Contacts of the strand formed by residues 5 - 12 (chain Q) 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 VAL 5 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3Q  LYS      3.4    16.4    -      -       -      +
      4Q  LYS*     1.3    79.6    -      -       -      +
      6Q  LEU*     1.3    75.1    +      -       -      +
     58Q  GLU*     4.1    17.7    -      -       +      +
     59Q  ILE      2.8    18.6    -      -       -      +
     60Q  ILE*     4.1    10.8    -      -       +      -
     74Q  LEU*     3.8    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 6 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A    G      5.3     4.0    -      -       -      +
      4Q  LYS*     3.5    32.5    -      -       +      -
      5Q  VAL*     1.3    95.6    -      -       -      +
      7Q  THR*     1.3    62.8    +      -       -      +
     23Q  VAL*     4.1    21.8    -      -       +      -
     42Q  TYR*     3.4    43.5    -      -       +      +
     58Q  GLU*     3.1     2.8    -      -       -      -
     59Q  ILE*     2.4    55.1    +      -       +      +
     71Q  PHE*     4.7     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 7 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6Q  LEU*     1.3    76.9    +      -       -      +
      8Q  GLY*     1.3    63.5    +      -       -      +
     23Q  VAL*     3.3    19.8    -      -       -      +
     24Q  GLU      4.7     3.1    +      -       -      +
     56Q  VAL*     3.5    28.7    -      -       +      -
     57Q  VAL      3.1     8.1    -      -       -      +
     58Q  GLU*     4.1    17.5    +      -       -      +
     77Q  VAL*     4.5     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 8 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6Q  LEU      4.3     0.2    +      -       -      -
      7Q  THR*     1.3    76.4    -      -       -      +
      9Q  VAL*     1.3    63.9    +      -       -      -
     21Q  VAL*     3.2    18.6    -      -       -      +
     22Q  LEU      3.1    13.7    -      -       -      -
     23Q  VAL*     3.7     2.2    -      -       -      -
     56Q  VAL*     3.1    13.1    -      -       -      +
     57Q  VAL      2.8    27.9    +      -       -      -
     59Q  ILE*     5.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 9 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8Q  GLY*     1.3    78.6    -      -       -      +
     10Q  VAL*     1.3    68.7    -      -       -      +
     11Q  VAL*     3.1    12.4    +      -       +      +
     21Q  VAL*     3.3     3.9    -      -       -      +
     22Q  LEU*     2.8    42.0    +      -       +      +
     24Q  GLU*     6.4     1.6    -      -       +      -
     54Q  GLY*     4.1    18.6    -      -       -      +
     55Q  ASP      3.4     9.2    -      -       -      +
     56Q  VAL*     4.4     5.4    -      -       +      -
     81Q  ARG      4.7     0.4    -      -       -      +
     84Q  LEU*     3.8    45.3    -      -       +      -
     85Q  VAL*     4.6     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 10 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9Q  VAL*     1.3    68.6    -      -       -      +
     11Q  VAL*     1.3    61.0    -      -       -      +
     12Q  SER      3.8    20.4    -      -       -      +
     13Q  ASP*     5.2     0.7    -      -       +      -
     19Q  VAL*     3.9    20.2    -      -       +      -
     20Q  THR      3.3     4.9    -      -       -      -
     21Q  VAL*     4.4     8.3    -      -       +      -
     51Q  TYR*     4.3    10.5    -      -       +      -
     52Q  LYS*     3.4    30.1    -      -       -      +
     53Q  LEU*     2.9    20.4    -      -       -      +
     54Q  GLY      3.1     9.4    +      -       -      -
     55Q  ASP*     2.8    20.2    +      -       +      +
     57Q  VAL*     4.3    25.1    -      -       +      -
     85Q  VAL*     3.8     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 11 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9Q  VAL*     3.3    20.2    -      -       +      +
     10Q  VAL*     1.3    75.7    -      -       -      +
     12Q  SER*     1.3    61.8    +      -       -      +
     14Q  LYS*     5.1     6.1    +      -       -      -
     20Q  THR*     2.9    33.9    +      -       +      +
     22Q  LEU*     4.0    18.8    -      -       +      -
     41Q  LYS*     4.6     0.4    -      -       +      -
     53Q  LEU*     3.4    19.9    -      -       +      +
     84Q  LEU      5.6     0.4    -      -       -      +
     85Q  VAL*     4.4    19.3    -      -       +      +
     88Q  TYR*     3.9    44.7    -      -       +      +
     89Q  LEU*     5.2     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 12 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A    G      2.5    25.5    +      -       -      -
     10Q  VAL*     3.5     3.4    -      -       -      +
     11Q  VAL*     1.3    85.2    -      -       -      +
     13Q  ASP*     1.3    61.7    +      -       -      +
     14Q  LYS*     3.9    20.1    +      -       -      +
     15Q  MET*     4.4     4.3    -      -       -      +
     19Q  VAL*     3.6    12.6    -      -       -      +
     20Q  THR*     3.2    41.8    +      -       -      -
     53Q  LEU*     4.0     2.2    -      -       -      -
     88Q  TYR*     6.1     1.1    -      -       -      -
----------------------------------------------------------
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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