Contacts of the strand formed by residues 93 - 97 (chain H) in PDB entry 1XBT


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 93 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40H  VAL*     4.5    13.2    -      -       +      -
     43H  PHE*     3.7    46.4    -      -       +      -
     48H  TYR*     4.1    17.5    -      -       +      -
     49H  LYS      3.1     2.6    +      -       -      -
     50H  CYS*     3.3    17.8    -      -       -      +
     51H  LEU      2.9    26.0    +      -       -      +
     91H  VAL*     3.1     3.7    -      -       -      +
     92H  ALA*     1.3    83.7    -      -       -      +
     94H  ILE*     1.3    63.6    +      -       -      +
    118H  THR*     3.4    17.3    -      -       -      +
    120H  ILE*     4.4    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 94 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51H  LEU*     3.3     7.0    -      -       +      +
     53H  ILE*     3.7    28.9    -      -       +      -
     88H  ALA*     3.8    34.5    -      -       +      +
     91H  VAL*     3.7    13.5    -      -       +      -
     93H  VAL*     1.3    80.2    -      -       -      +
     95H  GLY*     1.3    55.4    +      -       -      +
     96H  ILE*     4.0    13.7    -      -       +      -
    108H  PHE*     4.4     7.0    -      -       +      -
    112H  MET*     4.0    27.1    -      -       +      -
    117H  LYS*     4.2    14.8    -      -       +      -
    118H  THR      2.8    12.3    +      -       -      +
    119H  VAL*     3.3     8.8    -      -       +      +
    120H  ILE*     2.8    32.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 95 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  LEU*     3.8    18.4    -      -       -      -
     40H  VAL*     4.2    11.7    -      -       -      +
     51H  LEU      2.7    13.6    +      -       -      +
     52H  VAL*     3.3     4.9    -      -       -      -
     53H  ILE*     2.7    32.8    +      -       -      +
     93H  VAL      4.2     0.6    -      -       -      -
     94H  ILE*     1.3    73.8    -      -       -      +
     96H  ILE*     1.3    60.0    +      -       -      +
     97H  ASP      4.2     0.4    -      -       -      -
    120H  ILE      3.3     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 96 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  LEU*     3.6     4.7    -      -       -      +
     53H  ILE*     3.5     7.0    -      -       +      +
     81H  LEU*     4.0    14.4    -      -       +      -
     94H  ILE*     4.0     9.6    -      -       +      -
     95H  GLY*     1.3    77.1    -      -       -      +
     97H  ASP*     1.3    62.1    +      -       -      +
     99H  GLY*     4.2     4.0    -      -       -      -
    102H  PHE*     3.8    32.8    -      -       +      -
    105H  ILE*     4.0    13.7    -      -       +      -
    108H  PHE*     3.9    26.0    -      -       +      -
    109H  CYS*     3.9    24.2    -      -       -      -
    119H  VAL*     4.1     9.6    -      -       +      -
    120H  ILE      2.7    13.5    +      -       -      +
    121H  VAL*     3.5     6.5    -      -       +      +
    122H  ALA      2.9    29.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 97 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  SER*     2.6    35.1    +      -       -      -
     36H  LEU*     3.8    11.8    -      -       +      +
     37H  MET*     5.9     0.4    -      -       +      -
     52H  VAL*     5.3     4.0    -      -       +      -
     53H  ILE      2.8    16.5    +      -       -      +
     54H  LYS*     4.2    18.4    -      -       +      +
     55H  TYR      3.8     8.5    +      -       -      -
     96H  ILE*     1.3    72.5    -      -       -      +
     98H  GLU*     1.3    92.9    +      -       -      +
    102H  PHE*     3.7    14.2    -      -       -      -
    122H  ALA*     3.9    11.4    -      -       -      +
   8194H   MG      4.3     1.0    -      -       -      -
   8195H  TTP      4.7     0.5    +      -       -      -
----------------------------------------------------------
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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