Contacts of the strand formed by residues 33 - 44 (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 PHE 33 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14E  LEU*     3.5     2.3    -      -       -      +
     15E  LEU*     2.8    49.9    +      -       +      -
     16E  PRO*     4.7     6.3    -      -       +      -
     70E  LEU*     3.5    23.1    -      -       +      +
     74E  LYS*     3.8    40.4    -      -       +      -
     79E  ASN*     3.9    32.3    -      -       -      -
     80E  THR      5.0     2.0    -      -       -      -
     81E  PRO*     4.4     9.0    -      -       +      -
     31F  PRO*     4.0    22.2    -      -       +      -
     32F  TRP*     1.3    90.0    -      -       -      +
     34F  LEU*     1.3    61.0    +      -       -      +
     58F  TYR*     3.6    19.1    -      +       -      +
     59F  ASN*     3.4     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 34 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12E  PHE*     3.6    31.0    -      -       +      -
     13E  TYR      3.5    14.8    -      -       -      +
     14E  LEU*     4.0     6.7    -      -       +      -
     70E  LEU*     4.0     4.6    -      -       -      +
    113E  SER*     4.2     2.2    -      -       -      +
    115E  PRO*     3.9    18.6    -      -       +      -
    143E  HIS      5.4     0.4    -      -       -      +
    145E  PHE*     3.8    30.1    -      -       +      -
     32F  TRP*     3.7    24.9    -      -       +      -
     33F  PHE*     1.3    75.0    -      -       -      +
     35F  GLU*     1.3    57.5    +      -       -      +
     36F  TYR*     4.0    15.5    -      -       +      -
     57F  PHE      3.7     0.5    -      -       -      +
     58F  TYR*     3.3    11.3    -      -       -      -
     59F  ASN*     2.9    42.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 35 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  GLN      4.0     0.2    -      -       -      +
     12E  PHE*     3.1    24.9    -      -       -      -
     13E  TYR      3.1    11.1    +      -       -      +
     66E  ASN*     3.5    42.4    +      -       +      +
     69E  ASN*     3.7    15.2    +      -       +      +
     70E  LEU*     3.8    16.7    -      -       +      +
     73E  MET*     3.3    23.8    -      -       -      +
     13F  LYS*     2.7    32.3    +      -       -      -
     34F  LEU*     1.3    71.9    -      -       -      +
     36F  TYR*     1.3    62.8    +      -       -      +
     37F  CYS*     4.4     0.5    +      -       -      +
     56F  TYR*     4.3     9.9    -      -       -      -
     57F  PHE      3.9     7.3    -      -       -      +
     58F  TYR*     4.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 36 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  ALA*     4.3     4.9    -      -       +      +
     11E  GLN      3.2    23.3    -      -       -      -
     12E  PHE*     3.6    12.3    -      +       +      -
    138E  LEU      5.0     0.2    -      -       -      -
    139E  PRO*     3.6    19.2    -      -       -      +
    143E  HIS      4.0    18.8    -      -       -      -
    144E  LEU      4.7     1.7    +      -       -      -
    145E  PHE*     3.5    37.8    -      +       -      -
     34F  LEU*     4.0    17.3    -      -       +      -
     35F  GLU*     1.3    77.4    -      -       -      +
     37F  CYS*     1.3    63.8    +      -       -      +
     38F  LYS*     3.3    42.9    +      -       +      +
     56F  TYR*     3.6     2.4    -      -       -      +
     57F  PHE*     2.7    67.1    +      +       +      +
     59F  ASN      5.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 37 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  GLN      3.7     0.9    -      -       -      +
     10E  ALA*     3.6     2.1    -      -       -      -
     11E  GLN*     3.0    43.2    +      -       +      +
     66E  ASN*     4.7     5.8    -      -       -      +
     10F  GLU*     2.7    37.9    -      -       -      +
     35F  GLU*     4.3     1.3    -      -       -      +
     36F  TYR*     1.3    75.2    -      -       -      +
     38F  LYS*     1.3    68.6    +      -       -      +
     39F  SER*     4.2     8.5    -      -       -      -
     54F  VAL*     3.9    21.1    -      -       -      -
     55F  ARG      3.4     5.6    -      -       -      +
     56F  TYR*     4.0    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 38 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  ILE*     4.2    11.7    -      -       +      -
      9E  GLN      3.2     5.2    -      -       -      +
     10E  ALA*     4.0     7.4    -      -       +      -
    139E  PRO*     3.9    13.0    -      -       +      -
    140E  ARG      3.0    22.2    +      -       -      +
    141E  ASP      4.1     4.4    -      -       -      -
    142E  ASP      2.6    26.5    +      -       -      -
    144E  LEU      5.5     0.2    +      -       -      -
     36F  TYR*     3.3    33.0    +      -       +      +
     37F  CYS*     1.3    81.4    -      -       -      +
