Contacts of the strand formed by residues 65 - 74 (chain A) in PDB entry 3OOT


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 65 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  SER      5.3     2.2    +      -       -      -
     63A  SER*     3.9    19.2    +      -       -      +
     64A  TYR*     1.3    81.6    +      -       -      +
     66A  HIS*     1.3    65.6    +      -       -      +
     85A  SER      3.9     0.3    -      -       -      -
     86A  GLN*     2.8    71.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  TYR*     3.3    41.1    -      +       +      +
     65A  LYS*     1.3    77.7    -      -       -      +
     67A  ASN*     1.3    84.6    +      -       -      +
     68A  GLY*     4.1     9.5    -      -       -      -
     83A  PHE*     5.8     3.1    -      +       -      -
    367A  NAG      4.3    11.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  TYR*     4.6     0.2    +      -       -      -
     65A  LYS      3.9     1.3    +      -       -      +
     66A  HIS*     1.3    88.8    +      -       -      +
     68A  GLY*     1.3    60.4    +      -       -      +
     69A  THR*     2.8    33.3    +      -       -      -
     84A  LEU*     3.7    22.9    +      -       -      +
     85A  SER*     4.5     2.0    -      -       -      +
     86A  GLN*     6.0     0.2    -      -       +      -
    100A  MET*     3.6    19.0    -      -       +      +
    367A  NAG      1.5    80.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  HIS*     4.1    12.4    +      -       -      -
     67A  ASN*     1.3    74.0    -      -       -      +
     69A  THR*     1.3    64.6    +      -       -      +
     70A  GLU*     3.4     6.8    +      -       -      +
     83A  PHE*     3.6    20.9    -      -       -      +
     84A  LEU      2.9    16.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  ASN*     2.8    24.1    +      -       -      -
     68A  GLY*     1.3    74.9    -      -       -      +
     70A  GLU*     1.3    73.3    +      -       -      +
     83A  PHE*     3.0     1.7    -      -       -      -
     84A  LEU*     2.7    46.7    +      -       +      +
    367A  NAG      4.1    14.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  GLY      3.4     5.5    +      -       -      +
     69A  THR*     1.3    87.4    -      -       -      +
     71A  LEU*     1.3    62.4    +      -       -      +
     82A  GLY      3.4    12.1    -      -       -      +
     83A  PHE*     4.8     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ASN*     3.8    25.1    -      -       +      +
     38A  VAL      6.1     0.2    -      -       -      +
     69A  THR      4.7     0.7    -      -       -      +
     70A  GLU*     1.3    76.0    -      -       -      +
     72A  THR*     1.3    62.7    +      -       -      +
     73A  LEU*     3.9    25.5    -      -       +      +
     80A  VAL      4.2     0.2    -      -       -      +
     81A  SER*     3.4     4.2    -      -       -      -
     82A  GLY*     2.9    36.3    +      -       -      +
     83A  PHE      3.7    33.7    -      -       -      +
     84A  LEU*     4.1    20.9    -      -       +      +
    102A  GLY*     4.1    15.7    -      -       -      +
    104A  VAL*     6.4     1.3    -      -       +      -
    130A  ILE*     4.4    15.3    -      -       +      +
    131A  GLY*     6.0     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU*     1.3    72.8    -      -       -      +
     73A  LEU*     1.3    64.8    +      -       -      +
     74A  ARG*     3.6    43.4    +      -       +      +
     79A  THR*     3.9    17.5    -      -       +      -
     80A  VAL      3.6     2.5    -      -       -      -
     81A  SER*     3.0    21.5    +      -       -      +
    130A  ILE*     3.5    21.7    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     37A  ASN*     3.6    35.9    -      -       +      +
     39A  TRP*     3.5    37.5    -      -       +      -
     71A  LEU*     3.9    23.8    -      -       +      -
     72A  THR*     1.3    72.5    -      -       -      +
     74A  ARG*     1.3    61.6    +      -       -      +
     75A  TYR*     3.8    24.0    -      -       +      +
     79A  THR*     3.4     4.4    -      -       -      -
     80A  VAL*     2.9    43.5    +      -       +      +
    102A  GLY*     5.8     0.7    -      -       -      -
    104A  VAL*     5.2     2.5    -      -       +      -
    130A  ILE*     3.8    22.2    -      -       +      -
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Residues in contact with ARG 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  THR*     3.6    36.1    +      -       +      +
     73A  LEU*     1.3    73.3    -      -       -      +
     75A  TYR*     1.3    68.8    +      -       -      +
     79A  THR*     3.9    22.8    -      -       +      +
    130A  ILE*     5.7     2.6    -      -       -      +
----------------------------------------------------------
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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