Contacts of the strand formed by residues 456 - 461 (chain B) in PDB entry 2PMW


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 456 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413B  GLN*     3.4    25.3    -      -       +      +
    414B  ARG*     3.6    46.0    -      -       +      -
    417B  HIS*     3.3    53.6    -      +       +      -
    418B  PHE*     4.9     5.4    -      +       -      -
    454B  GLN*     3.6    32.5    +      -       +      -
    455B  LEU*     1.3    79.1    -      -       -      +
    457B  CYS*     1.3    59.6    +      -       -      +
    527B  CYS*     3.1     4.5    -      -       -      +
    528B  LEU*     3.0    44.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 457 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413B  GLN*     3.3     9.6    -      -       -      +
    416B  ILE*     5.1     7.4    -      -       -      +
    455B  LEU*     4.0    10.3    +      -       -      -
    456B  PHE*     1.3    73.4    -      -       -      +
    458B  ARG*     1.3    59.2    +      -       -      +
    525B  ARG*     3.6    31.7    +      -       +      +
    526B  CYS      3.2     5.6    -      -       -      +
    527B  CYS*     2.0    45.8    -      -       -      -
    631B  THR*     3.7    21.7    -      -       +      +
    632B  LEU      3.9     6.7    -      -       -      -
    633B  THR*     4.3     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 458 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360B  ASP*     5.5     1.4    +      -       -      -
    409B  ALA      5.6     0.2    -      -       -      -
    412B  ARG*     3.7    44.9    -      -       -      +
    413B  GLN*     3.4    18.6    -      -       -      +
    416B  ILE*     3.9    26.4    -      -       +      +
    457B  CYS*     1.3    75.5    -      -       -      +
    459B  THR*     1.3    62.3    +      -       -      +
    460B  VAL*     3.5    29.9    +      -       +      +
    476B  ARG      5.1     1.2    +      -       -      -
    477B  CYS*     4.8     1.0    -      -       -      +
    478B  ALA*     4.3     6.3    -      -       -      +
    481B  GLU*     2.8    44.6    +      -       -      -
    525B  ARG*     3.5    11.9    -      -       -      +
    526B  CYS*     2.9    39.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 459 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458B  ARG*     1.3    77.1    +      -       -      +
    460B  VAL*     1.3    62.8    +      -       -      +
    461B  TRP*     3.8    20.0    +      -       +      +
    523B  ILE*     3.5    28.3    -      -       +      -
    524B  ALA      3.4     4.5    -      -       -      +
    525B  ARG*     2.7    26.4    +      -       -      +
    648B  TYR*     5.4     0.2    -      -       +      -
    649B  ALA*     3.1    31.3    +      -       +      +
    651B  ASP      4.8     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 460 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458B  ARG*     3.5    42.6    -      -       +      +
    459B  THR*     1.3    76.7    -      -       -      +
    461B  TRP*     1.3    72.7    +      -       -      +
    462B  SER*     5.7     0.2    -      -       -      -
    475B  ALA*     3.7    10.2    -      -       +      +
    476B  ARG      3.8    18.4    -      -       -      +
    523B  ILE*     3.4     3.4    -      -       -      -
    524B  ALA*     2.8    46.9    +      -       +      +
    526B  CYS*     3.8    17.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 461 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357B  ARG*     3.9    28.9    +      -       +      +
    435B  VAL*     3.7    39.2    +      -       +      -
    436B  LEU*     3.3    31.4    -      -       +      -
    459B  THR*     3.8    27.1    +      -       +      +
    460B  VAL*     1.3    82.3    -      -       -      +
    462B  SER*     1.3    65.4    +      -       -      +
    489B  PHE*     3.9    13.2    -      +       -      -
    521B  TYR*     3.6    30.5    -      +       +      -
    522B  ALA      3.7     3.1    -      -       -      -
    523B  ILE*     3.5    28.0    -      -       +      -
    648B  TYR*     3.7    36.5    -      +       +      +
    649B  ALA      5.3     1.2    +      -       -      -
----------------------------------------------------------
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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