Contacts of the strand formed by residues 237 - 241 (chain B) in PDB entry 1IR1


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 GLY 237 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  LEU*     3.8     6.0    -      -       -      +
    198B  ASP      3.2     7.4    +      -       -      +
    199B  PHE*     3.2    38.4    -      -       -      -
    200B  THR      3.3     2.9    +      -       -      -
    225B  LEU*     4.0    10.3    -      -       -      -
    236B  LYS*     1.3    78.1    -      -       -      +
    238B  HIS*     1.3    61.4    +      -       -      +
    263B  PRO*     4.0    13.2    -      -       -      -
    264B  ILE*     4.3     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  ILE*     4.5     0.4    -      -       +      -
    185B  TYR*     4.1     6.1    -      +       -      -
    189B  VAL*     3.6    29.3    -      -       +      +
    193B  LEU*     5.3     0.2    -      -       +      -
    200B  THR*     2.7    28.8    +      -       -      +
    201B  KCX      3.5    26.9    -      -       -      -
    202B  ASP*     2.7    24.2    +      -       -      -
    221B  CYS*     3.8    17.1    -      -       +      -
    225B  LEU*     3.7    19.3    -      -       +      +
    237B  GLY*     1.3    73.7    -      -       -      -
    239B  TYR*     1.3    62.5    +      -       -      +
    240B  LEU*     2.9    39.6    +      -       +      +
    262B  VAL*     5.8     1.0    -      -       -      +
    263B  PRO*     5.3     0.4    -      -       -      +
    264B  ILE*     3.4    13.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 239 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  PHE*     3.4    44.5    -      +       +      +
    200B  THR      3.0     7.3    +      -       -      -
    201B  KCX      3.3    26.0    -      -       +      -
    202B  ASP*     3.3    24.1    +      -       -      +
    238B  HIS*     1.3    70.4    -      -       -      +
    240B  LEU*     1.3    61.4    +      -       -      +
    241B  ASN      3.5     2.4    +      -       -      -
    264B  ILE*     3.6    37.9    -      -       +      -
    265B  VAL      4.6     0.2    -      -       -      -
    266B  MET*     3.7    18.7    -      -       +      +
    292B  HIS*     3.3    37.2    -      +       +      -
    325B  HIS*     3.6    12.1    +      +       -      -
    399B  VAL*     3.8     3.8    -      -       -      +
    401B  GLN*     2.9    33.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 240 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202B  ASP*     3.7     4.0    -      -       -      +
    217B  ARG*     4.9     0.9    -      -       -      +
    218B  PHE*     3.7    65.6    -      -       +      +
    221B  CYS*     4.2     9.2    -      -       +      -
    222B  ALA*     6.0     0.7    -      -       -      +
    225B  LEU*     6.2     1.1    -      -       +      -
    238B  HIS*     2.9    36.0    +      -       +      +
    239B  TYR*     1.3    71.6    -      -       -      +
    241B  ASN*     1.3    63.9    +      -       -      +
    242B  ALA*     3.4     1.7    +      -       -      +
    257B  ALA*     4.4     4.3    -      -       +      -
    260B  LEU*     4.8     4.3    -      -       +      -
    262B  VAL*     4.0    30.7    -      -       +      -
    264B  ILE      3.6     7.9    +      -       -      +
    265B  VAL*     3.3    11.3    -      -       +      +
    266B  MET      2.9    18.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 241 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202B  ASP*     2.9    18.6    +      -       +      +
    203B  ASP      3.4    10.5    +      -       -      -
    204B  GLU      3.2    25.5    +      -       -      -
    206B  VAL      3.2    25.2    +      -       -      +
    207B  ASN*     3.5     7.7    -      -       -      +
    217B  ARG*     4.0     4.6    +      -       -      +
    218B  PHE*     3.6    17.7    -      -       -      -
    239B  TYR      3.5     2.2    +      -       -      -
    240B  LEU*     1.3    68.3    -      -       -      +
    242B  ALA*     1.3    60.5    +      -       -      +
    243B  THR*     2.7    31.7    +      -       -      +
    253B  ARG*     4.4     6.4    -      -       -      -
    266B  MET*     3.4    31.2    -      -       +      +
    268B  ASP*     4.0     2.1    +      -       -      +
----------------------------------------------------------
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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