Contacts of the strand formed by residues 7 - 18 (chain F) in PDB entry 1R5I


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 7 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14E  LEU*     3.6     3.6    -      -       -      +
     15E  ASN*     3.0    45.6    +      -       +      -
     16E  PRO*     5.3     1.1    -      -       +      -
     70E  LEU*     3.3    10.5    -      -       +      +
     74E  THR*     3.4    36.3    -      -       +      +
     79E  TYR*     3.5    31.2    -      +       +      -
     80E  THR      3.3    21.1    -      -       -      -
     81E  PRO*     3.6    11.2    -      -       +      -
      5F  PRO*     4.1    26.2    -      -       +      -
      6F  ARG*     1.3    76.3    -      -       -      +
      8F  LEU*     1.3    60.2    +      -       -      +
     32F  TYR*     3.2    21.8    -      -       -      +
     33F  ASN*     3.7     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 8 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12E  PHE*     4.1    13.2    -      -       +      -
     13E  TYR      3.7    14.1    -      -       -      +
     14E  LEU*     3.9    15.5    -      -       +      -
     70E  LEU*     3.7     2.2    -      -       -      +
     82E  ILE*     4.0     8.7    -      -       +      -
    113E  THR*     3.9    20.2    -      -       -      +
    115E  PRO*     3.7    26.7    -      -       +      -
    145E  PHE*     4.0     6.1    -      -       +      -
      6F  ARG      4.2     0.2    -      -       -      -
      7F  PHE*     1.3    73.9    -      -       -      +
      9F  TRP*     1.3    59.6    +      -       -      +
     10F  GLN*     3.3    34.5    -      -       +      +
     32F  TYR*     3.5     9.0    -      -       -      -
     33F  ASN*     2.6    50.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 9 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12E  PHE*     3.1     4.7    -      -       -      +
     13E  TYR*     3.0    35.5    +      -       +      +
     66E  ASP*     3.8    42.2    +      -       +      -
     69E  ASN*     3.9    20.5    -      -       +      +
     70E  LEU*     3.4    26.5    -      -       +      -
     73E  MSE      3.5    37.7    -      -       +      -
      8F  LEU*     1.3    73.3    -      -       -      +
     10F  GLN*     1.3    71.6    +      -       -      +
     11F  LEU*     4.6     5.2    -      -       +      +
     30F  CYS*     3.4    41.3    -      -       +      -
     31F  ILE      3.6     8.7    -      -       -      -
     32F  TYR*     4.0    19.1    -      +       +      -
     37F  SER*     4.5     0.9    -      -       -      -
     61F  TRP*     5.8     0.2    -      +       -      -
    313G  THR*     5.3     0.2    +      -       -      -
    316G  LEU*     4.0    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 10 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  GLU      3.4     6.5    -      -       -      +
     12E  PHE*     3.8    15.7    -      -       +      +
    139E  PRO*     5.7     0.9    -      -       -      +
    143E  HIS*     3.2    30.3    +      -       -      +
    144E  LEU      5.3     0.3    -      -       -      +
    145E  PHE*     3.5    21.1    -      -       -      -
      8F  LEU*     3.3    26.6    -      -       +      +
      9F  TRP*     1.3    82.4    -      -       -      +
     11F  LEU*     1.3    60.8    -      -       -      +
     12F  LYS*     3.7    23.6    +      -       -      -
     30F  CYS*     3.6     2.6    -      -       -      -
     31F  ILE*     2.8    51.1    +      -       +      +
     33F  ASN      3.5    10.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 11 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  GLN      4.5     0.2    -      -       -      -
     10E  ALA*     3.6     0.7    -      -       -      -
     11E  GLU*     2.9    45.6    +      -       +      +
     66E  ASP*     3.9    10.1    -      -       -      +
      9F  TRP*     4.6     7.2    -      -       +      +
     10F  GLN*     1.3    74.3    -      -       -      +
     12F  LYS*     1.3    69.4    +      -       -      +
     13F  PHE*     3.5    37.5    -      -       +      -
     28F  GLU*     4.5    10.5    -      -       +      +
     29F  ARG      3.3    21.5    -      -       -      +
     30F  CYS*     4.0    17.3    -      -       -      -
    313G  THR*     3.2    35.0    -      -       -      +
    314G  LEU      5.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 12 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  ILE*     4.5    14.8    -      -       +      +
      9E  GLN      3.4     5.8    -      -       -      +
     10E  ALA*     4.5     9.4    -      -       +      -
     11E  GLU      5.5     0.4    -      -       -      +
    139E  PRO*     3.8    23.8    -      -       +      +
    140E  ARG      3.0    29.1    +      -       -      +
    141E  GLU*     4.9     1.2    -      -       -      +
    143E  HIS*     3.2    26.6    -      -       +      +
    144E  LEU      5.5     0.2    +      -       -      -
     10F  GLN*     3.7    22.6    +      -       +      -
     11F  LEU*     1.3    82.2    -      -       -      +
