Contacts of the strand formed by residues 67 - 74 (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 LEU 67 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  MET*     4.2    20.9    -      -       +      -
     23A  PRO*     5.1     3.8    -      -       +      -
     24A  TYR*     3.3    42.0    -      -       +      +
     61A  GLY*     3.1     4.5    -      -       -      -
     62A  LEU*     2.9    43.8    +      -       +      -
     65A  LYS*     3.8    10.1    -      -       +      +
     66A  ASN*     1.3    77.8    -      -       -      +
     68A  TYR*     1.3    66.8    +      -       -      +
     82A  LEU*     3.7    25.8    -      -       +      -
     83A  GLU      3.5     8.3    -      -       -      +
     84A  SER*     3.5    21.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  SER*     4.0    13.2    +      -       -      -
     45A  SER*     3.8     7.1    +      -       -      -
     59A  ALA*     3.9    21.1    -      -       +      -
     60A  LEU      3.5    16.6    -      -       -      -
     61A  GLY*     3.5    19.4    -      -       -      -
     62A  LEU      5.7     1.3    -      -       -      -
     66A  ASN*     5.6     3.1    -      -       -      -
     67A  LEU*     1.3    87.4    -      -       -      +
     69A  LEU*     1.3    65.7    +      -       -      +
     70A  SER*     3.3     4.3    +      -       -      -
     82A  LEU*     3.8     1.7    -      -       -      -
     83A  GLU*     2.9    31.7    +      -       -      +
     85A  VAL*     3.7    24.0    -      -       +      -
     90A  TYR*     4.5    12.8    -      +       +      -
     91A  PRO*     3.2    28.8    -      -       +      +
     95A  MET*     3.9    17.7    -      -       +      -
     99A  PHE*     3.6    26.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     6.4     0.7    -      -       +      -
     26A  LEU*     4.4     6.5    -      -       +      -
     42A  PHE*     4.3    17.3    -      -       +      -
     60A  LEU*     2.8    40.8    +      -       +      +
     62A  LEU*     3.8    27.4    -      -       +      -
     68A  TYR*     1.3    72.1    -      -       -      +
     70A  SER*     1.3    59.3    +      -       -      +
     80A  LEU*     4.1    19.3    -      -       +      -
     81A  GLN      3.6     5.6    -      -       -      -
     82A  LEU*     4.2    16.8    -      -       +      -
     99A  PHE*     3.4    21.1    -      -       -      +
    101A  PHE*     3.4    16.5    -      -       +      -
    122A  ILE*     4.2    22.7    -      -       +      -
    132A  VAL*     6.1     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  TYR      3.3     0.6    +      -       -      -
     69A  LEU*     1.3    73.7    -      -       -      +
     71A  CYS*     1.3    64.0    +      -       -      +
     72A  VAL*     4.2     2.0    -      -       -      +
     80A  LEU*     3.3     6.6    -      -       -      +
     81A  GLN*     3.0    44.7    +      -       -      +
     83A  GLU*     2.8    26.6    +      -       -      +
     98A  ARG*     3.3    19.5    -      -       -      -
     99A  PHE*     3.5    23.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  SER*     1.3    75.5    -      -       -      +
     72A  VAL*     1.3    62.4    +      -       -      +
     79A  THR      3.4     4.7    -      -       -      -
     98A  ARG*     2.9    33.7    +      -       -      +
    101A  PHE*     3.4    33.2    -      -       -      -
    114A  SER*     3.1    28.9    -      -       -      +
    116A  GLN*     4.2     3.2    -      -       +      +
    117A  PHE*     3.7    21.8    -      -       +      -
    134A  LEU*     3.7    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  SER*     4.2     8.9    -      -       -      +
     71A  CYS*     1.3    80.8    -      -       -      +
     73A  LEU*     1.3    70.8    +      -       -      +
     74A  LYS*     4.6     5.6    -      -       +      +
     78A  PRO*     3.7     1.7    -      -       -      +
     79A  THR*     2.9    45.9    +      -       -      +
     81A  GLN*     3.1    35.9    -      -       +      +
     83A  GLU*     4.9     2.0    -      -       -      +
     98A  ARG*     4.5    14.1    -      -       -      -
    117A  PHE*     3.8     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL*     1.3    79.0    -      -       -      +
     74A  LYS*     1.3    59.8    +      -       -      +
     75A  ASP      4.0     0.6    +      -       -      -
     76A  ASP*     3.6    37.0    -      -       -      +
     77A  LYS      3.7    20.0    -      -       -      +
     78A  PRO*     4.0     4.3    -      -       +      -
    117A  PHE*     3.7    31.1    -      -       +      -
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Residues in contact with LYS 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL*     3.5     8.2    +      -       +      -
     73A  LEU*     1.3    72.3    -      -       -      +
     75A  ASP*     1.3    94.7    +      -       -      +
     77A  LYS*     3.1    21.9    +      -       -      +
     79A  THR*     3.1    29.7    -      -       +      +
     81A  GLN*     5.5     2.2    -      -       -      +
----------------------------------------------------------
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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