Contacts of the strand formed by residues 74 - 78 (chain F) in PDB entry 1XWD


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 74 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  HIS*     5.3     5.3    -      -       -      -
     85D  SER*     3.1    26.7    +      -       -      -
     86D  THR*     3.4    16.3    +      -       -      +
     88D  TYR*     5.4     0.6    +      -       -      -
     49F  ILE      3.2     2.2    +      -       -      -
     50F  GLU*     3.3    37.0    +      -       +      +
     51F  LEU      3.0    23.7    +      -       -      +
     72F  LEU*     3.9     1.9    -      -       -      +
     73F  GLU*     1.3    91.2    -      -       +      +
     75F  ILE*     1.3    65.5    +      -       -      +
     76F  GLU*     4.1     1.1    -      -       +      +
     98F  HIS*     5.8     1.3    -      -       +      -
     99F  GLU*     3.4    36.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 75 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51F  LEU*     3.4     9.6    -      -       +      +
     53F  PHE*     4.5     3.4    -      -       +      -
     66F  PHE*     3.8    41.3    -      -       +      -
     72F  LEU*     3.6    27.8    -      -       +      -
     74F  LYS*     1.3    78.2    -      -       -      +
     76F  GLU*     1.3    60.3    +      -       -      +
     77F  ILE*     4.1    18.3    -      -       +      +
     91F  PHE*     3.8    25.6    -      -       +      -
     94F  LEU*     4.5     2.5    -      -       +      -
     97F  LEU*     3.7    21.1    -      -       +      -
     99F  GLU*     3.0    10.0    +      -       -      +
    100F  ILE*     3.6     4.0    -      -       +      +
    101F  ARG*     2.8    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 76 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96E  VAL*     5.2     4.7    -      -       -      +
     97E  ARG*     4.9    14.5    -      -       -      +
     50F  GLU*     4.2     8.2    +      -       -      +
     51F  LEU      2.8    12.4    +      -       -      +
     52F  ARG*     3.6    36.5    -      -       +      -
     53F  PHE*     2.9    26.0    +      -       -      -
     54F  VAL*     3.9     9.6    -      -       +      +
     74F  LYS*     4.1     1.9    -      -       +      -
     75F  ILE*     1.3    72.3    -      -       -      +
     77F  ILE*     1.3    65.3    +      -       -      +
     78F  SER*     3.8    25.8    +      -       -      +
     99F  GLU*     5.6     3.0    -      -       -      +
    101F  ARG*     3.6    38.9    +      -       +      +
    103F  GLU*     5.4     0.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 77 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53F  PHE*     3.6    22.9    -      -       +      +
     58F  LEU*     5.8     1.1    -      -       +      -
     61F  ILE*     3.4    26.7    -      -       +      -
     66F  PHE*     5.1     3.8    -      -       +      -
     75F  ILE*     4.1    12.1    -      -       +      -
     76F  GLU*     1.3    76.6    -      -       -      +
     78F  SER*     1.3    59.2    +      -       -      +
     80F  ASN*     3.7    12.8    -      -       -      +
     83F  LEU*     3.7    27.6    -      -       +      -
     86F  ILE*     5.4     1.1    -      -       +      -
     91F  PHE*     4.2    23.1    -      -       +      -
    100F  ILE*     6.1     0.2    -      -       +      -
    101F  ARG      2.7    15.4    +      -       -      +
    102F  ILE*     3.3    16.1    -      -       +      +
    103F  GLU      2.9    25.8    +      -       -      +
    105F  ALA*     6.1     1.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 78 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95E  THR*     5.5     0.7    -      -       -      +
     97E  ARG      5.2     3.5    +      -       -      -
     53F  PHE      2.8     9.9    +      -       -      -
     54F  VAL*     3.1    31.0    -      -       -      +
     76F  GLU*     3.8    28.1    +      -       -      -
     77F  ILE*     1.3    74.8    -      -       -      +
     79F  GLN*     1.3    76.7    +      -       -      +
     80F  ASN*     3.0    12.0    +      -       -      +
    101F  ARG*     5.7     0.2    +      -       -      -
    103F  GLU*     3.4    16.6    +      -       -      +
    104F  LYS*     3.8    12.1    +      -       -      -
----------------------------------------------------------
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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