     13F  PHE*     1.3    63.5    -      -       -      +
     14F  GLU*     4.0    15.3    -      -       +      +
     27F  LEU      3.5     1.6    -      -       -      +
     28F  GLU*     3.2     4.5    -      -       -      +
     29F  ARG*     2.7    45.1    +      -       +      +
     31F  ILE*     4.3    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 13 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  ILE      3.6     2.3    -      -       -      +
      8E  ILE*     3.3     3.9    -      -       -      -
      9E  GLN*     2.8    70.1    +      -       +      +
     11E  GLU*     4.3     1.6    -      -       -      -
     11F  LEU*     3.5    38.8    -      -       +      -
     12F  LYS*     1.3    72.3    -      -       -      +
     14F  GLU*     1.3    60.9    +      -       -      +
     26F  LEU*     4.7     5.8    -      -       +      -
     27F  LEU      3.5     3.6    -      -       -      -
     28F  GLU*     3.2    41.5    -      -       +      +
     71F  ARG*     4.2     4.0    -      -       -      -
     78F  TYR*     3.3    24.3    +      +       +      +
    311G  GLN*     3.3    33.2    -      -       +      -
    312G  ASN      4.1    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 14 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  VAL*     4.7     0.2    -      -       +      -
      7E  ILE      3.7     3.4    -      -       -      -
      8E  ILE*     4.1    26.4    -      -       +      +
    141E  GLU*     6.2     0.6    -      -       -      +
     12F  LYS*     4.7    13.1    -      -       +      +
     13F  PHE*     1.3    74.1    -      -       -      +
     15F  CYS*     1.3    59.8    +      -       -      +
     16F  HIS*     2.7    41.1    +      -       +      +
     25F  ARG      3.5     1.4    -      -       -      +
     26F  LEU*     3.3     8.9    -      -       -      +
     27F  LEU*     2.7    53.3    +      -       +      +
     29F  ARG*     3.0    41.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 15 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  VAL*     3.2     6.3    -      -       -      +
      7E  ILE*     2.8    44.0    +      -       +      +
     14F  GLU*     1.3    70.8    -      -       -      +
     16F  HIS*     1.3    62.4    +      -       -      +
     17F  PHE*     3.6    21.8    -      -       +      -
     24F  VAL*     5.5     0.2    -      -       -      -
     25F  ARG      3.6     3.8    -      -       -      -
     26F  LEU*     3.7     1.3    -      -       -      -
     78F  TYR*     3.5    24.9    -      -       -      -
     79F  CYS*     2.1    53.6    -      -       -      -
     82F  ASN*     5.6     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 16 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  GLU*     2.8    33.3    +      -       -      +
      5E  HIS      3.6     3.8    -      -       -      -
      6E  VAL*     3.6    19.9    -      -       +      +
      8E  ILE*     6.2     0.2    -      -       +      -
     14F  GLU*     2.7    45.8    +      -       +      +
     15F  CYS*     1.3    71.7    -      -       -      +
     17F  PHE*     1.3    61.0    +      -       -      +
     18F  PHE*     3.5    17.6    -      +       +      -
     24F  VAL*     3.4     7.7    -      -       -      +
     25F  ARG*     2.8    47.0    +      -       +      +
     27F  LEU*     4.6    14.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 17 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  GLU*     4.0     1.2    -      -       -      +
      4E  GLU*     3.0    24.9    +      -       -      +
      5E  HIS*     2.9    29.1    +      -       +      +
      7E  ILE*     4.0    15.9    -      -       +      -
     15F  CYS*     3.6    27.4    -      -       +      -
     16F  HIS*     1.3    70.8    -      -       -      +
     18F  PHE*     1.3    65.0    +      -       -      +
     20F  GLY      3.4    11.4    -      -       -      +
     21F  THR*     3.8    12.3    -      -       +      -
     23F  ARG      3.7     1.8    -      -       -      -
     24F  VAL*     3.5    28.0    -      -       +      -
     79F  CYS*     3.1    41.7    -      -       +      -
     80F  ARG*     4.1     1.3    -      -       -      -
     83F  TYR*     3.5    42.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with PHE 18 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1E  ILE*     3.9    26.5    -      -       +      +
      2E  LYS      3.1    26.5    -      -       -      +
      3E  GLU*     3.4    27.8    -      -       +      -
      4E  GLU      4.5     0.7    -      -       -      +
     16F  HIS*     3.5    34.3    -      +       +      -
     17F  PHE*     1.3    75.0    -      -       -      +
     19F  ASN*     1.3    75.0    +      -       +      +
     20F  GLY      3.5     1.0    +      -       -      +
     22F  GLU      3.5     1.9    +      -       -      -
     23F  ARG*     2.9    77.8    +      -       +      +
     25F  ARG*     4.4    10.5    -      -       +      -
----------------------------------------------------------
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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