D  ILE*     4.3     4.5    -      -       +      -
   4292D  SER*     1.3    73.0    -      -       -      +
   4294D  LYS*     1.3   103.0    +      -       +      +
   4295D  GLY      3.3     0.9    -      -       -      -
   4296D  GLU*     2.7    28.9    +      -       -      +
   4298D  ILE*     3.8    23.4    -      -       +      +
   4308D  TRP*     4.7     7.4    -      +       +      -
   4315D  THR*     3.4    30.3    -      -       +      -
   4318D  GLU*     2.7    27.7    +      -       -      +
   4319D  ILE*     3.8    31.8    +      -       +      +
   4322D  LYS*     4.5     6.8    +      -       -      +
----------------------------------------------------------
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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