Contacts of the strand formed by residues 92 - 95 (chain B) 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 THR 92 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  LYS*     3.7    10.5    +      -       -      +
     53A  VAL*     3.3    16.7    -      -       +      +
     54A  THR      4.2     0.7    -      -       -      -
     55A  SER*     3.5    32.8    -      -       -      +
     52B  THR*     4.8     3.4    +      -       -      +
     53B  PHE*     3.5    18.9    -      -       -      -
     87B  CYS*     4.3     6.5    -      -       +      -
     88B  ASP      2.7    22.7    +      -       -      -
     89B  SER*     3.5    21.8    -      -       -      +
     90B  ASP      3.6     0.4    -      -       -      -
     91B  SER*     1.3    93.0    +      -       -      +
     93B  ASP*     1.3    65.8    +      -       -      +
     94B  CYS*     3.7     5.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  THR*     5.1     0.2    -      -       -      +
     47A  MET*     5.0     8.2    -      -       -      +
     51A  LYS*     4.0    19.8    +      -       +      +
     53A  VAL      2.9    14.7    +      -       -      +
     54A  THR*     3.7    17.4    +      -       -      +
     55A  SER      2.9    31.4    +      -       -      +
     92B  THR*     1.3    71.8    -      -       -      +
     94B  CYS*     1.3    61.1    +      -       -      +
     95B  THR*     3.3    25.9    +      -       -      +
    104C  LYS*     3.3    27.7    +      -       -      +
    129C  ASN*     5.0     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  SER*     3.8     6.5    -      -       -      -
     90A  HIS*     3.9    16.2    +      -       +      +
     91A  LYS*     3.8    30.7    +      -       +      +
     87B  CYS*     2.0    48.7    -      -       -      -
     89B  SER*     4.2     8.1    -      -       -      -
     92B  THR      3.7    15.9    +      -       -      -
     93B  ASP*     1.3    73.6    +      -       -      +
     95B  THR*     1.3    63.7    +      -       -      +
    101C  ARG*     4.6     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  THR*     4.2     4.9    -      -       -      +
     55A  SER      3.1    21.6    +      -       -      +
     56A  GLU*     3.4     7.3    -      -       -      -
     57A  SER*     3.4    10.9    +      -       -      +
     90A  HIS*     5.1     1.4    +      -       -      -
     93B  ASP*     3.3    18.1    +      -       -      +
     94B  CYS*     1.3    79.1    -      -       -      +
     96B  VAL*     1.3    64.9    +      -       -      +
     97B  ARG*     3.5    25.2    +      -       -      +
     98B  GLY*     3.9     2.4    +      -       -      -
     76C  GLU*     6.1     0.4    -      -       -      -
    101C  ARG*     3.7     6.3    -      -       -      +
    103C  GLU*     3.1    24.5    -      -       -      +
    104C  LYS*     3.2    25.4    -      -       -      +
----------------------------------------------------------
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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