Contacts of the strand formed by residues 453 - 458 (chain R) in PDB entry 5A31


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 THR 453 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176R  TYR*     3.2    40.7    +      -       +      +
    195R  TRP*     4.4     7.9    -      -       +      -
    446R  THR      4.1     0.2    -      -       -      +
    447R  LEU*     3.6     4.7    -      -       -      +
    448R  SER*     2.7    51.1    +      -       -      -
    451R  GLY      3.6     0.4    -      -       -      -
    452R  THR*     1.3    85.2    +      -       -      +
    454R  VAL*     1.3    73.7    +      -       -      +
    455R  VAL      4.2     0.2    +      -       -      -
    465R  TYR*     4.0    14.8    -      -       +      -
    466R  TRP      3.4    11.1    +      -       -      +
    467R  LYS*     4.3     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 454 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402R  VAL*     4.7     4.9    -      -       +      -
    411R  VAL*     4.6    11.4    -      -       +      -
    421R  LEU*     4.5     9.4    -      -       +      -
    445R  LEU*     3.5    34.1    -      -       +      -
    446R  THR      3.4    10.1    -      -       -      +
    447R  LEU*     4.0     9.4    -      -       +      -
    453R  THR*     1.3    76.9    -      -       -      +
    455R  VAL*     1.3    61.7    +      -       -      +
    465R  TYR*     3.7     0.2    -      -       -      -
    466R  TRP*     2.9    37.0    +      -       +      +
    468R  LEU*     3.6    28.9    -      -       +      -
    469R  PHE*     3.7    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 455 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193R  ILE*     3.3    27.3    -      -       +      +
    195R  TRP*     3.3    42.0    -      -       +      -
    201R  LEU*     4.2     4.3    -      -       +      -
    445R  LEU*     3.3     6.4    -      -       -      +
    446R  THR*     2.9    38.1    +      -       +      +
    454R  VAL*     1.3    75.0    -      -       -      +
    456R  SER*     1.3    64.5    +      -       -      +
    463R  LEU*     4.1     9.6    -      -       +      -
    464R  ARG      3.2     5.6    -      -       -      +
    465R  TYR*     3.7    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 456 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193R  ILE*     4.5     1.1    -      -       -      -
    421R  LEU*     3.7     7.4    -      -       -      +
    438R  HIS*     3.2    15.6    +      -       -      -
    442R  VAL*     3.6    24.0    -      -       -      -
    444R  HIS      3.3     4.0    -      -       -      -
    445R  LEU*     3.7    13.5    -      -       -      -
    455R  VAL*     1.3    76.7    -      -       -      +
    457R  GLY*     1.3    58.7    +      -       -      +
    463R  LEU*     3.2     4.6    -      -       -      +
    464R  ARG      2.7    37.6    +      -       -      -
    466R  TRP*     2.8    31.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 457 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184R  LEU*     4.0     2.9    -      -       -      -
    193R  ILE*     4.4     0.8    -      -       -      +
    438R  HIS*     4.1     3.1    -      -       -      -
    442R  VAL*     3.8     2.4    -      -       -      -
    443R  LEU      3.2     7.8    +      -       -      -
    444R  HIS*     2.7    46.7    +      -       -      +
    456R  SER*     1.3    75.4    -      -       -      +
    458R  ALA*     1.3    61.6    +      -       -      +
    462R  THR      3.4    10.3    -      -       -      -
    463R  LEU*     3.9    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 458 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184R  LEU*     3.5    18.8    -      -       -      +
    438R  HIS*     3.6    15.0    -      -       +      -
    440R  PHE*     3.6    15.0    -      -       +      +
    441R  ARG      3.2    23.1    -      -       -      +
    442R  VAL*     4.3     0.4    -      -       -      -
    444R  HIS*     4.1     5.4    -      -       -      -
    457R  GLY*     1.3    73.5    -      -       -      +
    459R  GLY*     1.3    58.6    +      -       -      +
    460R  ASP*     2.9    16.1    -      -       -      +
    461R  GLU*     2.9    19.2    +      -       -      -
    462R  THR      3.6     5.5    +      -       -      -
----------------------------------------------------------
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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