Contacts of the strand formed by residues 201 - 204 (chain D) in PDB entry 2J2M


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 201 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  TRP*     6.0     0.4    -      -       -      -
    127D  VAL      6.4     0.2    -      -       -      -
    197D  SER*     4.4    17.5    -      -       -      -
    199D  HIS*     3.7    27.4    -      +       +      -
    200D  SER*     1.3    78.3    -      -       -      +
    202D  LYS*     1.3    65.0    +      -       -      +
    203D  TRP*     5.0     3.1    -      -       +      +
    212D  TYR*     3.3     6.9    -      -       -      -
    213D  ILE*     2.7    51.3    +      -       +      -
    215D  LEU*     5.9     2.9    -      -       +      -
    317D  PRO*     3.4    32.3    -      -       +      -
    318D  GLY*     5.6     0.4    -      -       -      -
    320D  LEU*     4.2    17.9    -      -       +      -
    324D  MET*     6.2     0.7    -      -       +      -
    325D  LEU      3.8    12.6    -      -       -      +
    326D  PRO*     4.3     7.4    -      -       +      -
    327D  SER*     4.1     5.6    -      -       -      +
    332D  LEU*     3.8    28.3    -      -       +      -
    335D  ARG*     5.4     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 202 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410A  HIS*     5.0     2.2    +      -       -      -
    201D  PHE*     1.3    75.8    -      -       -      +
    203D  TRP*     1.3    70.8    +      -       -      +
    204D  VAL*     4.2     1.5    +      -       +      -
    210D  THR*     4.0    14.8    -      -       -      +
    211D  VAL      3.4     3.8    -      -       -      -
    212D  TYR*     3.5    36.2    +      -       +      -
    267D  PRO*     6.2     1.3    -      -       -      -
    324D  MET*     3.4     0.5    -      -       -      -
    325D  LEU*     2.8    52.0    +      -       +      +
    326D  PRO      3.7    17.2    +      -       -      +
    327D  SER*     4.3     0.6    -      -       -      +
    328D  GLU*     3.4    25.7    +      -       -      -
    403D  GLN*     2.7    47.9    +      -       +      +
    404D  PRO*     4.7     6.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 203 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72D  MET*     4.0    26.9    -      -       +      -
     75D  TYR*     3.3    30.8    -      -       +      +
     76D  THR*     3.7    21.8    -      -       +      -
     81D  LEU*     4.2    21.3    -      -       +      -
    124D  TRP*     5.3     2.0    -      +       -      -
    201D  PHE*     4.1     3.4    +      -       +      +
    202D  LYS*     1.3    83.1    -      -       -      +
    204D  VAL*     1.3    58.0    +      -       -      +
    209D  ASN      3.7     0.2    -      -       -      +
    210D  THR*     3.1     2.6    -      -       -      -
    211D  VAL*     2.9    32.6    +      -       +      -
    213D  ILE*     3.6    45.8    -      -       +      +
    215D  LEU*     4.1    17.9    -      -       +      +
    260D  LEU*     6.2     1.1    -      -       +      -
    262D  VAL*     3.8    26.2    -      -       +      -
    294D  VAL*     5.0     4.5    -      -       +      -
    323D  GLY      3.3     2.0    -      -       -      -
    324D  MET*     3.7    33.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 204 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75D  TYR      3.8     2.9    -      -       -      -
     76D  THR*     3.4     0.7    -      -       -      -
     77D  LYS*     3.0    24.2    +      -       -      +
    202D  LYS*     4.8     2.9    -      -       +      +
    203D  TRP*     1.3    78.7    -      -       -      +
    205D  ASN*     1.3    70.2    +      -       -      +
    208D  GLY*     4.3     9.9    -      -       -      +
    209D  ASN      3.4     7.6    -      -       -      +
    210D  THR*     3.7    17.9    -      -       +      +
    323D  GLY*     2.9    25.1    +      -       -      +
    325D  LEU*     4.1    25.4    -      -       +      -
    401D  ASP*     3.4    38.4    -      -       -      +
----------------------------------------------------------
 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