Contacts of the strand formed by residues 460 - 466 (chain B) in PDB entry 1PG3


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 460 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  LEU*     4.1     7.0    -      -       +      -
    456B  GLN*     3.5    39.9    +      -       +      +
    457B  GLU      3.5    11.4    -      -       -      +
    458B  GLY      3.0    16.0    +      -       -      +
    459B  ALA*     1.3    74.8    -      -       -      +
    461B  GLU*     1.3    88.9    +      -       -      +
    503B  ARG*     3.2     4.7    -      -       -      +
    504B  ARG*     2.8    33.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 461 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  LEU*     3.9     6.1    -      -       -      -
    456B  GLN*     4.3     7.8    +      -       -      +
    460B  THR*     1.3    97.8    +      -       -      +
    462B  GLY*     1.3    58.6    +      -       -      +
    502B  ALA      3.1    14.6    -      -       -      +
    503B  ARG*     3.6    18.1    -      -       +      +
    513B  THR*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 462 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  LEU*     4.0    13.2    -      -       -      +
    449B  VAL      3.9     8.7    -      -       -      -
    450B  ASP*     5.5     1.6    -      -       -      -
    456B  GLN*     5.1     1.3    -      -       -      -
    461B  GLU*     1.3    75.6    -      -       -      +
    463B  ASN*     1.3    66.2    +      -       -      -
    464B  LEU      3.5     0.2    +      -       -      -
    501B  GLY*     3.4     3.8    -      -       -      -
    502B  ALA*     2.9    31.7    +      -       -      +
    516B  VAL*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 463 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    447B  ALA      3.3     6.8    -      -       -      +
    448B  LEU*     3.3     1.2    -      -       -      -
    449B  VAL*     2.9    56.8    +      -       +      +
    450B  ASP*     3.3    13.5    +      -       -      +
    451B  ASN*     3.3    24.7    +      -       -      +
    462B  GLY*     1.3    71.2    -      -       -      -
    464B  LEU*     1.3    62.6    +      -       -      +
    465B  VAL      3.4     1.2    +      -       -      -
    492B  PHE*     3.6    12.6    -      -       +      -
    497B  PHE*     3.7    15.3    -      -       +      -
    500B  ASP      4.0     3.1    -      -       -      -
    501B  GLY*     4.6     0.9    -      -       -      -
    516B  VAL*     3.7    28.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 464 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413B  TRP*     3.5    37.9    -      -       +      -
    423B  ILE*     4.2     9.2    -      -       +      -
    446B  PRO*     4.2    17.7    -      -       +      -
    447B  ALA      3.6     9.4    -      -       -      +
    448B  LEU*     4.1    11.9    -      -       +      -
    462B  GLY      3.5     2.4    +      -       -      -
    463B  ASN*     1.3    70.5    -      -       -      +
    465B  VAL*     1.3    73.1    +      -       -      +
    466B  ILE*     4.8     2.7    -      -       +      -
    497B  PHE*     3.5     2.6    -      -       -      -
    498B  SER*     2.8    34.8    +      -       -      +
    500B  ASP*     2.9    24.2    +      -       +      +
    502B  ALA*     4.4    10.5    -      -       +      -
    510B  TYR*     4.6     3.6    -      -       +      -
    512B  ILE*     3.6    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 465 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446B  PRO*     3.4     4.7    -      -       -      +
    447B  ALA*     2.9    52.8    +      -       +      +
    449B  VAL*     4.1     9.9    -      -       +      -
    463B  ASN      4.0     5.6    -      -       -      +
    464B  LEU*     1.3    81.1    -      -       -      +
    466B  ILE*     1.3    67.0    +      -       -      +
    467B  THR*     4.8     0.9    -      -       +      -
    492B  PHE*     3.7    20.9    -      -       +      -
    495B  MET*     3.7    30.1    -      -       +      -
    496B  TYR      3.1    16.8    -      -       -      +
    497B  PHE*     3.6    18.6    -      -       +      -
    498B  SER      4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 466 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  PHE*     3.7     1.7    -      -       -      -
    413B  TRP*     4.5    20.6    -      -       +      -
    422B  MET*     4.1    13.0    -      -       +      -
    423B  ILE*     5.7     0.2    -      -       +      -
    444B  VAL*     4.1    16.8    -      -       +      -
    445B  GLN      3.4    24.0    -      -       -      +
    446B  PRO*     4.0    14.4    -      -       +      -
    464B  LEU*     4.8     2.7    -      -       +      -
    465B  VAL*     1.3    83.3    -      -       -      +
    467B  THR*     1.3    62.0    +      -       -      +
    468B  ASP      3.3    21.6    +      -       -      +
    470B  TRP*     3.7    17.0    -      -       +      -
    495B  MET*     4.8     0.2    -      -       -      -
    496B  TYR*     3.0    51.3    +      -       +      +
    498B  SER*     5.8     0.4    -      -       -      -
----------------------------------------------------------
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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