Contacts of the strand formed by residues 2 - 10 (chain F) in PDB entry 1IBM


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 2 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    738A    C      2.6    38.2    +      -       -      -
    739A    C      3.2    29.1    +      -       -      -
      1F  MET*     1.3    79.0    -      -       -      +
      3F  ARG*     1.3    65.4    +      -       -      +
      4F  TYR*     3.8    24.1    +      -       +      +
     66F  GLU*     3.3     2.7    -      -       -      -
     67F  MET      3.0    29.6    +      -       -      +
     69F  GLU*     3.1    34.7    +      -       +      +
     92F  LYS*     4.3    13.1    -      -       +      +
      2O  PRO*     3.6    29.1    -      -       -      +
----------------------------------------------------------
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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      5.7     0.2    -      -       -      +
      2F  ARG*     1.3    73.9    -      -       -      +
      4F  TYR*     1.3    63.4    +      -       -      +
     38F  GLU*     2.6    44.9    +      -       -      +
     39F  LYS*     5.7     0.6    -      -       -      +
     64F  GLN*     2.8    23.8    +      -       +      +
     65F  VAL      3.4     7.2    -      -       -      +
     66F  GLU*     3.9    13.5    -      -       +      +
     92F  LYS*     3.9     3.8    -      -       -      +
     93F  SER*     2.7    46.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 4 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    737A    A      4.1     4.7    -      -       -      -
    738A    C      3.0    24.0    +      -       -      -
      2F  ARG*     3.8    23.5    -      -       +      +
      3F  ARG*     1.3    80.0    -      -       -      +
      5F  GLU*     1.3    74.2    +      -       -      +
     64F  GLN*     3.5    18.0    -      -       -      +
     65F  VAL*     3.0    19.6    +      -       +      +
     67F  MET*     3.6    31.9    -      -       +      -
     69F  GLU*     3.2    17.3    -      -       -      +
     72F  VAL*     3.0    45.3    -      -       +      +
     90F  VAL*     3.9    10.3    -      -       +      -
     91F  VAL      3.1    15.7    -      -       -      +
     92F  LYS*     3.7    21.8    -      -       +      -
     93F  SER*     3.3    10.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 5 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4F  TYR*     1.3    88.9    -      -       -      +
      6F  VAL*     1.3    62.4    +      -       -      +
      7F  ASN      3.8     1.1    -      -       -      -
     62F  TRP*     3.2    36.8    +      -       +      +
     63F  TYR      3.3     7.0    -      -       -      -
     64F  GLN*     4.6     8.0    -      -       +      +
     89F  MET      3.3     2.1    -      -       -      +
     90F  VAL*     3.1     3.3    -      -       -      -
     91F  VAL*     2.8    36.0    +      -       +      +
     92F  LYS      4.4     3.3    -      -       -      +
     93F  SER*     4.0    18.5    +      -       -      +
     94F  GLN      4.3     5.5    +      -       -      +
     34R  TYR*     3.1    33.8    +      -       -      +
     35R  ARG*     5.4     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 6 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5F  GLU*     1.3    74.1    -      -       -      +
      7F  ASN*     1.3    63.8    +      -       -      +
      8F  ILE*     3.5    26.6    +      -       +      +
     30F  LEU*     4.6    10.1    -      -       +      -
     62F  TRP*     3.6     4.9    +      -       -      -
     63F  TYR*     2.7    43.3    +      -       +      +
     65F  VAL*     4.2    26.2    -      -       +      -
     67F  MET*     6.1     1.6    -      -       -      -
     75F  LEU*     4.9     4.0    -      -       +      -
     79F  LEU*     3.9    20.2    -      -       +      -
     88F  VAL*     4.3     0.7    -      -       +      -
     89F  MET      4.1     1.3    -      -       -      -
     90F  VAL*     4.1    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 7 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5F  GLU      4.4     0.4    +      -       -      -
      6F  VAL*     1.3    71.1    -      -       -      +
      8F  ILE*     1.3    64.5    +      -       -      +
      9F  VAL*     5.0     1.6    -      -       +      -
     60F  PHE*     6.3     0.9    -      -       +      -
     61F  LEU      4.0     7.5    -      -       -      +
     62F  TRP*     3.6    14.6    -      -       -      +
     87F  ARG      4.5     0.2    -      -       -      -
     88F  VAL*     3.2     3.0    -      -       -      +
     89F  MET*     2.7    61.1    +      -       +      +
     91F  VAL*     3.2    11.9    -      -       -      +
     34R  TYR*     2.9    39.6    +      -       -      -
     35R  ARG*     4.1     2.1    -      -       -      -
     76R  LEU*     3.5    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 8 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  VAL*     3.5    17.9    +      -       +      +
      7F  ASN*     1.3    79.9    -      -       -      +
      9F  VAL*     1.3    77.3    +      -       -      +
     10F  LEU*     4.6     3.4    -      -       +      -
     26F  ILE*     4.0    33.9    -      -       +      -
     59F  TYR      3.9     0.2    -      -       -      +
     60F  PHE*     3.3     2.1    -      -       -      +
     61F  LEU*     2.8    60.6    +      -       +      +
     63F  TYR*     5.1     5.2    -      -       +      -
     79F  LEU*     3.7    28.9    -      -       +      -
     85F  VAL*     4.4    12.3    -      -       +      -
     87F  ARG      3.3     7.0    -      -       -      +
     88F  VAL*     4.0     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 9 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  ILE*     1.3    83.8    -      -       -      +
     10F  LEU*     1.3    61.8    +      -       -      +
     48F  LEU*     5.3     4.3    -      -       +      -
     52F  ILE*     5.9     1.8    -      -       +      -
     58F  GLY*     4.3     6.5    -      -       -      -
     59F  TYR      3.4    18.4    -      -       -      +
     60F  PHE*     3.1    49.4    -      -       +      -
     85F  VAL*     3.8     1.3    -      -       -      -
     86F  ARG*     2.8    33.1    +      -       +      +
     87F  ARG*     2.8    38.6    +      -       +      +
     76R  LEU*     4.5     9.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 10 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  ILE*     4.6     2.9    -      -       +      -
      9F  VAL*     1.3    76.2    -      -       -      +
     11F  ASN*     1.3    68.1    +      -       -      +
     12F  PRO*     3.3     5.0    -      -       -      +
     14F  LEU*     4.1    17.9    -      -       +      -
     19F  LEU*     5.2     3.8    -      -       +      +
     22F  GLU*     4.1    20.9    -      -       +      -
     23F  LYS*     5.4     3.1    -      -       +      +
     26F  ILE*     4.7     7.0    -      -       +      -
     58F  GLY*     4.4     1.0    -      -       -      -
     59F  TYR*     2.8    74.0    +      -       +      +
     61F  LEU*     4.2    22.9    -      -       +      -
     84F  ASN      2.9    23.1    -      -       -      +
     85F  VAL*     4.1     6.3    -      -       +      -
     86F  ARG*     3.8     7.7    -      -       -      -
----------------------------------------------------------
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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