Contacts of the strand formed by residues 216 - 220 (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 HIS 216 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  LEU*     3.9    38.4    +      -       +      +
    181B  ARG      3.8     3.0    +      -       -      -
    182B  LEU*     3.2    18.6    -      -       +      +
    183B  VAL      3.1    21.1    +      -       -      -
    214B  VAL*     3.3     9.4    -      -       -      +
    215B  GLU*     1.3   106.6    +      -       +      +
    217B  VAL*     1.3    64.5    +      -       -      +
    218B  ILE*     5.5     0.2    -      -       +      -
    232B  GLY      3.2    27.6    +      -       -      -
    233B  ARG*     3.2    10.5    +      -       -      +
    235B  LEU*     4.0    15.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  VAL*     3.2    20.0    -      -       +      +
    185B  THR*     4.0    16.6    -      -       +      -
    199B  LYS*     4.5     4.7    -      -       +      -
    202B  VAL*     4.2    10.5    -      -       +      -
    206B  LEU*     3.7    30.3    -      -       +      -
    214B  VAL*     4.2     1.3    -      -       +      -
    216B  HIS*     1.3    79.6    -      -       -      +
    218B  ILE*     1.3    62.9    +      -       -      +
    219B  VAL*     3.7    19.8    +      -       +      +
    233B  ARG*     3.0    19.8    +      -       -      +
    234B  ASP*     3.3    14.0    -      -       -      +
    235B  LEU*     2.9    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  PHE*     3.7    25.6    -      -       +      -
    123B  THR*     4.6     2.7    -      -       +      -
    124B  LEU*     4.6     2.9    -      -       +      -
    127B  LEU*     4.0    16.4    -      -       +      -
    182B  LEU*     3.9    29.6    -      -       +      +
    183B  VAL      2.8     8.9    +      -       -      +
    184B  ILE*     3.6     7.1    -      -       +      -
    185B  THR*     2.9    27.9    +      -       -      +
    217B  VAL*     1.3    74.4    -      -       -      +
    219B  VAL*     1.3    63.6    +      -       -      +
    235B  LEU*     3.3     6.7    -      -       +      +
    237B  TRP*     3.8    44.2    -      -       +      +
    240B  LEU*     3.8    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  THR*     3.4     2.9    -      -       +      +
    186B  ALA      3.9     4.0    -      -       -      -
    187B  ASP*     3.7    25.6    -      -       -      +
    199B  LYS*     3.6    30.7    -      -       +      -
    217B  VAL*     3.9    16.4    -      -       +      +
    218B  ILE*     1.3    78.7    -      -       -      +
    220B  LEU*     1.3    62.7    +      -       -      +
    227B  ILE*     4.4     8.3    -      -       +      -
    229B  TRP*     3.9    17.0    -      -       +      -
    234B  ASP*     4.8     0.9    -      -       +      -
    235B  LEU      2.7    12.6    +      -       -      +
    236B  TRP*     3.2    25.2    -      -       +      -
    237B  TRP*     2.9    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  MET*     4.0     9.0    -      -       +      -
    142B  VAL*     4.0    14.8    -      -       +      -
    144B  GLU*     3.7    49.8    -      -       +      +
    185B  THR      2.9    16.5    +      -       -      +
    186B  ALA*     3.2     9.6    -      -       +      -
    187B  ASP*     2.9    25.1    +      -       -      -
    218B  ILE*     5.2     0.2    -      -       -      +
    219B  VAL*     1.3    75.2    -      -       -      +
    221B  LYS*     1.3    75.5    +      -       -      +
    222B  ARG*     3.2    14.8    +      -       +      +
    237B  TRP*     3.8    26.2    -      -       +      +
    901B   CL      4.1     6.5    -      -       +      -
----------------------------------------------------------
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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