     39F  SER*     1.3    63.2    +      -       -      +
     40F  GLU*     3.9     9.9    +      -       +      +
     53F  LEU      3.7     1.7    -      -       -      +
     54F  VAL*     3.4     1.7    -      -       -      -
     55F  ARG*     2.8    47.6    +      -       +      +
     57F  PHE*     3.5    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 39 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  ILE      3.7     1.0    -      -       -      +
      8E  ILE*     3.2     4.2    -      -       -      -
      9E  GLN*     2.8    39.2    +      -       -      +
      8F  PHE*     3.3    50.3    -      -       -      +
     10F  GLU*     5.1     2.1    +      -       -      -
     37F  CYS*     4.2     7.1    -      -       -      -
     38F  LYS*     1.3    72.1    -      -       -      +
     40F  GLU*     1.3    62.0    +      -       -      +
     41F  CYS      4.0     0.4    +      -       -      -
     53F  LEU      3.7     3.6    -      -       -      -
     54F  VAL*     3.9    21.9    -      -       -      +
     97F  LYS*     5.7     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 40 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  THR*     4.7     0.4    -      -       +      -
      7E  ILE      3.5     3.1    -      -       -      -
      8E  ILE*     3.9    31.6    -      -       +      +
    140E  ARG      5.2     1.9    -      -       -      +
    141E  ASP*     5.5     1.9    -      -       -      -
     38F  LYS*     4.5    14.6    +      -       +      +
     39F  SER*     1.3    75.2    -      -       -      +
     41F  CYS*     1.3    60.0    +      -       -      +
     42F  HIS*     3.3    31.7    +      -       +      +
     51F  ARG      3.5     5.0    -      -       -      +
     52F  LEU*     3.5     6.1    -      -       -      +
     53F  LEU*     2.7    58.1    +      -       -      +
     55F  ARG*     3.1    33.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 41 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  THR*     3.2     7.5    -      -       -      +
      7E  ILE*     2.7    45.8    +      -       +      +
      8F  PHE*     3.3    27.1    -      -       -      -
     39F  SER      4.0     0.2    +      -       -      -
     40F  GLU*     1.3    70.5    -      -       -      +
     42F  HIS*     1.3    61.2    +      -       -      +
     43F  PHE*     3.4    22.5    -      -       +      -
     51F  ARG      3.8     1.1    -      -       -      -
     52F  LEU*     4.1     0.2    -      -       -      -
    104F  VAL*     4.8     0.7    -      -       -      -
    105F  CYS*     2.0    56.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 42 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  HIS      3.7     3.1    -      -       -      +
      6E  THR*     3.6    22.0    +      -       +      +
     40F  GLU*     3.3    41.9    +      -       +      +
     41F  CYS*     1.3    71.9    -      -       -      +
     43F  PHE*     1.3    60.0    +      -       -      +
     44F  TYR*     4.1    29.2    +      -       +      +
     49F  ARG      3.7     1.0    -      -       -      +
     50F  VAL*     3.3     9.1    -      -       -      +
     51F  ARG*     2.9    57.5    +      -       +      +
     53F  LEU*     4.3    15.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 43 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  GLU      4.2     2.0    -      -       -      +
      4E  GLU*     3.1     6.8    -      -       -      +
      5E  HIS      2.8    44.2    +      -       -      +
      7E  ILE*     3.5    22.9    -      -       +      -
     41F  CYS*     3.4    33.4    -      -       +      -
     42F  HIS*     1.3    70.6    -      -       -      +
     44F  TYR*     1.3    70.5    +      -       -      +
     45F  ASN      4.1     0.4    -      -       -      -
     46F  GLY      3.5    17.7    -      -       -      +
     47F  THR*     4.5     0.9    -      -       +      -
     49F  ARG      3.7     1.3    -      -       -      -
     50F  VAL*     3.7    24.7    -      -       +      -
    105F  CYS*     3.3    31.6    -      -       +      -
    106F  ARG*     4.1     2.7    -      -       -      -
    109F  TYR*     3.4    44.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 44 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  GLU*     3.8    27.6    -      -       +      +
     42F  HIS*     4.1    33.4    +      -       +      +
     43F  PHE*     1.3    80.1    -      -       -      +
     45F  ASN*     1.3    75.5    +      -       -      +
     46F  GLY      3.5     0.5    +      -       -      +
     48F  GLN*     3.7     1.6    +      -       -      +
     49F  ARG*     2.8    86.9    +      -       +      +
     51F  ARG*     4.8     9.4    +      -       +      -
     67H  ASP*     4.8     4.0    +      -       -      -
     70H  VAL*     3.7    26.3    -      -       +      +
----------------------------------------------------------
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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