Contacts of the strand formed by residues 67 - 72 (chain D) in PDB entry 1F11


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 ALA 67 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48D  ILE*     3.6    31.4    -      -       +      -
     59D  TYR*     3.8    14.0    -      -       +      -
     63D  PHE*     2.9    20.7    +      -       +      +
     65D  GLY      4.1     8.0    +      -       -      -
     66D  LYS*     1.3    76.3    -      -       +      +
     68D  THR*     1.3    69.0    +      -       -      +
     69D  LEU*     4.1     4.5    -      -       +      -
     80D  MET*     4.3     5.4    -      -       -      -
     81D  GLN      3.4     4.7    -      -       -      -
     82D  LEU*     3.9    14.1    -      -       +      -
----------------------------------------------------------
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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     7.0    -      -       -      +
     65D  GLY*     5.1     1.4    +      -       -      -
     67D  ALA*     1.3    80.2    +      -       -      +
     69D  LEU*     1.3    69.5    +      -       -      +
     70D  THR*     3.7    10.0    +      -       -      +
     79D  TYR      4.0     0.3    -      -       -      +
     80D  MET*     3.7     1.0    -      -       -      -
     81D  GLN*     2.9    45.6    +      -       +      +
     82D  ASN*     3.8    14.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 69 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  TRP*     3.4    35.7    -      -       +      +
     48D  ILE*     4.6     3.6    -      -       +      -
     49D  GLY*     3.4    22.9    -      -       -      +
     50D  ASP      3.4    22.0    -      -       -      +
     51D  ILE*     4.1    18.2    -      -       +      +
     57D  THR*     4.3     5.7    +      -       -      +
     59D  TYR*     2.9    31.0    +      -       +      +
     67D  ALA*     4.4     3.8    -      -       +      -
     68D  THR*     1.3    82.5    -      -       -      +
     70D  THR*     1.3    62.0    +      -       -      +
     79D  TYR      3.4     5.8    -      -       -      +
     80D  MET*     4.0    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 70 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  LYS*     5.2     6.1    -      -       -      +
     36D  TRP*     5.6     0.2    +      -       -      -
     51D  ILE*     3.6    10.6    -      -       -      +
     68D  THR*     4.4    10.1    +      -       -      +
     69D  LEU*     1.3    76.0    +      -       -      +
     71D  VAL*     1.3    72.2    +      -       -      +
     78D  ALA*     3.8     2.6    -      -       -      +
     79D  TYR*     2.8    59.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 71 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  PHE*     3.1    41.3    -      -       +      -
     51D  ILE*     3.3    27.4    -      -       +      -
     52D  PRO*     4.0    25.4    -      -       -      +
     55D  GLY*     4.4     9.2    -      -       -      -
     70D  THR*     1.3    85.6    -      -       -      +
     72D  ASP*     1.3    75.7    +      -       -      +
     73D  LYS*     4.1     5.6    -      -       -      +
     77D  THR      3.5     6.5    -      -       -      +
     78D  ALA*     4.8     1.6    -      -       +      -
     79D  TYR*     4.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 72 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  VAL*     1.3    77.5    -      -       -      +
     73D  LYS*     1.3    66.5    +      -       -      +
     74D  SER*     2.8    23.9    +      -       -      -
     75D  SER*     2.9    23.2    +      -       -      +
     76D  SER*     3.0    17.3    +      -       -      -
     77D  THR      2.8    18.1    +      -       -      +
     79D  TYR*     3.9    16.7    +      -       +      -
----------------------------------------------------------
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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