Contacts of the strand formed by residues 49 - 58 (chain F) in PDB entry 1I3R


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 ARG 49 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42F  HIS      3.7     1.6    -      -       -      +
     43F  PHE*     3.7     0.3    -      -       -      -
     44F  TYR*     2.8    84.4    +      -       +      +
     46F  GLY      3.9     0.7    -      -       -      +
     48F  GLN*     1.3    85.1    -      -       +      +
     50F  VAL*     1.3    71.2    +      -       -      +
     51F  ARG*     4.3    18.2    -      -       -      +
     69F  ASP*     4.3    13.1    +      -       -      -
    106F  ARG*     4.6     0.4    -      -       -      +
     67H  ASP*     5.5     0.6    +      -       -      -
     69H  ASP*     3.2    45.6    +      -       -      +
     70H  VAL*     4.0     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 50 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42F  HIS      3.3    11.4    -      -       -      +
     43F  PHE*     3.7    24.7    -      -       +      -
     47F  THR*     3.6    19.1    -      -       -      +
     49F  ARG*     1.3    90.1    +      -       -      +
     51F  ARG*     1.3    65.5    +      -       -      +
     52F  LEU      4.3     0.2    -      -       -      -
     68F  SER*     4.2     3.8    +      -       -      -
     69F  ASP*     4.6     6.1    -      -       -      +
    101F  VAL*     3.9    23.2    -      -       +      +
    105F  CYS*     3.8    32.8    -      -       +      -
    106F  ARG*     3.7    20.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 51 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40F  GLU      3.5     2.3    -      -       -      +
     41F  CYS*     3.8     1.0    -      -       -      -
     42F  HIS*     2.9    55.2    +      -       +      +
     44F  TYR*     4.8     8.4    +      -       +      -
     49F  ARG*     4.3    13.5    -      -       -      +
     50F  VAL*     1.3    78.4    -      -       -      +
     52F  LEU*     1.3    63.9    +      -       -      +
     53F  LEU*     4.0    29.9    -      -       -      +
     65F  ARG*     4.7     4.9    -      -       -      +
     67F  ASP*     2.5    41.9    +      -       -      +
     68F  SER*     3.3     4.3    -      -       -      +
     69F  ASP*     3.1    24.4    +      -       -      +
     51H  ARG*     3.0    40.6    -      -       -      +
     65H  ARG*     6.1     0.8    -      -       -      +
     67H  ASP*     4.4     5.2    +      -       -      -
     69H  ASP*     5.8     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 52 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  PHE*     3.3    42.4    -      -       +      -
     40F  GLU      3.5    19.5    -      -       -      +
     50F  VAL*     4.3     0.4    -      -       -      +
     51F  ARG*     1.3    74.1    -      -       -      +
     53F  LEU*     1.3    62.4    +      -       -      +
     54F  VAL*     4.3    17.0    -      -       +      -
     66F  PHE*     3.3    16.3    -      -       +      +
     67F  ASP*     3.4     4.3    -      -       -      +
     68F  SER*     2.5    49.2    +      -       -      -
     97F  LYS*     4.1    20.2    -      -       -      +
    100F  GLU*     4.2     9.6    -      -       +      +
    101F  VAL*     4.0    13.9    -      -       +      +
    105F  CYS*     3.6    11.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 53 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38F  LYS      3.7     0.2    -      -       -      +
     39F  SER*     3.7     0.2    -      -       -      -
     40F  GLU*     2.7    62.6    +      -       -      +
     42F  HIS*     4.3    11.9    -      -       +      +
     51F  ARG*     3.9    32.5    +      -       -      +
     52F  LEU*     1.3    76.1    -      -       -      +
     54F  VAL*     1.3    62.1    +      -       -      +
     55F  ARG*     4.1    17.4    +      -       +      +
     65F  ARG*     4.2    31.4    -      -       -      +
     66F  PHE      3.4    10.3    -      -       -      +
     67F  ASP*     4.0    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 54 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  PHE*     5.5     0.9    -      -       +      -
     10F  GLU*     4.6     1.6    -      -       -      +
     37F  CYS*     3.9     9.6    -      -       -      -
     38F  LYS      3.4     3.1    -      -       -      +
