Contacts of the strand formed by residues 358 - 363 (chain A) in PDB entry 2PDA


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 ILE 358 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324A  ILE*     3.2    16.6    -      -       +      +
    326A  VAL*     3.8    16.8    -      -       +      -
    341A  TYR*     3.6    35.0    +      -       +      -
    344A  VAL*     4.7     2.9    -      -       +      -
    345A  CYS*     4.4     9.4    -      -       -      -
    348A  PHE*     3.6    48.2    -      -       +      -
    355A  MET*     5.1     5.2    -      -       +      -
    356A  PRO*     4.9     2.5    -      -       +      -
    357A  LYS*     1.3   101.9    +      -       -      +
    359A  LEU*     1.3    61.9    +      -       -      +
    388A  ASN*     4.0     7.1    +      -       -      -
    349B  VAL*     4.9    18.7    -      -       +      +
    350B  GLU*     6.1     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  VAL*     4.2    16.4    -      -       +      -
    324A  ILE      2.9     6.8    +      -       -      +
    325A  THR*     3.0    16.2    -      -       +      -
    326A  VAL*     2.9    24.3    +      -       -      +
    341A  TYR*     4.4     1.8    -      -       -      -
    357A  LYS*     3.4    38.4    -      -       +      +
    358A  ILE*     1.3    79.7    -      -       -      +
    360A  ALA*     1.3    61.8    +      -       -      +
    381A  ASN*     3.8    14.6    -      -       -      +
    382A  MET*     4.4     7.6    -      -       +      -
    386A  LYS*     3.7    36.3    -      -       +      +
    387A  LYS      3.8    13.0    -      -       -      +
    388A  ASN*     3.7    11.4    -      -       +      +
    390A  PHE*     5.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  THR*     5.1     0.2    -      -       -      -
    326A  VAL      3.8     4.3    -      -       -      -
    338A  ASP*     5.7     2.0    -      -       -      +
    341A  TYR*     3.5    41.3    -      -       +      -
    359A  LEU*     1.3    75.0    -      -       -      +
    361A  GLY*     1.3    59.4    +      -       -      +
    388A  ASN*     2.9    14.1    +      -       -      +
    389A  HIS*     2.9    40.9    +      -       +      -
    390A  PHE*     3.3     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  VAL      3.1    10.9    +      -       -      +
    327A  LEU*     3.3    11.4    -      -       -      +
    328A  ASP*     2.9    28.1    +      -       -      +
    338A  ASP*     5.0     2.0    -      -       -      +
    360A  ALA*     1.3    75.0    -      -       -      +
    362A  ARG*     1.3    61.2    +      -       -      +
    389A  HIS*     5.1     0.2    -      -       -      -
    390A  PHE*     3.5    28.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328A  ASP      3.4     8.5    -      -       -      +
    330A  THR      2.8    31.4    +      -       -      +
    331A  LYS*     3.6    21.8    -      -       -      +
    332A  GLU      4.8     0.2    -      -       -      +
    338A  ASP*     2.5    40.0    +      -       -      +
    361A  GLY*     1.3    75.0    -      -       -      +
    363A  TYR*     1.3    67.9    +      -       -      +
    365A  LEU*     3.9     8.7    -      -       +      -
    389A  HIS      6.0     1.4    +      -       -      -
    390A  PHE*     3.1    15.5    +      -       -      +
    391A  THR*     3.3    10.8    -      -       +      +
    392A  VAL*     2.9    29.5    +      -       -      +
    226B  PHE*     3.7    13.7    -      -       +      -
    230B  GLU*     2.9    33.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  HIS*     4.3     0.2    -      -       -      -
    275A  SER*     3.8     2.3    +      -       -      -
    276A  MET      3.2    17.0    +      -       -      -
    279A  SER*     2.4    38.0    +      -       -      -
    327A  LEU*     3.7    30.8    +      -       +      -
    328A  ASP      3.3    25.2    +      -       -      +
    329A  ARG*     3.5    49.9    +      -       +      +
    362A  ARG*     1.3    77.5    -      -       -      +
    364A  GLY*     1.3    63.9    +      -       -      +
    365A  LEU*     2.8    16.0    +      -       -      +
    370A  PHE*     3.6    39.5    -      +       +      -
    392A  VAL*     4.0    17.9    -      -       +      +
    226B  PHE*     4.0     4.5    -      -       -      -
----------------------------------------------------------
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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