Contacts of the strand formed by residues 614 - 618 (chain A) in PDB entry 2PMF


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 614 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555A  ALA*     4.4     2.9    -      -       +      -
    561A  LYS*     2.8    18.7    +      -       +      +
    562A  CYS*     3.4     7.7    -      -       -      -
    563A  SER*     3.0    21.5    +      -       -      -
    604A  TYR*     5.2     0.4    -      -       -      -
    612A  VAL*     3.4    12.4    -      -       -      +
    613A  ALA*     1.3    96.1    -      -       +      +
    615A  GLY*     1.3    58.5    +      -       -      +
    632A  LEU*     4.2    12.1    -      -       +      -
    633A  ARG      3.5    13.9    -      -       -      +
    634A  ASP*     3.9    21.3    -      -       -      -
    635A  ARG      4.9     0.4    -      -       -      +
    652A  VAL*     4.2    15.9    -      -       +      -
    655A  LEU*     3.4    52.3    -      -       +      -
    656A  ALA*     4.0    16.6    -      -       +      -
    662A  TRP*     4.4     7.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLY 615 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562A  CYS*     4.4     0.4    -      -       -      -
    563A  SER      3.2    11.2    -      -       -      -
    604A  TYR*     3.2    25.3    +      -       -      -
    614A  PHE*     1.3    78.5    -      -       -      +
    616A  VAL*     1.3    63.6    +      -       -      -
    631A  THR      3.5     0.5    -      -       -      +
    632A  LEU*     3.3     6.4    -      -       -      +
    633A  ARG*     2.7    36.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 616 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562A  CYS*     3.9    16.2    -      -       -      -
    563A  SER      2.7    10.9    +      -       -      +
    564A  VAL*     3.1     4.6    -      -       -      +
    565A  LEU      2.6    30.1    +      -       -      -
    580A  LEU*     3.7    31.2    -      -       +      -
    584A  LEU*     6.1     0.7    -      -       +      -
    604A  TYR*     3.5     2.9    -      -       -      -
    615A  GLY*     1.3    77.8    -      -       -      +
    617A  THR*     1.3    57.0    +      -       -      +
    618A  ILE*     3.9     3.1    +      -       +      +
    630A  ALA*     3.8    24.9    -      -       +      -
    631A  THR      3.2     4.3    -      -       -      +
    632A  LEU*     3.8    17.3    -      -       +      -
    648A  LEU*     3.8    19.7    -      -       +      -
    652A  VAL*     4.8     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 617 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    565A  LEU*     3.0    12.8    -      -       -      -
    600A  ILE*     4.0    24.4    -      -       +      +
    604A  TYR*     2.9    33.4    -      -       +      +
    616A  VAL*     1.3    71.5    -      -       -      +
    618A  ILE*     1.3    64.0    +      -       -      +
    619A  ASP*     4.0     6.6    +      -       -      +
    622A  THR*     4.5     0.2    +      -       -      -
    630A  ALA*     3.3    18.4    -      -       -      +
    631A  THR*     3.0    39.0    +      -       +      +
    640A  GLN*     4.2     9.0    -      -       -      +
    642A  ARG*     4.7     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 618 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564A  VAL*     5.2     4.7    -      -       +      -
    565A  LEU      2.6    13.0    +      -       -      +
    566A  PRO*     3.4     6.8    -      -       +      +
    567A  LEU*     3.2    26.2    +      -       -      +
    573A  PHE*     3.9    22.8    -      -       +      -
    576A  PHE*     4.2    10.5    -      -       +      +
    577A  VAL*     3.9    35.4    -      -       +      +
    580A  LEU*     4.3    11.4    -      -       +      -
    616A  VAL*     4.5     7.2    -      -       +      +
    617A  THR*     1.3    76.2    -      -       -      +
    619A  ASP*     1.3    61.9    +      -       -      +
    622A  THR*     3.8    21.8    -      -       +      -
    623A  VAL*     4.6     1.6    -      -       +      -
    630A  ALA*     4.3     5.2    -      -       +      -
    645A  ILE*     3.9    24.7    -      -       +      -
----------------------------------------------------------
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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