Contacts of the strand formed by residues 227 - 232 (chain B) in PDB entry 2PHA


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 ILE 227 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  HIS*     4.3     2.7    -      -       -      -
    119B  GLY*     3.3     7.0    -      -       -      +
    121B  ILE*     3.8    31.9    -      -       +      -
    216B  LEU*     5.5     2.7    -      -       +      -
    219B  LEU*     4.3    21.8    -      -       +      -
    220B  LEU*     3.6    28.9    -      -       +      -
    225B  ARG*     4.8     0.2    -      -       -      -
    226B  PRO*     1.3    77.5    -      -       -      +
    228B  HIS*     1.3    67.2    +      -       -      +
    229B  LEU*     4.3     0.7    -      -       -      +
    264B  ILE*     4.2    14.8    -      -       +      -
    267B  THR*     4.7     6.5    -      -       -      +
    269B  LEU*     2.5    41.1    +      -       +      +
    270B  LEU*     3.3    10.2    -      -       +      +
    271B  SER      2.7    28.8    +      -       -      -
    272B  GLY      3.3     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 228 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  SER*     5.2     0.9    -      -       -      -
    107B  SER*     2.8    37.8    +      -       -      -
    108B  ILE*     3.3    29.6    -      -       +      +
    111B  HIS*     3.0    31.9    +      -       +      +
    118B  LEU*     4.3     9.6    -      -       +      -
    119B  GLY      2.7    14.1    +      -       -      +
    120B  VAL*     3.4     5.6    -      -       +      +
    121B  ILE      2.9    25.7    +      -       -      +
    227B  ILE*     1.3    73.4    -      -       -      +
    229B  LEU*     1.3    65.7    +      -       -      +
    230B  SER*     4.2     2.5    -      -       -      -
    272B  GLY*     3.4    19.1    -      -       -      +
    274B  ASP*     2.7    26.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 229 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  ILE*     3.2    40.8    -      -       +      +
    123B  VAL*     3.7    18.8    -      -       +      -
    227B  ILE*     5.0     0.2    -      -       +      -
    228B  HIS*     1.3    74.3    -      -       -      +
    230B  SER*     1.3    64.3    +      -       -      +
    231B  PHE*     4.5     8.1    -      -       +      +
    260B  ILE*     5.0     1.3    -      -       +      -
    261B  THR*     3.9    24.0    -      -       +      -
    264B  ILE*     3.6    24.7    -      -       +      -
    270B  LEU*     4.0    16.4    -      -       +      +
    272B  GLY      2.9     9.1    +      -       -      -
    273B  LEU*     3.3    21.9    -      -       +      +
    274B  ASP*     2.9    24.3    +      -       -      +
    303B  CYS*     4.3     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 230 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  HIS*     2.7    29.7    +      -       -      -
    104B  ALA*     4.0     1.4    -      -       -      +
    120B  VAL*     5.1     0.2    -      -       -      -
    121B  ILE      2.8     8.6    +      -       -      -
    122B  TRP*     3.5    34.2    -      -       -      -
    123B  VAL      3.1    26.0    +      -       -      +
    228B  HIS*     3.7     7.9    +      -       -      -
    229B  LEU*     1.3    71.4    -      -       -      +
    231B  PHE*     1.3    60.0    +      -       -      +
    232B  ASP      3.9     0.4    +      -       -      -
    274B  ASP*     3.1    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 231 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  HIS*     4.5     2.7    -      -       -      -
    123B  VAL*     3.7    34.8    -      -       +      -
    229B  LEU*     3.7    17.7    +      -       +      -
    230B  SER*     1.3    73.1    +      -       -      +
    232B  ASP*     1.3    64.9    +      -       -      +
    233B  VAL*     3.5    25.5    +      -       +      -
    236B  LEU*     3.7    24.0    -      -       +      -
    241B  THR*     6.2     0.9    -      -       +      -
    257B  GLY*     5.1     3.8    -      -       -      -
    260B  ILE*     5.7     3.1    -      -       +      -
    261B  THR*     4.9     5.8    -      -       +      -
    273B  LEU*     4.8     0.9    -      -       +      -
    274B  ASP*     3.0    18.8    +      -       -      +
    275B  ILE*     3.7    11.2    -      -       +      -
    276B  MET*     2.9    27.9    +      -       -      -
    296B  ALA*     6.2     2.0    -      -       -      -
    299B  ILE*     3.4    47.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 232 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  HIS*     3.5    11.4    -      -       +      +
    123B  VAL      3.1     9.0    +      -       -      +
    124B  ASP*     3.4    20.9    -      -       -      +
    230B  SER      3.9     1.2    +      -       -      -
    231B  PHE*     1.3    74.8    -      -       -      +
    233B  VAL*     1.3    54.1    +      -       -      +
    234B  ASP*     2.7    17.2    +      -       -      +
    235B  GLY*     2.6    32.2    +      -       -      -
    276B  MET*     4.3     4.5    -      -       -      -
    277B  GLU*     3.0    28.9    -      -       -      +
    323B   MN      2.3    33.1    +      -       -      -
    324B   MN      2.5    13.2    +      -       -      -
----------------------------------------------------------
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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