Contacts of the strand formed by residues 50 - 63 (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 50 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  SER*     3.4     7.8    -      -       -      -
     55A  SER*     4.1    14.6    -      -       -      +
     56A  GLU      4.4     0.3    +      -       -      -
     57A  SER*     2.6    36.5    -      -       -      +
     87A  CYS*     5.8     0.9    -      -       -      -
     90A  HIS*     4.5    10.3    -      -       +      +
     32B  CYS*     3.8     5.6    -      -       -      -
     49B  LYS*     1.3    75.8    -      -       -      +
     51B  CYS*     1.3    74.5    +      -       -      +
     52B  THR*     3.5    13.8    +      -       +      +
     83B  HIS      3.4     0.2    -      -       -      +
     84B  CYS*     3.2     1.9    -      -       -      -
     85B  GLY      2.6    36.7    +      -       -      +
     87B  CYS*     4.2    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  SER*     3.0    32.6    +      -       -      +
     35A  ARG      4.1    16.1    +      -       -      +
     36A  ALA*     4.4     0.5    -      -       -      +
     55A  SER*     4.7     1.0    +      -       -      -
      3B  CYS*     2.1    49.1    -      -       +      -
     28B  CYS*     3.9     6.5    -      -       -      -
     29B  ALA      3.6    31.6    -      -       -      -
     30B  GLY      4.4     1.3    -      -       -      +
     32B  CYS*     3.6     7.6    -      -       -      -
     50B  THR*     1.3    78.3    +      -       -      +
     52B  THR*     1.3    63.3    +      -       -      +
     83B  HIS      3.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ALA*     4.1    11.6    -      -       -      +
     55A  SER*     5.2     2.5    -      -       -      -
     28B  CYS*     3.4    13.9    -      -       -      -
     50B  THR*     3.8    21.5    -      -       +      +
     51B  CYS*     1.3    81.1    -      -       -      +
     53B  PHE*     1.3    92.5    +      -       -      +
     82B  CYS*     3.3     2.1    -      -       -      -
     83B  HIS*     2.9    38.6    +      -       +      +
     85B  GLY      4.6     0.9    -      -       -      +
     86B  LYS      4.0    19.3    -      -       -      +
     87B  CYS*     4.3     8.8    -      -       -      +
     88B  ASP      5.4     0.8    +      -       -      +
     92B  THR*     4.8     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ALA*     4.7     0.6    -      -       -      +
     53A  VAL*     4.3    10.1    -      -       +      -
     27B  TRP*     4.0    26.7    -      +       +      -
     28B  CYS*     3.5     8.7    -      -       -      -
     52B  THR*     1.3    92.7    +      -       -      +
     54B  LYS*     1.3    62.5    +      -       -      +
     55B  GLU*     4.0    15.0    -      -       -      +
     56B  LEU*     3.6    43.1    -      -       +      -
     79B  ALA*     4.5     4.0    -      -       +      -
     81B  GLN      3.4     9.4    -      -       -      +
     83B  HIS*     3.1    13.6    -      -       -      -
     88B  ASP*     5.1     9.2    -      -       +      -
     91B  SER*     3.6    21.5    -      -       -      -
     92B  THR*     3.5    22.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  PHE*     1.3    78.6    -      -       -      +
     55B  GLU*     1.3    81.7    +      -       +      +
     81B  GLN*     2.6    45.3    +      -       +      +
     82B  CYS      4.4     1.1    -      -       -      +
     83B  HIS*     3.7    42.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  PHE*     4.0     5.9    -      -       -      +
     54B  LYS*     1.3    96.6    -      -       +      +
     56B  LEU*     1.3    58.6    +      -       -      +
     57B  VAL*     6.5     0.2    -      -       +      -
     79B  ALA*     3.9     1.4    -      -       -      -
     80B  THR*     2.8    41.0    +      -       +      -
     81B  GLN*     3.3    28.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  VAL*     3.8    26.9    -      -       +      -
