Contacts of the strand formed by residues 93 - 98 (chain B) in PDB entry 1PG4


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 93 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ASP      3.6     2.8    +      -       -      -
     92B  ARG*     1.3    80.0    -      -       -      +
     94B  ALA*     1.3    63.8    +      -       -      +
     95B  ILE      3.5    23.3    -      -       -      +
     96B  ILE*     3.6    25.4    -      -       +      -
    107B  HIS*     4.1    19.5    -      -       +      +
    108B  ILE      3.8    11.2    -      -       -      +
    109B  SER*     3.9     3.9    -      -       -      +
    110B  TYR*     3.8     1.0    -      -       -      -
    326B  THR*     2.8    34.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  ARG      3.3     2.6    +      -       -      -
     93B  THR*     1.3    73.1    -      -       -      +
     95B  ILE*     1.3    60.0    +      -       -      +
    108B  ILE      2.7    15.2    +      -       -      +
    109B  SER      4.0     0.2    -      -       -      -
    110B  TYR*     3.4    47.8    -      -       +      +
    113B  LEU*     3.9    20.4    -      -       +      -
    321B  LEU*     4.0     2.6    -      -       +      +
    325B  ALA      3.6     2.1    -      -       -      +
    326B  THR*     3.6     1.6    -      -       -      -
    327B  THR*     2.9    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  THR*     3.5     5.1    -      -       -      +
     94B  ALA*     1.3    85.8    -      -       +      +
     96B  ILE*     1.3    74.9    +      -       -      +
     97B  TRP*     3.8     4.7    +      -       +      +
    106B  LYS      3.7     0.7    -      -       -      +
    107B  HIS*     3.6     0.7    -      -       -      -
    108B  ILE*     2.8    52.6    +      -       +      +
    113B  LEU*     3.8    31.6    -      -       +      -
    143B  PRO*     5.2     6.7    -      -       +      +
    146B  ALA*     4.0    25.4    -      -       +      -
    316B  LEU*     6.2     0.2    -      -       +      -
    317B  LEU*     4.4    10.5    -      -       +      -
    321B  LEU*     4.7     3.1    -      -       +      -
    327B  THR*     3.2    17.9    -      -       +      +
    329B  MET*     4.2    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  THR*     3.6    19.7    -      -       +      -
     95B  ILE*     1.3    74.0    -      -       -      +
     97B  TRP*     1.3    62.6    +      -       -      +
    106B  LYS      3.4     7.6    -      -       -      +
    107B  HIS*     3.9    18.6    -      -       +      +
    300B  ILE*     4.3    22.4    -      -       +      -
    326B  THR*     3.7    20.9    -      -       +      -
    327B  THR      2.9     8.7    +      -       -      +
    328B  LEU*     3.3    16.3    -      -       +      +
    329B  MET      2.8    25.8    +      -       -      +
    349B  HIS*     3.7    45.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  ILE*     3.8     5.1    +      -       +      -
     96B  ILE*     1.3    76.1    -      -       -      +
     98B  GLU*     1.3    57.6    +      -       -      +
     99B  GLY*     3.8    12.3    -      -       -      -
    104B  GLN*     4.1    24.2    -      -       +      -
    105B  SER*     3.1    22.3    -      -       -      -
    106B  LYS*     2.7    59.5    +      -       +      +
    108B  ILE*     5.2     0.7    -      -       +      -
    141B  MET      3.0    23.0    +      -       -      -
    142B  VAL*     3.7     9.8    -      -       +      +
    143B  PRO*     3.5    36.3    -      -       +      -
    222B  ARG*     3.9    18.2    -      -       -      -
    329B  MET*     3.3    23.1    -      -       -      -
    331B  GLU*     3.5    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ILE      3.9     1.0    +      -       -      -
     97B  TRP*     1.3    74.2    +      -       -      +
     99B  GLY*     1.3    62.3    +      -       -      +
    102B  THR*     2.9    25.6    +      -       -      -
    104B  GLN      4.1     0.4    -      -       -      -
    105B  SER*     4.0     2.9    -      -       -      -
    328B  LEU*     4.2    15.3    -      -       +      -
    329B  MET      3.0     6.9    +      -       -      +
    330B  PHE*     3.4    22.7    -      -       +      -
    331B  GLU*     2.8    28.6    +      -       -      +
    341B  ARG*     3.0    19.8    +      -       -      +
    345B  VAL*     4.2    13.1    -      -       +      +
    348B  LYS*     2.9    26.5    +      -       -      +
    349B  HIS*     2.9    24.6    +      -       +      +
----------------------------------------------------------
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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