Contacts of the strand formed by residues 104 - 108 (chain H) in PDB entry 1XFB


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 VAL 104 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19H  ILE*     4.2     4.7    -      -       +      +
     22H  ARG*     3.8    39.3    -      -       +      +
     23H  ILE*     3.7    24.5    -      -       +      -
     75H  GLY      2.9    20.1    +      -       -      +
     76H  GLY*     3.2     1.6    -      -       -      -
     77H  VAL*     2.9    27.0    +      -       -      -
     98H  ILE*     4.2     1.3    -      -       -      +
    102H  GLY      4.8     0.4    -      -       -      +
    103H  ILE*     1.3    73.9    -      -       -      +
    105H  VAL*     1.3    64.6    +      -       -      +
    144H  ASP*     3.8    26.2    -      -       +      +
    145H  PHE*     3.6    21.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77H  VAL      3.8     2.5    -      -       -      -
     79H  PHE*     3.6    24.5    -      -       +      -
     84H  LEU*     3.9    20.9    -      -       +      -
     95H  VAL*     4.0    10.5    -      -       +      +
     98H  ILE*     3.9    16.6    -      -       +      -
     99H  GLN*     3.7    30.7    -      -       +      -
    103H  ILE      4.3     0.7    -      -       -      +
    104H  VAL*     1.3    76.0    -      -       -      +
    106H  GLY*     1.3    63.2    +      -       -      +
    142H  GLY      3.3    19.3    +      -       -      +
    143H  ALA*     3.3     3.8    -      -       -      -
    144H  ASP*     2.8    29.6    +      -       -      -
    145H  PHE*     3.2    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 106 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77H  VAL      2.9    11.0    +      -       -      -
     78H  ILE*     4.1     3.8    -      -       -      -
     79H  PHE*     2.6    39.4    +      -       -      +
     84H  LEU*     5.0     0.2    -      -       -      +
    105H  VAL*     1.3    78.1    -      -       -      +
    107H  ILE*     1.3    59.0    +      -       -      -
    143H  ALA*     4.4     0.2    -      -       -      -
    145H  PHE*     2.9    28.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 107 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78H  ILE*     4.3     4.2    -      -       -      +
     79H  PHE*     3.4    18.2    -      -       +      +
     81H  HIS*     4.1    17.3    -      -       -      +
     84H  LEU*     4.1    21.3    -      -       +      -
    106H  GLY*     1.3    75.8    -      -       -      +
    108H  LYS*     1.3    71.0    +      -       -      +
    109H  VAL*     3.6     1.5    -      -       +      +
    138H  TYR*     3.8    37.0    -      -       +      -
    143H  ALA*     3.6    24.2    -      -       +      -
    145H  PHE      3.2    18.0    +      -       -      +
    146H  ALA*     3.2    17.3    -      -       +      +
    147H  LYS      3.0    21.4    +      -       -      -
    183H  ILE*     4.8     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 108 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34H  ASP*     3.5    52.8    +      -       +      +
     35H  GLU*     5.1     0.6    -      -       -      +
     36H  SER*     4.2    20.6    +      -       -      +
     39H  SER*     5.3     0.6    +      -       -      -
     78H  ILE*     4.1     1.4    -      -       -      +
     79H  PHE      3.2     8.9    +      -       -      +
     80H  PHE*     4.7    13.2    -      -       +      -
     81H  HIS*     5.0     5.4    +      -       -      +
    107H  ILE*     1.3    81.8    -      -       -      +
    109H  VAL*     1.3    60.7    +      -       -      +
    110H  ASP*     3.5    38.4    -      -       -      +
    134H  ARG*     4.5     3.3    +      -       -      -
    138H  TYR*     4.9     2.3    +      -       -      -
    147H  LYS*     3.4    18.6    -      -       +      +
    149H  ARG*     5.7     3.4    -      -       -      +
----------------------------------------------------------
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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