Contacts of the strand formed by residues 1 - 10 (chain F) in PDB entry 4IHB


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 MET 1 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      0F  PHE      1.3    80.0    -      -       -      +
      2F  LEU*     1.3    64.9    +      -       -      +
      3F  ARG      3.7     0.4    +      -       -      -
     51F  GLU*     3.9    37.9    -      -       +      +
     52F  TRP      3.4     8.7    -      -       -      +
     53F  ASP*     3.5    38.4    -      -       +      +
     54F  LEU*     3.4     9.1    -      -       -      +
    123F  TYR*     3.5     5.4    -      -       -      -
    124F  THR*     2.4    56.8    +      -       +      +
    125F  ALA      4.0    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 2 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1F  MET*     1.3    71.7    -      -       -      +
      3F  ARG*     1.3    58.9    +      -       -      +
      4F  VAL*     4.2    16.6    -      -       +      -
     28F  PHE*     3.6    43.7    -      -       +      -
     50F  PHE      3.6     1.4    -      -       -      +
     51F  GLU*     3.2     5.2    -      -       -      -
     52F  TRP*     3.0    40.9    +      -       +      +
     54F  LEU*     3.4    22.5    -      -       +      +
     59F  LEU*     5.4     6.5    -      -       +      -
     65F  LEU*     5.1     2.2    -      -       +      -
     88F  LEU*     4.2    15.9    -      -       +      -
     91F  VAL*     5.4     5.4    -      -       +      -
    121F  VAL*     3.6    27.4    -      -       +      -
    122F  SER      3.6     8.3    -      -       -      +
    123F  TYR*     5.0     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 3 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1F  MET      3.7     1.0    +      -       -      -
      2F  LEU*     1.3    72.3    -      -       -      +
      4F  VAL*     1.3    62.9    +      -       -      +
      5F  PHE*     3.8    36.5    -      -       +      -
     49F  GLY*     5.8     0.4    -      -       -      -
     50F  PHE      3.3     9.9    -      -       -      +
     51F  GLU*     4.1    19.8    +      -       +      -
    120F  GLN*     3.8     2.4    -      -       -      +
    121F  VAL*     3.4     4.0    -      -       -      +
    122F  SER*     2.8    63.7    +      -       -      +
    123F  TYR      5.3     0.4    +      -       -      -
    124F  THR*     3.5    38.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 4 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2F  LEU*     4.2     8.3    -      -       +      -
      3F  ARG*     1.3    78.8    -      -       -      +
      5F  PHE*     1.3    74.4    +      -       -      +
      6F  ILE*     4.1    17.3    -      -       +      -
     26F  ALA*     5.7     0.7    -      -       +      -
     48F  GLU      3.6     1.4    -      -       -      +
     49F  GLY*     3.2     2.1    -      -       -      -
     50F  PHE*     2.7    41.6    +      -       +      -
     52F  TRP*     3.5    31.9    -      -       +      -
     65F  LEU*     4.0    24.7    -      -       +      -
    119F  LEU*     4.2     5.6    -      -       +      -
    120F  GLN      3.4     5.8    -      -       -      +
    121F  VAL*     3.9    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 5 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3F  ARG*     3.8    39.9    -      -       +      -
      4F  VAL*     1.3    72.6    -      -       -      +
      6F  ILE*     1.3    62.1    +      -       -      +
      7F  LEU*     3.5    21.5    +      -       +      +
     47F  ASN*     5.5     4.5    -      -       -      -
     48F  GLU      3.3     6.3    -      -       -      +
     49F  GLY*     3.7    24.5    -      -       -      -
    119F  LEU*     3.2     7.6    -      -       -      +
    120F  GLN*     2.9    59.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 6 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4F  VAL*     4.0    13.0    -      -       +      -
      5F  PHE*     1.3    74.2    -      -       -      +
      7F  LEU*     1.3    59.8    +      -       -      +
     24F  CYS*     3.9    34.8    -      -       +      +
     26F  ALA*     4.0    20.4    -      -       +      -
     33F  LYS      5.9     0.2    -      -       -      +
     35F  THR*     3.9    11.9    -      -       +      -
     46F  TRP*     3.8    26.5    -      -       +      +
     47F  ASN      3.1    19.1    +      -       -      -
     48F  GLU      2.9    18.2    +      -       -      +
     50F  PHE*     3.5    26.9    -      -       +      -
     67F  VAL*     5.2     1.8    -      -       +      -
    117F  LEU*     4.0    11.9    -      -       +      -
    118F  VAL      4.2     2.7    -      -       -      +
    119F  LEU*     4.3     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 7 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5F  PHE*     3.8    29.2    -      -       +      +
      6F  ILE*     1.3    72.6    -      -       -      +
      8F  TYR*     1.3    80.1    +      -       +      +
     45F  VAL*     3.6     6.2    -      -       -      +
     46F  TRP*     3.0    24.0    +      -       -      -
     47F  ASN*     3.0    28.9    +      -       -      +
    118F  VAL*     3.0    30.1    +      -       +      +
    119F  LEU*     4.6     3.4    -      -       -      -
    120F  GLN*     4.9    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 8 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  ILE*     3.9     0.4    -      -       -      +
      7F  LEU*     1.3    95.2    -      -       +      +
      9F  ALA*     1.3    59.9    -      -       -      +
     10F  GLU*     3.5    41.3    +      -       +      -
     43F  ASN*     3.7     9.0    -      -       -      +
     44F  PRO      3.2    16.4    -      -       -      +
     45F  VAL*     3.9    17.9    -      -       +      -
     46F  TRP*     3.8    10.5    -      -       -      -
    102F  ASN*     5.2     1.6    +      -       -      -
    117F  LEU*     3.6     2.8    -      -       -      +
    118F  VAL*     2.8    64.8    +      -       +      +
    201F  FMT      5.3     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 9 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  TYR*     1.3    75.3    -      -       -      +
     10F  GLU*     1.3    63.4    +      -       -      +
     12F  VAL*     3.6    19.3    -      -       +      -
     43F  ASN*     2.9    29.3    +      -       -      -
     44F  PRO*     3.1     7.2    +      -       +      +
     46F  TRP*     3.6    25.0    -      -       +      -
     69F  VAL*     4.8     7.0    -      -       +      -
    105F  LEU*     5.0     1.8    -      -       +      -
    116F  SER      3.2    13.7    -      -       -      +
    117F  LEU*     4.1     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 10 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  TYR*     3.5    34.6    +      -       +      -
      9F  ALA*     1.3    72.6    -      -       -      +
     11F  ASN*     1.3    81.2    +      -       -      +
     12F  VAL*     3.3     4.5    +      -       -      +
     42F  VAL      4.1     1.1    -      -       -      -
     43F  ASN*     3.7    17.2    +      -       +      +
    102F  ASN*     5.7     3.4    +      -       -      -
    115F  ALA*     3.3     2.8    -      -       -      +
    116F  SER*     2.9    43.8    +      -       -      +
    118F  VAL*     5.5     0.9    -      -       +      -
----------------------------------------------------------
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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