Contacts of the strand formed by residues 210 - 214 (chain A) in PDB entry 1PSN


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 CYS 210 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  THR*     3.4     7.5    -      -       -      +
    194A  VAL*     2.7    48.4    +      -       -      -
    197A  ILE*     4.7     1.3    -      -       -      -
    206A  CYS*     2.0    48.7    -      -       +      -
    209A  GLY*     1.3    72.8    -      -       -      +
    211A  GLN*     1.3    64.8    +      -       -      +
    297A  GLU      5.0     3.4    -      -       -      +
    299A  TRP*     3.8    32.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  THR*     2.7    30.2    +      -       -      +
    186A  VAL*     5.0     0.3    -      -       -      +
    191A  GLN*     3.1    27.6    +      -       -      +
    192A  ILE      3.5     2.6    -      -       -      +
    193A  THR*     3.0    28.3    +      -       -      +
    210A  CYS*     1.3    78.4    +      -       -      +
    212A  ALA*     1.3    59.7    +      -       -      +
    295A  SER*     3.3    30.5    -      -       -      +
    297A  GLU      4.0     3.4    +      -       -      +
    298A  LEU*     3.5    15.9    -      -       +      -
    299A  TRP*     2.9    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  GLN*     3.3     5.1    -      -       -      +
    192A  ILE*     2.7    42.8    +      -       +      +
    194A  VAL*     3.7    27.4    -      -       +      -
    211A  GLN*     1.3    75.0    -      -       -      +
    213A  ILE*     1.3    63.0    +      -       -      +
    298A  LEU*     4.8     0.2    -      -       -      -
    299A  TRP*     3.2    21.8    -      -       +      +
    301A  LEU*     4.1    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  GLY*     4.8     1.8    -      -       -      -
    189A  TYR*     3.6    50.0    -      -       +      -
    190A  TRP      3.3     7.0    -      -       -      +
    191A  GLN*     4.2    10.8    -      -       +      -
    212A  ALA*     1.3    77.9    -      -       -      +
    214A  VAL*     1.3    57.6    +      -       -      +
    215A  ASP*     3.4    23.8    +      -       +      +
    298A  LEU*     4.0    23.1    -      -       +      -
    299A  TRP      2.9     7.5    +      -       -      -
    300A  ILE*     3.5    34.3    -      -       +      -
    301A  LEU*     2.8    33.6    +      -       -      +
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Residues in contact with VAL 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR*     2.9    20.1    +      -       -      +
     34A  GLY*     5.3     0.2    -      -       -      -
    190A  TRP*     2.9    25.1    +      -       +      +
    192A  ILE*     4.4    13.0    -      -       +      -
    213A  ILE*     1.3    72.1    -      -       -      +
    215A  ASP*     1.3    60.8    +      -       -      +
    301A  LEU*     3.6    23.6    -      -       +      +
    305A  PHE*     5.6     5.4    -      -       +      -
    306A  ILE*     4.0    18.8    -      -       +      -
    311A  THR*     3.9    12.8    -      -       +      +
    313A  PHE*     3.6    32.3    -      -       +      -
    320A  VAL*     4.3    19.1    -      -       +      -
    322A  LEU*     5.6     2.5    -      -       +      -
----------------------------------------------------------
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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