Contacts of the strand formed by residues 182 - 186 (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 LEU 182 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  LEU*     3.5    32.5    -      -       +      -
    127B  LEU*     4.4     5.6    -      -       +      -
    129B  ILE*     4.0    21.3    -      -       +      -
    134B  VAL      4.0     1.4    +      -       -      -
    135B  VAL*     3.9    18.8    -      -       +      -
    136B  ALA*     2.8    29.3    +      -       -      +
    180B  SER*     3.4     2.4    -      -       -      -
    181B  ARG*     1.3    83.0    -      -       -      +
    183B  VAL*     1.3    76.0    +      -       -      +
    184B  ILE*     4.1     3.8    -      -       +      -
    214B  VAL*     4.6     0.4    -      -       -      -
    216B  HIS*     3.2    39.0    -      -       +      +
    218B  ILE*     3.9    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136B  ALA*     3.3    13.9    -      -       +      +
    138B  TYR*     4.7     6.7    -      -       +      -
    171B  VAL*     6.1     0.9    -      -       +      -
    175B  ILE*     3.8    28.7    -      -       +      -
    180B  SER*     5.3     0.2    -      -       -      -
    182B  LEU*     1.3    80.7    -      -       -      +
    184B  ILE*     1.3    71.2    +      -       -      +
    185B  THR*     4.6     1.8    -      -       -      -
    202B  VAL*     3.9    30.3    -      -       +      -
    206B  LEU*     4.7     3.1    -      -       +      -
    214B  VAL*     4.0    20.9    -      -       +      -
    216B  HIS      3.1     5.7    +      -       -      -
    217B  VAL*     3.2    15.5    -      -       +      +
    218B  ILE      2.8    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  PHE*     3.6    29.6    -      -       +      -
    124B  LEU*     4.5     1.3    -      -       +      -
    135B  VAL*     3.7    28.3    -      -       +      -
    136B  ALA      2.8    12.3    +      -       -      +
    137B  ILE*     3.6     7.6    -      -       +      -
    138B  TYR*     2.8    29.5    +      -       -      +
    139B  MET*     3.7    13.8    -      -       +      +
    148B  ALA*     3.8    17.5    -      -       +      -
    152B  CYS*     4.9     1.6    -      -       -      -
    182B  LEU*     4.1    12.8    -      -       +      -
    183B  VAL*     1.3    75.5    -      -       -      +
    185B  THR*     1.3    62.9    +      -       -      +
    218B  ILE*     3.6    13.5    -      -       +      +
    237B  TRP*     3.9    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  TYR*     2.8    27.1    +      -       -      -
    139B  MET*     3.4    13.1    -      -       -      +
    183B  VAL*     4.6     0.9    -      -       -      -
    184B  ILE*     1.3    75.3    -      -       -      +
    186B  ALA*     1.3    76.5    +      -       -      +
    198B  LEU*     3.5    11.6    -      -       -      +
    199B  LYS*     4.2    14.1    -      -       +      -
    202B  VAL*     4.0    19.6    -      -       +      +
    217B  VAL*     4.0    19.3    -      -       +      -
    218B  ILE      2.9    17.6    +      -       -      +
    219B  VAL*     4.4     2.5    -      -       +      -
    220B  LEU*     2.9    20.8    +      -       -      +
    237B  TRP*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  TYR      4.1     1.2    +      -       -      -
    139B  MET*     3.9     1.9    -      -       -      -
    140B  PRO*     4.0    21.8    -      -       +      -
    185B  THR*     1.3    78.1    +      -       -      +
    187B  ASP*     1.3    68.3    +      -       -      +
    188B  GLU      3.9    15.7    -      -       -      +
    198B  LEU*     3.4     6.2    -      -       +      +
    199B  LYS*     3.1    17.0    +      -       -      +
    219B  VAL*     3.9     4.9    -      -       -      -
    220B  LEU*     3.2    25.4    -      -       +      +
    222B  ARG*     4.3     6.7    -      -       +      -
----------------------------------------------------------
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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