Contacts of the strand formed by residues 38 - 44 (chain A) in PDB entry 1O3Q


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 THR 38 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  GLU*     1.3    86.1    +      -       -      +
     39A  LEU*     1.3    79.5    +      -       -      +
     40A  TYR*     4.0    18.0    +      -       +      +
     71A  GLY      3.1     4.3    -      -       -      +
     82A  ARG*     2.6    31.1    +      -       -      +
     96A  GLU*     4.1    13.5    -      -       +      +
     97A  ILE      3.3    22.0    -      -       -      +
     98A  SER*     4.7     2.3    -      -       -      +
     99A  TYR*     3.0    15.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  PHE*     4.5     1.6    -      -       +      -
     38A  THR*     1.3    78.5    -      -       -      +
     40A  TYR*     1.3    69.9    +      -       -      +
     69A  PHE*     4.0    14.6    -      -       +      -
     70A  ILE      3.7     7.9    -      -       -      +
     71A  GLY      3.4    16.8    -      -       -      +
     72A  GLU*     3.7    26.0    -      -       +      -
     75A  LEU*     4.3     8.7    -      -       +      -
     95A  ALA      3.9     0.2    -      -       -      +
     96A  GLU*     3.5     4.2    -      -       -      -
     97A  ILE*     3.0    40.0    +      -       +      +
     99A  TYR*     3.9     9.6    -      -       +      -
    102A  PHE*     3.6    49.4    -      -       +      -
    116A  LEU*     4.4     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  PHE*     5.9     0.4    -      -       -      -
     23A  TYR*     3.7     9.3    +      -       -      -
     29A  LEU*     3.7    29.0    +      -       +      -
     30A  ILE*     3.6    23.1    -      -       +      +
     38A  THR*     4.0    16.2    -      -       +      -
     39A  LEU*     1.3    78.4    -      -       -      +
     41A  TYR*     1.3    60.5    +      -       -      +
     69A  PHE*     3.3    12.5    -      -       -      -
     70A  ILE*     2.6    51.4    +      -       +      +
     82A  ARG*     3.5    24.4    +      -       -      -
     94A  VAL*     3.5    17.7    -      -       +      -
     95A  ALA      3.3     4.9    -      -       -      -
     96A  GLU*     3.2    42.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     3.4    35.9    -      -       +      +
     14A  PHE*     3.9    18.6    -      +       +      -
     15A  LEU*     4.1    10.3    -      -       +      -
     40A  TYR*     1.3    75.5    -      -       -      +
     42A  ILE*     1.3    79.2    +      -       -      +
     43A  VAL*     3.3    16.0    +      -       +      -
     67A  GLY*     3.3    37.5    +      -       -      -
     68A  ASP      3.5     4.3    -      -       -      -
     69A  PHE*     3.6    34.5    -      +       -      -
     94A  VAL*     3.3     3.1    -      -       -      -
     95A  ALA*     2.7    47.1    +      -       +      +
    115A  ARG*     5.7     0.7    +      -       -      -
    119A  GLN*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  TYR*     1.3    77.6    -      -       -      +
     43A  VAL*     1.3    59.7    +      -       -      +
     44A  LYS      3.6    22.2    -      -       -      +
     45A  GLY      3.8    16.6    -      -       -      +
     47A  VAL*     3.6    17.3    -      -       +      -
     64A  LEU*     3.9    27.1    -      -       +      +
     65A  ASN      3.7    15.7    -      -       -      +
     66A  GLN*     3.5     0.5    -      -       -      -
     67A  GLY      2.9    29.1    +      -       -      -
     68A  ASP      2.8    16.4    +      -       -      +
     70A  ILE*     3.5    32.5    -      -       +      -
     92A  CYS*     4.6     2.5    -      -       -      -
     93A  GLU      4.0     4.3    -      -       -      +
     94A  VAL*     4.2     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     4.5    14.6    -      -       +      -
     20A  ILE*     4.6     4.9    -      -       +      -
     41A  TYR*     3.9    13.5    -      -       +      +
     42A  ILE*     1.3    72.4    -      -       -      +
     44A  LYS*     1.3    62.3    +      -       +      +
     66A  GLN*     3.7    11.3    -      -       -      +
     93A  GLU*     2.9    35.6    +      -       +      +
     94A  VAL      4.5     0.7    -      -       -      -
     95A  ALA*     3.8    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ILE*     3.4     5.2    -      -       -      +
     43A  VAL*     1.3    84.3    -      -       +      +
     45A  GLY*     1.3    66.5    +      -       -      +
     66A  GLN*     3.4    23.3    +      -       +      +
     91A  ALA      5.3     1.8    -      -       -      +
     92A  CYS*     3.3     4.3    -      -       -      +
     93A  GLU*     2.9    48.7    +      -       +      +
----------------------------------------------------------
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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