Contacts of the strand formed by residues 2 - 8 (chain P) in PDB entry 1IBL


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 VAL 2 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A    C      5.8     2.9    -      -       -      +
    227A    G      6.3     0.4    -      -       -      +
    228A    A      3.3    30.5    -      -       -      +
    229A    U      3.9    20.1    +      -       -      +
      1P  MET*     1.3    76.0    -      -       -      +
      3P  LYS*     1.3    64.2    -      -       -      +
     21P  VAL*     3.2    33.4    -      -       +      -
     22P  THR      3.0    12.6    -      -       -      +
     23P  ASP*     4.3     2.7    -      -       -      +
     33P  ILE*     4.1     4.7    -      -       +      -
     59P  TRP*     4.2     9.6    -      -       +      -
     62P  VAL      5.5     0.7    -      -       -      +
     63P  GLY*     4.1     3.5    -      -       -      +
     64P  ALA*     3.1    22.0    -      -       +      +
     65P  GLN      3.0    18.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 3 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377A    G      2.4    49.1    +      -       -      +
    378A    G      4.5     8.9    +      -       -      -
      1P  MET*     3.3    36.9    -      -       +      +
      2P  VAL*     1.3    81.3    -      -       -      +
      4P  ILE*     1.3    68.7    +      -       -      +
      5P  ARG*     3.8     8.3    -      -       -      -
     20P  VAL      3.5     0.3    -      -       -      +
     21P  VAL*     3.1     5.5    -      -       -      -
     22P  THR*     2.5    36.7    +      -       -      +
     24P  ALA*     3.4    13.2    -      -       +      +
     65P  GLN*     3.1    19.1    -      -       +      +
     66P  PRO      5.1     0.9    -      -       -      -
     67P  THR*     4.5    13.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 4 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3P  LYS*     1.3    73.0    -      -       -      +
      5P  ARG*     1.3    61.4    +      -       -      +
     19P  ILE*     3.9    15.3    -      -       +      -
     20P  VAL      3.2     4.5    -      -       -      +
     21P  VAL*     4.0     6.3    -      -       +      -
     36P  ILE*     3.5    28.7    -      -       +      -
     56P  ALA*     4.6     3.8    -      -       -      +
     59P  TRP*     3.9    14.8    -      -       +      -
     60P  LEU*     4.1    23.3    -      -       +      -
     64P  ALA*     3.4    33.7    -      -       +      -
     65P  GLN      3.0     6.5    +      -       -      -
     66P  PRO*     4.0     7.9    -      -       +      -
     67P  THR      3.1    10.9    +      -       -      -
     70P  ALA*     3.0    19.8    -      -       +      +
     74P  LEU*     4.2    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 5 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376A    G      3.0    40.0    +      -       -      +
    377A    G      2.9    20.3    +      -       -      +
      3P  LYS*     4.6     5.5    -      -       +      +
      4P  ILE*     1.3    74.7    -      -       -      +
      6P  LEU*     1.3    70.4    +      -       -      +
      7P  ALA*     6.1     0.4    -      -       +      -
     18P  ARG      3.3     1.7    -      -       -      +
     19P  ILE*     3.6     1.2    -      -       -      -
     20P  VAL*     2.7    40.6    +      -       +      +
     22P  THR*     3.8    25.3    -      -       +      +
     24P  ALA*     3.2    31.3    +      -       -      +
     26P  ARG*     2.8    29.3    +      -       -      +
     27P  LYS      2.9    18.6    +      -       -      -
     28P  ARG*     3.6     9.5    +      -       -      +
     67P  THR*     3.1    21.1    -      -       -      +
     70P  ALA*     4.0     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 6 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A    U      3.1    39.2    +      -       -      +
    376A    G      3.0    18.3    +      -       -      +
      5P  ARG*     1.3    85.7    -      -       -      +
      7P  ALA*     1.3    60.7    +      -       -      +
     17P  TYR*     3.7    26.7    -      -       +      -
     18P  ARG      3.7     2.0    -      -       -      -
     19P  ILE*     4.4    11.4    -      -       +      -
     28P  ARG*     4.6     3.5    -      -       -      +
     39P  TYR*     3.6    32.3    -      -       +      -
     69P  THR*     4.0    13.0    -      -       +      -
     70P  ALA*     3.9    22.9    -      -       +      +
     73P  LEU*     3.9    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 7 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5P  ARG*     6.1     0.7    -      -       +      -
      6P  LEU*     1.3    75.3    -      -       -      +
      8P  ARG*     1.3    62.3    +      -       -      +
      9P  PHE*     3.7    20.3    -      -       +      -
     16P  HIS      3.6     0.2    -      -       -      +
     17P  TYR*     2.9    11.2    -      -       -      -
     18P  ARG*     2.9    38.9    +      -       +      +
     20P  VAL*     4.6    11.2    -      -       +      -
     28P  ARG*     3.8    19.7    -      -       -      +
     29P  ASP*     4.1     2.5    -      -       -      +
     32P  TYR*     5.5     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 8 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A    A      5.7     2.2    +      -       +      -
    375A    U      5.3     1.3    -      -       -      -
    391A    G      2.8    47.6    +      -       -      +
    392A    G      3.3    10.7    +      -       -      -
      7P  ALA*     1.3    68.4    -      -       -      +
      9P  PHE*     1.3    75.8    +      -       -      +
     10P  GLY      4.8     1.1    -      -       -      +
     11P  SER      3.4    31.3    +      -       -      +
     15P  PRO*     3.6    31.3    -      -       -      +
     16P  HIS      3.9     1.8    -      -       -      -
     17P  TYR*     3.6    31.6    +      -       +      +
     28P  ARG*     3.3    39.4    -      -       -      +
     29P  ASP*     3.1    23.8    +      -       -      +
----------------------------------------------------------
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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