Contacts of the strand formed by residues 258 - 262 (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 ILE 258 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  ILE*     3.6    28.0    -      -       +      -
    198A  THR      3.4     4.5    -      -       -      +
    199A  MET*     3.8    21.5    -      -       +      -
    204A  ILE*     4.1    11.7    -      -       +      -
    231A  ILE*     4.3     2.0    -      -       +      -
    235A  ILE*     4.1    14.8    -      -       +      -
    256A  PRO      3.8     0.8    +      -       -      -
    257A  ASP*     1.3    73.2    -      -       -      +
    259A  VAL*     1.3    61.8    +      -       -      +
    260A  PHE*     4.0    15.4    +      -       +      -
    267A  TYR      4.0     0.7    -      -       -      +
    269A  VAL*     2.8    36.1    +      -       +      +
    274A  TYR*     3.7    30.9    -      -       +      +
    286A  PHE*     3.9    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  SER      3.6     1.0    -      -       -      +
    197A  ILE*     3.3     6.6    -      -       -      -
    198A  THR*     2.7    53.7    +      -       -      +
    199A  MET*     5.8     0.7    -      -       -      -
    200A  ASN      6.2     0.4    -      -       -      +
    257A  ASP*     4.3    11.7    -      -       +      +
    258A  ILE*     1.3    76.7    -      -       -      +
    260A  PHE*     1.3    63.6    +      -       -      +
    261A  THR*     3.8     8.9    +      -       -      +
    266A  GLN*     3.4    48.7    -      -       +      +
    267A  TYR      3.8     9.6    -      -       -      +
    268A  PRO*     4.2    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  VAL*     4.1    10.8    -      -       +      -
    196A  SER      3.8     2.5    -      -       -      -
    197A  ILE*     3.7    38.8    -      -       +      -
    221A  LEU*     4.2    25.6    -      -       +      -
    258A  ILE*     4.2    15.3    -      -       +      -
    259A  VAL*     1.3    73.6    -      -       -      +
    261A  THR*     1.3    58.8    +      -       -      +
    262A  ILE*     4.3     8.1    -      -       +      -
    267A  TYR*     2.8    47.8    +      -       +      +
    269A  VAL*     3.9    28.9    -      -       +      -
    286A  PHE*     4.6     9.4    -      +       -      -
    299A  TRP*     4.8     8.7    -      +       +      -
    301A  LEU*     3.8    26.7    -      -       +      -
    305A  PHE*     4.2    19.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with THR 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  VAL*     3.6     3.1    -      -       -      +
    195A  ASP*     2.7    50.4    +      -       +      +
    196A  SER*     3.0    29.9    +      -       -      +
    198A  THR*     5.0     3.1    +      -       -      +
    259A  VAL*     3.8     6.4    +      -       -      +
    260A  PHE*     1.3    71.5    -      -       -      +
    262A  ILE*     1.3    58.8    +      -       -      +
    264A  GLY*     4.2     6.5    -      -       -      +
    265A  VAL      3.2    22.0    -      -       -      +
    266A  GLN*     4.0    17.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  VAL*     3.6    32.1    -      -       +      +
    192A  ILE*     3.8    17.0    -      -       +      -
    193A  THR      3.5    17.7    -      -       -      +
    194A  VAL*     4.2    13.2    -      -       +      -
    195A  ASP*     4.3     0.2    -      -       -      -
    260A  PHE*     4.2     8.3    -      -       +      +
    261A  THR*     1.3    78.5    -      -       -      +
    263A  ASN*     1.3    65.6    +      -       -      +
    264A  GLY      3.2     1.1    -      -       -      -
    265A  VAL*     2.8    32.6    +      -       -      +
    267A  TYR*     3.7    26.3    +      -       +      -
    301A  LEU*     4.3     7.9    -      -       +      -
    305A  PHE*     3.9    25.1    -      -       +      -
    322A  LEU*     4.1     8.7    -      -       +      -
----------------------------------------------------------
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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