Contacts of the strand formed by residues 130 - 139 (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 130 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  VAL*     3.9    13.9    -      -       +      -
     43A  SER      3.8     4.0    -      -       -      +
     44A  PRO*     4.4     3.6    -      -       +      -
     45A  GLN*     3.6    12.3    +      -       -      -
     53A  ALA*     3.9    32.1    -      -       +      +
     56A  ALA*     6.1     2.9    -      -       +      -
     57A  VAL*     4.1    13.0    -      -       +      -
    124A  VAL*     3.6    23.8    -      -       +      +
    125A  PHE*     5.4     3.1    -      -       -      +
    127A  PHE*     3.1    27.0    +      -       +      +
    128A  LYS      3.1     1.3    -      -       -      +
    129A  ALA*     1.3    89.1    -      -       +      +
    131A  ARG*     1.3    61.2    +      -       -      +
    132A  ALA      4.3     7.9    -      -       -      +
    133A  LEU*     4.1    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  SER*     2.7    24.3    +      -       -      +
     44A  PRO      2.6    24.5    +      -       -      +
     45A  GLN*     3.6    30.2    -      -       -      +
     46A  PRO*     4.5     8.5    -      -       -      -
     94A  GLU*     3.9    14.1    +      -       -      +
     95A  ASN*     2.7    42.8    +      -       -      +
    130A  LEU*     1.3    74.3    -      -       -      +
    132A  ALA*     1.3    65.0    +      -       +      +
    307A  HIS*     4.9     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  VAL*     4.2     0.9    -      -       -      +
     43A  SER*     3.1    39.1    +      -       -      +
    125A  PHE      6.0     0.4    -      -       -      -
    130A  LEU*     3.5     7.2    -      -       -      +
    131A  ARG*     1.3    84.3    -      -       +      +
    133A  LEU*     1.3    64.3    +      -       -      +
    306A  ASN*     3.3    37.5    -      -       +      +
    307A  HIS*     3.7    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  PHE*     3.8    20.2    -      -       +      -
     41A  ARG      3.5     9.4    -      -       -      +
     42A  VAL*     3.6    32.3    -      -       +      -
     57A  VAL*     4.4     9.6    -      -       +      -
    124A  VAL*     3.7    44.2    -      -       +      +
    125A  PHE*     3.1    38.2    -      -       +      +
    130A  LEU*     4.1    13.5    -      -       +      -
    132A  ALA*     1.3    77.9    -      -       -      +
    134A  ARG*     1.3    62.5    +      -       -      +
    306A  ASN      3.6     2.9    +      -       -      -
    307A  HIS*     3.2     7.3    +      -       -      -
    308A  GLY      3.0    19.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  PHE*     3.4     6.1    -      -       -      -
     41A  ARG*     2.7    45.6    +      -       +      +
    125A  PHE*     4.5     0.4    -      -       -      -
    133A  LEU*     1.3    77.2    -      -       -      +
    135A  LEU*     1.3    65.8    +      -       -      +
    136A  GLU*     3.0    33.5    +      -       -      -
    302A  ASP      3.1    24.4    +      -       -      -
    304A  GLN      3.3    19.9    +      -       -      -
    305A  LYS*     3.3    27.6    -      -       -      +
    306A  ASN      4.0    10.5    -      -       -      +
    307A  HIS*     4.0     0.6    +      -       -      -
    308A  GLY      3.1    24.7    -      -       -      +
    309A  MET      4.4     2.2    -      -       -      +
    310A  HIS*     3.5    24.3    -      -       -      +
    473A  ASP*     2.7    30.5    +      -       -      -
    474A  THR      5.3     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ALA*     4.0     8.1    -      -       +      -
     39A  ALA      3.8     8.5    -      -       -      +
     40A  PHE*     3.8    26.7    -      -       +      -
    117A  PHE*     5.0     1.3    -      -       +      -
    120A  ILE*     4.2     7.9    -      -       +      -
    121A  VAL*     3.8    21.8    -      -       +      -
    125A  PHE*     4.0     5.8    -      -       +      -
    134A  ARG*     1.3    71.7    -      -       -      +
    136A  GLU*     1.3    58.2    +      -       -      +
    137A  ASP      3.6    19.5    -      -       -      +
    138A  LEU*     4.0    16.6    -      -       +      -
    308A  GLY      3.0     7.5    +      -       -      -
    309A  MET*     3.5    16.5    -      -       +      -
    310A  HIS*     3.0    25.5    +      -       -      +
    313A  VAL*     3.8    34.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ALA*     2.8    19.3    +      -       +      +
     41A  ARG*     2.8    54.6    +      -       +      +
     98A  ILE*     4.9     2.2    -      -       +      -
    134A  ARG*     3.0    31.7    +      -       -      +
    135A  LEU*     1.3    74.8    -      -       -      +
    137A  ASP*     1.3    57.8    +      -       -      +
    310A  HIS*     3.8     4.3    -      -       -      +
    312A  ARG*     2.7    55.2    +      -       -      +
    313A  VAL*     3.7     3.4    -      -       -      +
    363A  TYR*     3.8    29.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ALA*     3.1    23.8    +      -       +      -
    135A  LEU*     3.6     4.6    -      -       -      +
    136A  GLU*     1.3    79.8    -      -       -      +
    138A  LEU*     1.3    83.6    +      -       -      +
    312A  ARG*     3.9    15.1    -      -       -      +
    313A  VAL*     3.8     9.2    -      -       -      +
    316A  LYS*     3.0    29.1    +      -       -      +
    348A  LEU*     5.4     0.7    -      -       -      +
    362A  ILE*     4.0     8.5    -      -       -      +
    363A  TYR*     3.1    44.8    +      -       +      -
    364A  PHE*     3.5    17.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ILE*     4.4     3.6    -      -       +      -
     37A  LEU      3.2     6.7    -      -       -      +
     38A  ALA*     3.4    31.2    -      -       +      -
    116A  MET*     4.1    24.9    -      -       +      -
    117A  PHE*     4.4     3.4    -      -       +      -
    120A  ILE*     3.9    25.1    -      -       +      -
    135A  LEU*     4.0    13.2    -      -       +      -
    137A  ASP*     1.3    86.4    +      -       -      +
    139A  ARG*     1.3    57.2    +      -       -      +
    140A  ILE*     3.6    15.2    +      -       +      -
    313A  VAL*     3.9    26.2    -      -       +      +
    316A  LYS*     2.7    37.8    +      -       +      +
    364A  PHE*     3.9     3.4    -      -       -      -
    366A  GLN*     3.4     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  THR*     5.0     2.0    +      -       -      -
     32A  LEU      3.0    24.9    +      -       -      -
     33A  ASP*     4.1    18.0    +      -       -      +
     35A  ASP      2.9    28.9    +      -       -      +
     36A  ILE*     3.4     2.8    -      -       -      +
     37A  LEU*     2.7    68.8    +      -       +      +
    138A  LEU*     1.3    71.8    -      -       -      +
    140A  ILE*     1.3    70.8    +      -       -      +
    141A  PRO*     3.4    11.0    -      -       -      +
    364A  PHE*     3.7    19.8    -      -       +      -
    365A  THR      3.5    24.3    +      -       -      +
    366A  GLN*     3.7     5.4    -      -       -      +
----------------------------------------------------------
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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