     27B  TRP*     3.9     8.7    -      -       +      -
     53B  PHE*     3.6    33.2    -      -       +      -
     55B  GLU*     1.3    78.5    +      -       -      +
     57B  VAL*     1.3    70.1    +      -       -      +
     58B  TYR*     4.5    19.0    -      -       +      +
     77B  PRO*     4.0    13.5    -      -       +      -
     78B  VAL      3.3    16.2    -      -       -      +
     79B  ALA*     4.2     2.7    -      -       -      -
     80B  THR*     3.9     1.6    -      -       -      -
     91B  SER*     6.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  LEU*     1.3    79.3    -      -       -      +
     58B  TYR*     1.3    69.8    +      -       -      +
     59B  GLU*     4.2    20.9    -      -       +      +
     77B  PRO*     3.6     2.8    -      -       -      +
     78B  VAL*     2.8    44.6    +      -       +      +
     80B  THR*     3.4    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  ASN*     2.8    41.7    +      -       -      +
     53A  VAL*     5.5     0.7    -      -       -      +
     93A  NAG      3.2    29.2    +      -       -      +
     56B  LEU*     4.5    23.2    -      -       +      +
     57B  VAL*     1.3    83.3    -      -       -      +
     59B  GLU*     1.3    68.3    +      -       -      +
     75B  THR*     4.3    21.5    -      -       +      -
     76B  TYR*     3.4    22.9    -      -       -      -
     77B  PRO*     4.2    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  THR*     5.0     0.3    +      -       -      -
     57B  VAL*     4.2    12.4    -      -       +      +
     58B  TYR*     1.3    80.2    -      -       -      +
     60B  THR*     1.3    66.0    +      -       -      +
     75B  THR*     3.5     3.0    -      -       -      -
     76B  TYR*     3.1    55.6    +      -       +      +
     78B  VAL*     3.4    32.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  GLU*     1.3    76.4    -      -       -      +
     61B  VAL*     1.3    75.8    +      -       -      +
     73B  LEU*     3.9    32.8    -      -       +      -
     74B  TYR      3.3    13.2    -      -       -      +
     75B  THR*     3.4    20.8    -      -       +      +
     76B  TYR*     4.3     3.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ILE*     3.7    13.5    -      -       +      -
     21B  ILE*     4.9     3.1    -      -       +      -
     23B  ILE*     3.4    38.1    -      -       +      -
     60B  THR*     1.3    81.7    -      -       -      +
     62B  ARG*     1.3    72.0    +      -       -      +
     63B  VAL*     3.6     6.3    -      -       +      +
     73B  LEU*     3.4     4.9    -      -       -      -
     74B  TYR*     3.0    41.6    +      -       +      +
     76B  TYR*     4.1     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  ILE*     4.0     8.3    -      -       -      +
     61B  VAL*     1.3    85.6    -      -       -      +
     63B  VAL*     1.3    62.1    +      -       -      +
     64B  PRO*     4.1     2.4    -      -       -      +
     71B  ASP*     4.5    27.1    +      -       +      +
     72B  SER*     3.5    10.3    +      -       -      +
     73B  LEU*     3.6    37.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ILE*     4.3    13.0    -      -       +      +
     14B  LYS*     3.8    18.6    +      -       +      -
     19B  PHE*     5.2     1.3    -      -       +      -
     21B  ILE*     4.0    18.8    -      -       +      -
     61B  VAL*     3.6    15.0    -      -       +      +
     62B  ARG*     1.3    77.2    -      -       -      +
     64B  PRO*     1.3    81.7    -      -       +      +
     71B  ASP*     3.2     5.6    -      -       -      +
     72B  SER*     2.8    50.5    +      -       -      +
     73B  LEU      4.1     0.2    -      -       -      -
     74B  TYR*     3.8    23.3    -      -       +      +
----------------------------------------------------------
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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