Contacts of the strand formed by residues 375 - 379 (chain A) 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 LEU 375 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ILE*     4.0    25.0    -      -       +      +
    158A  GLU*     3.6    33.0    -      -       +      +
    159A  ARG*     5.4     8.1    -      -       +      +
    169A  LEU*     4.1    11.4    -      -       +      -
    324A  ASP      3.0    17.6    +      -       -      +
    325A  HIS*     3.3    14.8    -      -       +      +
    326A  ILE      3.1    23.6    +      -       -      -
    374A  VAL*     1.3    71.1    -      -       -      +
    376A  PRO*     1.3    65.9    -      -       -      +
    377A  VAL*     3.8     1.4    -      -       -      +
    397A  ASP*     3.5    41.1    -      -       +      +
    398A  SER*     3.6     5.4    -      -       -      +
    399A  VAL*     4.1    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 376 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  ILE*     3.5     9.4    -      -       +      +
    328A  SER*     3.6    21.3    -      -       -      +
    346A  VAL*     4.2    15.9    -      -       +      -
    349A  LEU*     4.7     6.7    -      -       +      -
    350A  ARG*     3.6    22.2    -      -       +      +
    374A  VAL      3.3     9.8    -      -       -      +
    375A  LEU*     1.3    84.6    -      -       -      +
    377A  VAL*     1.3    60.7    +      -       -      +
    378A  ALA      4.1     0.4    -      -       -      -
    394A  PHE*     4.6     5.4    -      -       +      -
    397A  ASP      3.3    24.7    -      -       -      +
    398A  SER*     3.2     8.8    -      -       -      -
    399A  VAL      3.0    22.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 377 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292A  HIS*     3.8    18.6    -      -       +      -
    325A  HIS*     3.8    19.1    -      -       +      +
    326A  ILE      2.9    13.0    +      -       -      +
    327A  HIS*     3.3    21.5    -      -       +      +
    328A  SER*     3.0    24.2    +      -       -      -
    329A  GLY      3.9     1.2    +      -       -      -
    375A  LEU      3.8     2.2    -      -       -      +
    376A  PRO*     1.3    77.2    -      -       -      +
    378A  ALA*     1.3    64.1    +      -       -      +
    379A  SER      3.7     2.1    +      -       -      -
    399A  VAL*     3.3    24.7    -      -       +      +
    401A  GLN*     3.4    38.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 378 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328A  SER*     4.3     0.2    +      -       -      -
    329A  GLY      3.5    20.6    -      -       -      +
    330A  THR*     3.8     9.0    -      -       +      -
    376A  PRO      4.1     1.4    +      -       -      -
    377A  VAL*     1.3    69.0    -      -       -      +
    379A  SER*     1.3    61.5    +      -       -      +
    382A  ILE*     3.8     3.4    -      -       +      +
    390A  LEU*     4.4     4.7    -      -       +      -
    394A  PHE*     3.7    24.9    -      -       +      -
    398A  SER*     5.7     0.8    -      -       -      -
    399A  VAL      2.8     8.2    +      -       -      +
    400A  LEU*     3.6    20.1    -      -       +      -
    401A  GLN*     2.9    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  THR*     4.6     1.4    +      -       -      -
    327A  HIS*     4.1     7.4    -      -       -      -
    329A  GLY*     4.5     1.9    +      -       -      -
    330A  THR*     3.2    18.2    +      -       -      +
    335A  LEU*     4.3     2.8    -      -       -      +
    377A  VAL*     3.7     2.8    +      -       -      -
    378A  ALA*     1.3    75.3    -      -       -      +
    380A  GLY*     1.3    60.9    +      -       -      +
    382A  ILE*     4.4     0.4    -      -       -      -
    401A  GLN*     3.6    40.0    +      -       -      +
    501A  CAP      2.8    58.3    +      -       -      +
----------------------------------------------------------
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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