Contacts of the strand formed by residues 326 - 330 (chain A) in PDB entry 2P2F


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 THR 326 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ARG*     4.1    13.2    -      -       -      +
     93A  THR*     2.7    36.6    +      -       +      +
     94A  ALA      3.8     0.9    -      -       -      +
     96A  ILE*     3.8    33.2    -      -       +      -
    295A  TYR*     4.6     0.2    +      -       -      -
    298A  GLY*     5.9     3.0    -      -       -      -
    299A  ASP      3.9     7.8    +      -       -      +
    300A  ILE*     4.4    21.6    -      -       +      +
    301A  TYR*     3.2    30.4    +      -       -      +
    324A  GLY      4.0     0.2    +      -       -      -
    325A  ALA*     1.3    73.6    -      -       -      +
    327A  THR*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ALA      3.1    18.1    +      -       -      +
     95A  ILE*     3.1    23.7    -      -       +      +
     96A  ILE      2.9    22.6    +      -       -      +
    300A  ILE*     6.3     0.2    -      -       -      -
    301A  TYR*     3.3    20.4    -      -       -      -
    303A  CYS      5.1     0.2    +      -       -      -
    316A  LEU*     3.0    38.2    +      -       +      +
    317A  LEU*     5.1     0.9    -      -       -      -
    320A  PRO*     3.9    13.0    -      -       +      -
    321A  LEU*     4.5    12.1    -      -       +      -
    325A  ALA      3.9     0.9    +      -       -      -
    326A  THR*     1.3    77.4    -      -       -      +
    328A  LEU*     1.3    66.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ILE*     3.3    23.1    -      -       +      +
     98A  GLU*     4.4     5.8    -      -       +      -
    300A  ILE*     5.1     1.8    -      -       +      -
    301A  TYR      2.9    16.6    +      -       -      +
    302A  TRP*     3.2    46.3    -      -       +      +
    303A  CYS      3.8     0.7    +      -       -      +
    316A  LEU*     3.6    15.1    -      -       -      +
    327A  THR*     1.3    75.7    +      -       -      +
    329A  MET*     1.3    75.5    +      -       -      +
    330A  PHE*     3.7     5.8    -      -       +      +
    345A  VAL*     4.0    11.7    -      -       +      -
    349A  HIS*     3.7    31.4    -      -       +      -
    351A  VAL*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  ILE*     4.1    15.7    -      -       +      -
     96A  ILE      2.8    10.2    +      -       -      +
     97A  TRP*     3.3    11.3    -      -       +      -
     98A  GLU      3.0    24.3    +      -       -      -
    141A  MET*     3.8    33.7    -      -       +      +
    142A  VAL      3.3    37.7    -      -       -      +
    143A  PRO*     3.7     6.3    -      -       +      -
    145A  ALA*     5.3     0.4    -      -       +      -
    146A  ALA*     4.2    24.2    -      -       +      +
    307A  VAL*     4.7     9.9    -      -       +      -
    316A  LEU*     3.8    30.1    -      -       +      -
    317A  LEU*     4.5     5.6    -      -       +      -
    327A  THR      4.0     0.6    +      -       -      -
    328A  LEU*     1.3    75.2    -      -       -      +
    330A  PHE*     1.3    58.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  GLU*     3.4    24.0    -      -       +      -
     99A  GLY      3.8     4.3    -      -       -      -
    141A  MET*     3.3    28.9    -      -       +      +
    302A  TRP*     3.5    40.7    -      +       +      +
    303A  CYS      5.6     0.2    +      -       -      -
    304A  THR*     5.9     4.7    -      -       -      +
    328A  LEU*     3.7     7.1    +      -       +      +
    329A  MET*     1.3    74.2    -      -       -      +
    331A  GLU*     1.3    62.7    +      -       -      +
    332A  GLY*     3.3    34.8    -      -       -      +
    333A  VAL      3.3    33.2    -      -       -      -
    334A  PRO*     3.7     9.2    -      -       +      -
    341A  ARG*     3.4    45.1    -      -       +      -
    342A  MET*     6.1     0.2    -      -       -      -
    345A  VAL*     4.3     4.7    -      -       +      -
----------------------------------------------------------
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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