Contacts of the strand formed by residues 373 - 377 (chain A) in PDB entry 2PME


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 LEU 373 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  LEU*     6.0     0.3    -      -       -      +
    320A  TYR*     3.9    15.2    +      -       -      +
    360A  TYR*     4.3    11.8    -      -       +      +
    363A  LEU*     3.8    37.7    -      -       +      -
    364A  THR*     4.3    19.5    -      -       +      -
    368A  ILE*     3.8    17.7    -      -       +      -
    369A  SER      3.5    10.3    -      -       -      +
    370A  PRO*     3.3    18.5    +      -       +      +
    371A  ASP      3.5     0.6    -      -       -      -
    372A  LYS*     1.3    80.9    -      -       -      +
    374A  ARG*     1.3    70.1    +      -       -      +
    375A  PHE*     3.7    33.2    -      -       +      -
    393A  ALA*     4.9     2.2    -      -       +      -
    394A  GLU      3.5     7.6    -      -       -      +
    395A  SER*     5.4     1.1    -      -       -      -
    401A  TRP*     4.3     0.8    -      -       -      -
    404A  ILE*     5.4     0.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 374 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  TYR*     3.6    20.2    -      -       +      +
    322A  TYR*     3.9    47.7    -      -       +      -
    333A  ALA*     4.8    11.6    -      -       +      +
    373A  LEU*     1.3    78.2    -      -       -      +
    375A  PHE*     1.3    65.9    +      -       -      +
    376A  ARG*     4.4     4.2    -      -       -      +
    393A  ALA*     3.6     2.1    -      -       -      -
    394A  GLU*     2.7    69.9    +      -       +      +
    401A  TRP*     3.4    64.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 375 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  LEU*     3.8    22.4    -      -       +      -
    320A  TYR      2.8    11.4    +      -       -      -
    321A  LEU*     3.6    16.1    -      -       +      -
    322A  TYR*     2.8    26.4    +      -       -      -
    356A  ILE*     3.5    42.4    -      -       +      -
    359A  ILE*     4.1    13.9    -      -       +      -
    360A  TYR*     3.7    33.2    -      +       +      -
    373A  LEU*     3.7    21.5    -      -       +      -
    374A  ARG*     1.3    74.8    -      -       -      +
    376A  ARG*     1.3    60.2    +      -       -      +
    391A  TRP*     3.2    20.9    -      -       +      -
    392A  ASP      3.5     2.9    -      -       -      +
    393A  ALA*     3.6    26.9    -      -       +      -
    407A  CYS*     6.4     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 376 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  TYR*     3.4    24.2    -      -       +      +
    327A  GLN*     3.4    29.0    +      -       -      +
    374A  ARG*     3.9     7.9    +      -       -      +
    375A  PHE*     1.3    73.7    -      -       -      +
    377A  GLN*     1.3    62.2    +      -       -      +
    378A  HIS*     3.8    42.7    +      -       -      +
    379A  MET*     6.1     1.8    -      -       -      +
    391A  TRP*     4.1     1.8    -      -       -      -
    392A  ASP*     2.6    52.8    +      -       -      +
    394A  GLU*     3.2    45.1    +      -       +      +
    403A  GLU*     6.1     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 377 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  TYR      3.1     9.0    +      -       -      +
    323A  SER*     3.4    11.1    -      -       -      -
    324A  ALA*     3.0    29.4    +      -       -      +
    327A  GLN*     2.5    28.1    +      -       -      -
    346A  VAL      4.6     5.0    +      -       -      +
    376A  ARG*     1.3    73.7    -      -       -      +
    378A  HIS*     1.3    68.5    +      -       -      +
    389A  ASP*     3.1    24.5    +      -       -      +
    390A  CYS      3.4    18.8    -      -       -      +
    391A  TRP*     3.6    34.0    -      -       +      +
----------------------------------------------------------
 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