Contacts of the strand formed by residues 77 - 84 (chain A) in PDB entry 1ITB


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 LYS 77 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  LEU*     3.8     4.2    -      -       -      +
     74A  LYS      3.1    29.4    +      -       -      +
     75A  ASP*     3.1     6.7    -      -       +      +
     76A  ASP*     1.3    81.9    -      -       -      +
     78A  PRO*     1.3    88.6    +      -       +      +
     79A  THR*     3.2    13.7    -      -       +      +
    120A  TRP*     3.6    30.3    -      -       +      -
    134A  LEU      5.1     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL      3.7     6.3    -      -       -      +
     73A  LEU*     4.3     9.2    -      -       +      -
     76A  ASP      4.4     2.2    -      -       -      +
     77A  LYS*     1.3    94.7    +      -       +      +
     79A  THR*     1.3    65.3    +      -       -      +
    117A  PHE*     3.7    38.8    -      -       +      -
    120A  TRP*     3.5    58.2    -      -       +      +
    134A  LEU*     4.3     8.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  CYS*     3.4     3.5    -      -       -      -
     72A  VAL*     2.9    40.7    +      -       -      +
     74A  LYS*     3.1    37.6    -      -       +      +
     77A  LYS*     3.2    26.2    -      -       +      +
     78A  PRO*     1.3    79.9    -      -       -      +
     80A  LEU*     1.3    66.6    +      -       -      +
     81A  GLN*     4.0     1.0    +      -       -      +
    134A  LEU*     4.1    10.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  LEU*     6.2     0.7    -      -       +      -
     69A  LEU*     4.1    24.7    -      -       +      -
     70A  SER      3.3    17.9    -      -       -      +
     79A  THR*     1.3    77.7    -      -       -      +
     81A  GLN*     1.3    67.5    +      -       -      +
     82A  LEU*     5.3     6.1    -      -       +      -
    101A  PHE*     4.1    22.9    -      -       +      -
    122A  ILE*     4.7     8.3    -      -       +      -
    132A  VAL*     3.8    37.9    -      -       +      +
    133A  PHE*     3.9    12.3    -      -       -      +
    134A  LEU*     3.7    33.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  TYR      5.4     1.3    -      -       -      +
     69A  LEU*     3.6     3.8    -      -       -      -
     70A  SER*     3.0    46.4    +      -       -      +
     72A  VAL*     3.1    35.9    -      -       +      +
     74A  LYS*     5.5     2.9    -      -       -      +
     79A  THR*     5.0     1.8    -      -       -      +
     80A  LEU*     1.3    80.6    -      -       -      +
     82A  LEU*     1.3    70.2    +      -       -      +
     83A  GLU*     4.1    21.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  MET*     4.5     2.0    -      -       -      -
     24A  TYR*     3.6    42.6    +      -       +      +
     25A  GLU*     3.7    23.3    -      -       -      +
     26A  LEU*     4.2    25.1    -      -       +      +
     62A  LEU*     4.0    14.4    -      -       +      -
     67A  LEU*     3.7    26.7    -      -       +      -
     68A  TYR      3.8     3.8    -      -       -      +
     69A  LEU*     4.2    24.2    -      -       +      -
     80A  LEU*     5.3     6.5    -      -       +      -
     81A  GLN*     1.3    85.9    +      -       -      +
     83A  GLU*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  TYR*     4.7     2.0    -      -       -      -
     67A  LEU*     3.5     5.1    -      -       -      +
     68A  TYR*     2.9    32.4    +      -       -      +
     70A  SER*     2.8    23.2    +      -       -      +
     72A  VAL*     4.9     2.4    -      -       -      +
     81A  GLN*     4.1    17.7    +      -       -      +
     82A  LEU*     1.3    75.0    -      -       -      +
     84A  SER*     1.3    70.0    +      -       -      +
     85A  VAL*     4.0     3.4    +      -       +      +
     98A  ARG*     3.6    24.8    +      -       -      -
     99A  PHE*     3.6    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  TYR*     3.1    21.2    +      -       -      -
     66A  ASN*     3.2    19.1    -      -       -      -
     67A  LEU*     3.5    10.7    -      -       -      +
     83A  GLU*     1.3    84.0    -      -       -      +
     85A  VAL*     1.3    68.2    +      -       -      +
----------------------------------------------------------
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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