Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 4PS1


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 LYS 353 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310A  PHE*     3.5     8.5    -      -       +      -
    340A  PHE*     3.0    36.2    +      -       +      +
    341A  THR*     5.2     1.3    -      -       -      +
    342A  GLY*     5.2     4.4    -      -       -      +
    348A  LEU*     2.8    44.3    +      -       +      -
    349A  ALA*     4.3     5.3    -      -       -      +
    350A  GLY      4.3     1.4    -      -       -      +
    351A  LYS      2.8    24.0    +      -       -      +
    352A  PRO*     1.3    74.5    -      -       -      +
    354A  VAL*     1.3    60.7    +      -       -      +
    355A  PHE*     4.2     8.7    -      -       +      -
    397A  ALA      3.8    15.5    +      -       -      -
    398A  ASP*     2.8    11.8    +      -       -      +
    399A  PHE*     3.3    36.2    -      -       +      -
    400A  LEU      2.9    25.1    +      -       -      +
    470A  LEU*     5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309A  CYS*     4.4    13.7    -      -       -      -
    310A  PHE      2.8    16.1    +      -       -      +
    311A  ILE*     3.2    12.7    -      -       +      +
    312A  CYS      2.8    32.4    +      -       -      +
    352A  PRO*     4.6     1.3    -      -       +      -
    353A  LYS*     1.3    79.4    -      -       -      +
    355A  PHE*     1.3    59.7    +      -       -      +
    356A  PHE*     3.5    39.9    -      -       +      -
    400A  LEU*     3.5    22.4    -      -       +      +
    439A  ILE*     5.8     0.2    -      -       +      -
    474A  LEU*     3.8    28.0    -      -       +      -
    476A  PHE*     4.6     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  LEU*     5.2     1.6    -      -       +      -
    310A  PHE*     4.3     8.3    -      +       -      -
    312A  CYS*     3.2    39.5    -      -       +      -
    314A  ILE*     4.8     3.4    -      -       +      -
    336A  LEU*     4.3     8.7    -      -       +      -
    337A  THR*     3.8    32.5    -      -       +      -
    340A  PHE*     3.7    30.3    -      +       -      -
    353A  LYS*     4.5     6.7    -      -       +      -
    354A  VAL*     1.3    78.6    -      -       -      +
    356A  PHE*     1.3    64.2    +      -       -      +
    357A  ILE*     4.5    12.3    -      -       +      -
    399A  PHE*     4.0    29.8    -      +       -      -
    400A  LEU      2.9     9.2    +      -       -      +
    401A  LEU*     3.5    20.3    -      -       +      +
    402A  GLY      2.8    26.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  PHE*     3.9    25.4    -      +       -      -
    311A  ILE*     4.1     6.1    -      -       +      -
    312A  CYS      3.0     7.1    +      -       -      -
    313A  CYS*     3.5    26.3    -      -       -      +
    314A  ILE      2.9    27.0    +      -       -      +
    315A  LEU*     5.6     0.2    -      -       -      +
    354A  VAL*     3.5    29.6    -      -       +      -
    355A  PHE*     1.3    75.8    -      -       -      +
    357A  ILE*     1.3    62.0    +      -       -      +
    358A  GLN      4.1     0.7    -      -       -      -
    400A  LEU*     4.9     0.7    -      -       +      -
    402A  GLY*     3.5     9.0    -      -       -      +
    421A  TYR*     3.6    24.2    -      -       +      -
    422A  ILE*     4.7     7.7    -      -       +      +
    425A  LEU*     3.7    39.9    -      -       +      -
    429A  LEU*     5.3     0.2    -      -       +      -
    439A  ILE*     4.5    14.1    -      -       +      -
    443A  LEU*     4.3    13.5    -      -       +      -
    476A  PHE*     5.8     1.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314A  ILE*     3.7    31.6    -      -       +      +
    323A  ILE*     3.6    27.8    -      -       +      -
    333A  ILE*     4.1    18.6    -      -       +      -
    355A  PHE*     4.5    13.5    -      -       +      -
    356A  PHE*     1.3    79.1    -      -       -      +
    358A  GLN*     1.3    59.6    +      -       -      +
    359A  ALA*     3.7     9.7    +      -       +      -
    401A  LEU*     3.8    13.2    -      -       +      -
    402A  GLY      2.9    10.3    +      -       -      +
    403A  MET*     3.7    37.8    -      -       +      +
    404A  ALA*     3.0    26.9    +      -       -      +
    421A  TYR*     4.3     2.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260A  ARG*     4.0     6.1    -      -       -      +
    266A  ASP*     4.2     1.6    -      -       -      +
    314A  ILE*     2.8    16.5    +      -       -      +
    315A  LEU*     3.9     6.3    -      -       +      +
    316A  SER      3.0    26.5    +      -       -      +
    356A  PHE      4.1     1.0    +      -       -      -
    357A  ILE*     1.3    69.9    -      -       -      +
    359A  ALA*     1.3    62.3    +      -       -      +
    404A  ALA*     3.2    20.0    -      -       +      +
    411A  SER*     2.9    25.4    +      -       -      -
    412A  TYR      4.2     3.6    +      -       -      -
    419A  THR*     3.5    34.9    +      -       +      +
    421A  TYR*     3.4    15.5    +      -       +      +
    422A  ILE*     3.7    21.5    -      -       +      -
    462A  GLN*     4.6     0.2    +      -       -      -
    405E  1U8      2.8    25.3    +      -       -      +
----------------------------------------------------------
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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