Contacts of the strand formed by residues 468 - 474 (chain A) in PDB entry 4KSP


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 GLY 468 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463A  GLY      4.4     0.7    -      -       -      +
    464A  SER*     4.1     0.7    -      -       -      -
    465A  GLY      2.5    40.1    +      -       -      +
    466A  SER      3.0     4.4    +      -       -      -
    467A  PHE*     1.3    74.7    -      -       -      +
    469A  THR*     1.3    62.3    +      -       -      -
    470A  VAL*     5.4     2.5    -      -       -      +
    482A  LYS*     4.6     8.5    -      -       -      -
    483A  MET      2.9    16.6    -      -       -      -
    484A  LEU*     4.5     6.1    -      -       -      -
    485A  ASN      5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  ARG*     3.8    23.1    -      -       +      -
    463A  GLY      3.6    11.0    -      -       -      +
    464A  SER*     3.8    18.9    +      -       -      +
    465A  GLY      5.1     0.3    +      -       -      -
    468A  GLY*     1.3    76.8    +      -       -      -
    470A  VAL*     1.3    66.7    +      -       -      +
    471A  TYR*     3.8    19.7    -      -       +      +
    481A  VAL      3.3     3.1    -      -       -      +
    482A  LYS*     3.3     0.7    -      -       -      -
    483A  MET*     2.7    39.5    +      -       -      +
    485A  ASN*     3.2    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 470 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  ARG*     3.7     2.8    -      -       -      +
    462A  ILE*     2.7    39.0    +      -       +      +
    463A  GLY*     3.0    20.2    +      -       -      +
    468A  GLY      5.4     1.6    -      -       -      +
    469A  THR*     1.3    77.9    -      -       -      +
    471A  TYR*     1.3    61.5    +      -       -      +
    480A  ALA*     4.7     1.3    -      -       +      -
    481A  VAL      3.3     8.1    -      -       -      +
    482A  LYS*     4.5    22.7    -      -       +      -
    530A  TRP*     5.6     0.2    -      -       +      -
    594A  PHE*     5.5     5.6    -      -       -      +
    595A  GLY      6.5     0.4    -      -       -      -
    901A  1SU      3.4    55.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458A  VAL*     3.3    36.1    -      -       +      -
    459A  GLY      3.6    12.6    -      -       -      -
    460A  GLN      3.6     4.3    -      -       -      +
    461A  ARG*     3.7    27.2    -      -       +      +
    462A  ILE*     4.3     3.6    -      -       -      -
    469A  THR*     3.8    32.6    -      -       +      +
    470A  VAL*     1.3    75.5    -      -       -      +
    472A  LYS*     1.3    65.4    +      -       -      +
    473A  GLY      3.7     0.3    +      -       -      -
    480A  ALA*     3.5     4.7    -      -       -      +
    481A  VAL*     2.9    42.2    +      -       +      +
    483A  MET*     4.5    17.0    -      -       +      -
    485A  ASN*     3.7    24.2    +      -       -      -
    530A  TRP*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459A  GLY*     2.7    35.8    +      -       -      -
    460A  GLN*     3.1    20.4    +      -       +      +
    462A  ILE*     3.9     6.6    -      -       +      +
    471A  TYR*     1.3    72.2    -      -       -      +
    473A  GLY*     1.3    58.7    +      -       -      +
    478A  ASP*     4.0    31.3    +      -       -      -
    479A  VAL      3.6     8.7    -      -       -      +
    530A  TRP*     3.4    50.8    -      -       +      +
    532A  GLU*     4.7     7.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457A  THR      3.2    14.1    -      -       -      -
    458A  VAL*     4.5     1.6    -      -       -      -
    459A  GLY*     4.1     2.2    -      -       -      -
    471A  TYR      3.7     1.8    +      -       -      -
    472A  LYS*     1.3    80.3    -      -       -      +
    474A  LYS*     1.3    66.0    +      -       -      +
    478A  ASP*     3.5     5.9    -      -       -      +
    479A  VAL*     2.8    39.9    +      -       -      +
    481A  VAL*     4.5     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455A  GLN      3.8     3.1    -      -       -      +
    456A  ILE*     3.7     2.6    -      -       -      +
    457A  THR*     2.9    45.1    +      -       +      +
    473A  GLY*     1.3    75.0    -      -       -      +
    475A  TRP*     1.3    64.0    +      -       -      +
    476A  HIS      4.3     0.2    -      -       -      -
    477A  GLY*     3.3    15.1    -      -       -      +
    478A  ASP*     3.8    20.9    +      -       -      +
    479A  VAL*     4.2     0.9    -      -       -      -
    561B  GLN*     4.6     9.5    -      -       -      +
    714B  GLU*     3.6    28.1    +      -       -      +
----------------------------------------------------------
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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