     39F  SER*     3.9    24.5    -      -       -      +
     52F  LEU*     4.3    19.3    -      -       +      -
     53F  LEU*     1.3    74.7    -      -       -      +
     55F  ARG*     1.3    64.6    +      -       -      +
     56F  TYR*     3.5    32.1    -      -       +      +
     65F  ARG*     3.1    12.4    -      -       -      +
     66F  PHE*     2.9    50.1    +      -       +      +
     97F  LYS*     4.5    14.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 55 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141E  ASP*     2.9    29.7    +      -       -      +
    142E  ASP*     4.1     4.8    -      -       -      +
     37F  CYS*     3.4     4.5    -      -       -      -
     38F  LYS*     2.8    43.1    +      -       +      +
     40F  GLU*     3.1    40.9    +      -       -      -
     53F  LEU*     4.1    19.0    -      -       +      +
     54F  VAL*     1.3    83.3    -      -       -      +
     56F  TYR*     1.3    63.6    +      -       -      +
     57F  PHE*     3.5    33.8    -      -       +      -
     62F  GLU*     3.1    33.3    +      -       -      +
     64F  LEU      3.8     2.9    -      -       -      -
     65F  ARG*     4.3     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 56 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66E  ASN*     6.1     0.4    -      -       -      -
     69E  ASN*     5.7     0.9    -      -       -      -
     10F  GLU*     2.7    39.9    +      -       +      +
     11F  GLY      4.8     2.4    +      -       -      -
     13F  LYS*     4.4    12.8    -      -       -      +
     35F  GLU*     4.3    15.7    -      -       -      +
     36F  TYR      3.6     2.2    -      -       -      +
     37F  CYS*     4.0    12.3    -      -       +      -
     54F  VAL*     3.5    24.7    -      -       +      +
     55F  ARG*     1.3    76.2    -      -       -      +
     57F  PHE*     1.3    63.1    +      -       -      +
     62F  GLU*     3.2     5.6    -      -       -      +
     63F  ASN*     2.9    41.3    +      -       -      +
     64F  LEU*     3.0    43.6    +      -       +      +
     65F  ARG*     5.2     0.7    -      -       -      -
     73F  PHE*     4.2    15.8    -      +       -      -
     87F  TRP*     3.9    26.1    -      +       -      -
     93F  PHE*     5.9     0.3    -      -       -      -
     97F  LYS*     5.0     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 57 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142E  ASP      3.8     2.5    -      -       -      -
    143E  HIS*     3.5    31.6    -      +       +      -
     13F  LYS*     6.3     0.2    -      -       -      -
     34F  LEU      3.7     0.7    -      -       -      +
     35F  GLU*     3.9     7.0    -      -       -      +
     36F  TYR*     2.7    67.1    +      +       +      +
     37F  CYS*     4.9     0.2    -      -       -      -
     38F  LYS*     3.5    28.0    -      -       +      -
     55F  ARG*     3.5    50.5    -      -       +      -
     56F  TYR*     1.3    78.0    -      -       -      +
     58F  TYR*     1.3    59.1    +      -       -      +
     59F  ASN      4.0     8.7    -      -       -      +
     61F  GLU      3.2     6.1    -      -       -      +
     62F  GLU*     3.6    34.3    -      -       +      -
     63F  ASN*     4.1     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 58 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70E  LEU*     4.1    16.2    -      -       +      -
     73E  MET*     3.6    38.1    -      -       +      -
     74E  LYS*     3.9     8.0    -      -       -      -
     77E  SER*     3.3    32.1    +      -       -      -
     79E  ASN*     5.0     0.5    -      -       -      -
     80E  THR      4.1    10.0    +      -       -      -
     82E  ASP*     4.4     1.7    -      -       -      +
     33F  PHE*     3.6    23.3    -      -       +      -
     34F  LEU      3.3    12.8    -      -       -      -
     35F  GLU*     4.5     2.5    -      -       -      +
     57F  PHE*     1.3    71.6    -      -       -      +
     59F  ASN*     1.3    91.3    +      -       +      +
     60F  LEU      3.1     2.9    +      -       -      -
     61F  GLU*     2.9    17.9    +      -       +      +
     63F  ASN*     3.5    19.9    -      -       -      +
     79F  LEU*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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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