Contacts of the strand formed by residues 39 - 45 (chain V) 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 39 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37V  LYS      4.9     4.0    -      -       -      +
     38V  TRP*     1.3    74.8    -      -       -      +
     40V  PRO*     1.3    70.5    -      -       -      +
     73V  PRO*     3.9     8.7    -      -       +      -
     74V  MET      3.8    29.2    -      -       -      +
     75V  PHE*     3.9    29.8    -      -       +      +
     76V  GLY      5.5     1.8    -      -       -      +
    102V  ILE      3.7     0.2    -      -       -      +
    103V  GLY*     3.3     3.6    -      -       -      -
    104V  PHE*     2.8    51.7    +      -       +      +
    106V  SER*     5.5    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 40 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30V  VAL*     6.0     0.7    -      -       +      -
     33V  LEU*     3.8    19.9    -      -       +      -
     34V  LEU*     4.0    13.2    -      -       +      -
     38V  TRP      3.5     9.4    -      -       -      +
     39V  VAL*     1.3    86.3    -      -       +      +
     41V  CYS*     1.3    63.3    +      -       -      +
     73V  PRO*     3.6     0.9    -      -       -      +
     74V  MET*     2.9    52.9    +      -       +      +
     77V  CYS*     4.2     4.3    -      -       +      +
     83V  VAL*     3.9    35.0    -      -       +      -
    101V  ILE*     5.2     1.6    -      -       +      -
    102V  ILE      3.4     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 41 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  ARG*     6.3     0.2    -      -       -      -
     40V  PRO*     1.3    76.0    -      -       -      +
     42V  LEU*     1.3    79.5    +      -       -      +
     43V  GLU*     5.0     1.8    -      -       -      -
     69V  MET*     3.9    22.7    -      -       -      -
     70V  TRP      4.9     1.1    -      -       -      -
     72V  LEU      4.4     3.4    -      -       -      -
     73V  PRO*     3.8    29.2    -      -       +      -
     74V  MET*     5.0     2.2    -      -       -      +
    101V  ILE*     3.7     3.3    -      -       -      +
    102V  ILE*     2.9    44.2    +      -       +      +
    104V  PHE*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 42 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41V  CYS*     1.3    89.9    -      -       -      +
     43V  GLU*     1.3    64.2    +      -       -      +
     69V  MET*     3.8     1.7    -      -       -      -
     70V  TRP*     2.9    47.6    +      -       +      +
     74V  MET*     5.0     6.3    -      -       -      -
     83V  VAL*     4.3    26.2    -      -       +      +
     86V  GLU*     3.8    16.6    -      -       +      +
     87V  LEU*     3.6    41.7    -      -       +      +
     90V  CYS*     4.4     7.4    -      -       +      -
     99V  ILE*     4.5     6.7    -      -       +      -
    100V  ARG      3.5     8.7    -      -       -      +
    101V  ILE*     4.3    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 43 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  ARG*     3.0    30.8    +      -       -      -
     41V  CYS*     5.0     3.0    -      -       -      -
     42V  LEU*     1.3    80.1    -      -       -      +
     44V  PHE*     1.3    62.2    +      -       -      +
     66V  TYR*     6.1     0.5    -      -       -      -
     67V  TRP*     3.9    22.8    +      -       +      +
     68V  THR      3.1    11.7    -      -       -      +
     69V  MET*     4.8     7.5    -      -       -      +
     70V  TRP*     4.5     0.4    -      -       -      +
     99V  ILE*     3.4     6.4    -      -       -      +
    100V  ARG*     2.8    76.1    +      -       +      +
    102V  ILE*     3.7    28.0    -      -       +      +
    111V  GLN*     5.1     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 44 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3S  VAL*     4.1    12.1    -      -       +      -
      6S  THR*     4.0    17.5    -      -       +      -
     43V  GLU*     1.3    76.4    -      -       -      +
     45V  GLU*     1.3    64.1    +      -       -      +
     46V  THR*     4.8     2.2    -      -       +      -
     67V  TRP*     4.0     2.9    -      -       -      -
     68V  THR*     2.8    64.6    +      -       +      -
     69V  MET      3.8    17.0    -      -       -      -
     70V  TRP*     4.1    20.6    -      +       +      -
     90V  CYS*     4.2    19.7    -      -       -      -
     94V  TYR*     3.5    50.5    -      +       -      -
     97V  ALA*     4.3     7.4    -      -       +      -
     98V  PHE      3.2    12.3    -      -       -      +
     99V  ILE*     4.3     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 45 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  LYS*     3.0    31.3    +      -       -      -
     44V  PHE*     1.3    78.0    -      -       -      +
     46V  THR*     1.3    64.3    +      -       -      +
     47V  ASP*     3.0    26.0    +      -       -      +
     48V  HIS*     3.1    41.9    +      -       -      +
     49V  GLY*     4.3     1.8    -      -       -      +
     67V  TRP*     3.5    36.8    -      -       +      +
     68V  THR*     4.5     3.6    +      -       -      -
     97V  ALA*     3.2     1.6    -      -       -      +
     98V  PHE*     2.9    34.7    +      -       +      -
----------------------------------------------------------
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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