Contacts of the strand formed by residues 67 - 71 (chain D) in PDB entry 6H7L


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 PHE 67 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  ARG*     4.3     0.7    -      -       -      -
     48D  VAL*     3.5    19.5    -      -       +      -
     59D  TYR*     3.4    16.7    -      -       +      -
     63D  VAL*     3.0    43.3    +      -       +      +
     65D  GLY*     4.8     3.8    +      -       -      -
     66D  ARG*     1.3   106.1    +      -       +      +
     68D  THR*     1.3    65.7    +      -       -      +
     80D  LEU*     4.0    12.6    -      -       +      -
     81D  GLN      3.4     4.0    -      -       -      +
     82D  MET*     3.6    51.6    -      -       +      -
     83D  ASN      3.9     2.9    -      -       -      -
     85D  LEU*     3.7    17.7    -      -       +      -
     89D  ASP*     3.9    16.8    -      -       -      -
     93D  TYR*     3.8    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 68 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59D  TYR*     3.5    10.2    +      -       -      +
     65D  GLY      6.0     0.3    -      -       -      -
     66D  ARG      4.5     3.9    +      -       -      -
     67D  PHE*     1.3    77.8    +      -       -      +
     69D  ILE*     1.3    68.1    +      -       -      +
     70D  SER*     4.2     6.3    +      -       -      -
     79D  TYR      3.6     1.4    -      -       -      +
     80D  LEU*     3.5     5.1    -      -       -      +
     81D  GLN*     2.8    48.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 69 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34D  MET      3.9     2.9    -      -       -      +
     35D  GLY*     4.2     0.4    -      -       -      -
     36D  TRP*     3.9    14.6    -      -       +      -
     49D  ALA*     3.4    37.7    -      -       +      +
     50D  ALA*     3.6    28.5    -      -       -      +
     51D  ILE*     3.9    10.9    -      -       +      +
     57D  THR*     4.0    12.3    -      -       +      +
     59D  TYR*     2.9    33.1    +      -       +      +
     68D  THR*     1.3    75.8    -      -       -      +
     70D  SER*     1.3    67.7    +      -       -      +
     78D  VAL*     3.7    24.2    -      -       +      -
     79D  TYR      3.3    10.8    -      -       -      +
     80D  LEU*     4.1     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 70 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  ARG*     5.0     2.4    +      -       -      -
     51D  ILE*     4.1     9.6    -      -       -      -
     68D  THR*     4.9     6.8    +      -       -      +
     69D  ILE*     1.3    78.0    -      -       -      +
     71D  ARG*     1.3    62.6    +      -       -      +
     78D  VAL*     3.5     5.1    -      -       -      +
     79D  TYR*     2.8    47.8    +      -       -      +
     81D  GLN*     6.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 71 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  ASN*     2.8    31.3    +      -       -      +
     34D  MET*     3.3    34.8    -      -       -      +
     51D  ILE*     3.7    31.7    +      -       +      +
     52D  HIS      3.9    13.7    -      -       -      -
     53D  SER*     3.6    27.0    +      -       -      +
     55D  GLY*     6.0     0.7    -      -       -      -
     70D  SER*     1.3    78.5    -      -       -      +
     72D  ASP*     1.3    73.5    +      -       -      +
     73D  ASN*     3.4     5.1    +      -       -      +
     75D  ALA      5.2     1.4    +      -       -      -
     76D  ASN*     4.1    17.8    +      -       -      +
     77D  THR      3.4    11.4    +      -       -      +
     78D  VAL*     4.4     3.8    -      -       +      -
     79D  TYR*     4.6     4.9    -      -       -      -
----------------------------------------------------------
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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