Contacts of the strand formed by residues 399 - 401 (chain C) 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 VAL 399 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169C  LEU*     3.4    27.1    -      -       +      +
    171C  GLY      4.3     6.3    -      -       -      +
    199C  PHE*     4.5     3.4    -      -       +      -
    239C  TYR*     3.8    19.5    -      -       -      +
    325C  HIS*     4.2    13.0    -      -       +      -
    375C  LEU*     4.1    20.9    -      -       +      -
    376C  PRO      3.0     7.9    +      -       -      +
    377C  VAL*     3.3    21.7    -      -       +      +
    378C  ALA      2.8    27.9    +      -       -      +
    398C  SER*     1.3    78.8    -      -       -      +
    400C  LEU*     1.3    64.3    +      -       -      +
    401C  GLN*     3.9    16.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 400 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168C  PRO*     4.0    25.1    -      -       +      -
    169C  LEU      2.9     7.8    +      -       -      +
    170C  LEU*     3.4    12.5    -      -       +      +
    171C  GLY      2.9    20.1    +      -       -      +
    378C  ALA*     3.5    25.4    -      -       +      +
    387C  MET*     4.0    24.7    -      -       -      -
    390C  LEU*     4.3    27.4    -      -       +      +
    391C  THR*     4.7     4.5    -      -       -      +
    394C  PHE*     4.6     5.4    -      -       +      -
    398C  SER*     3.9    14.8    -      -       -      +
    399C  VAL*     1.3    76.8    -      -       -      +
    401C  GLN*     1.3    60.5    +      -       -      +
    402C  PHE*     3.7    17.2    -      -       +      -
    424C  LEU*     4.2     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 401 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171C  GLY*     3.3    21.1    -      -       -      -
    172C  CYS*     4.1     4.3    -      -       -      +
    173C  THR*     4.4     2.6    +      -       -      +
    201C  KCX      3.4    22.0    -      -       -      +
    239C  TYR*     2.9    44.3    +      -       -      -
    292C  HIS*     3.9     1.0    -      -       -      -
    327C  HIS*     3.7    18.0    -      -       -      -
    377C  VAL*     3.4    25.1    -      -       +      +
    378C  ALA      2.9     9.9    +      -       -      -
    379C  SER*     3.8    22.4    +      -       -      +
    380C  GLY      4.3     1.6    +      -       -      -
    382C  ILE*     3.4    20.8    -      -       -      +
    399C  VAL*     3.9     3.5    -      -       +      +
    400C  LEU*     1.3    75.6    -      -       -      +
    402C  PHE*     1.3    63.5    +      -       -      +
    403C  GLY      4.1     1.4    +      -       -      -
    501C  CAP      4.4     0.7    +      -       -      -
----------------------------------------------------------
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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