Contacts of the strand formed by residues 565 - 573 (chain B) in PDB entry 1XI1


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 565 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  THR*     4.7     1.2    +      -       -      -
     16B  THR      4.9     0.3    -      -       -      +
     64B  LYS      4.6     5.6    -      -       -      +
     65B  PHE*     3.8    33.2    -      -       +      +
     68B  ALA*     3.2    28.3    -      -       +      -
     69B  PHE*     3.2    27.2    -      -       +      -
    558B  PRO*     3.7    18.4    -      -       +      -
    559B  VAL      3.5    22.4    -      -       -      +
    560B  GLN*     3.5    21.1    -      -       -      +
    564B  GLY*     1.3    74.4    -      -       -      +
    566B  VAL*     1.3    74.8    +      -       -      +
    567B  LEU*     4.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 566 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  THR      4.1    11.7    -      -       -      +
     17B  THR*     3.2    25.6    -      -       -      +
     18B  LYS      3.9    10.5    -      -       -      +
     19B  VAL*     4.2    16.2    -      -       +      -
     22B  CYS*     3.2    38.1    -      -       +      -
     65B  PHE*     5.1     1.6    -      -       -      -
    557B  LYS      3.7     0.2    -      -       -      +
    558B  PRO*     3.6     1.4    -      -       -      +
    559B  VAL*     2.9    35.7    +      -       +      +
    561B  VAL*     3.9    11.0    -      -       +      -
    565B  VAL*     1.3    72.4    -      -       -      +
    567B  LEU*     1.3    78.5    +      -       -      +
    568B  VAL*     4.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 567 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  THR*     4.8     5.7    -      -       -      +
     65B  PHE*     4.5    14.8    -      -       +      -
    556B  PRO*     4.3    18.6    -      -       +      -
    557B  LYS      3.6     3.4    -      -       -      +
    558B  PRO*     3.9    32.8    -      -       +      -
    566B  VAL*     1.3    84.8    -      -       -      +
    568B  VAL*     1.3    62.0    +      -       -      +
      4D    T      4.1    35.4    -      -       +      +
      5D    T      3.1    50.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 568 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     4.5    21.1    -      -       +      -
    556B  PRO*     2.9     4.2    -      -       -      +
    557B  LYS*     2.6    40.4    +      -       +      +
    559B  VAL*     3.6    31.9    -      -       +      -
    566B  VAL*     4.3     3.6    -      -       +      +
    567B  LEU*     1.3    78.8    -      -       -      +
    569B  ASP*     1.3    81.6    +      -       +      +
    570B  ASP*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 569 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553B  LYS*     3.9    29.6    -      -       +      +
    554B  MET*     3.8    10.5    -      -       -      +
    555B  LYS      3.6     2.9    -      -       -      +
    556B  PRO*     3.8    21.3    -      -       -      +
    568B  VAL*     1.3    85.3    -      -       +      +
    570B  ASP*     1.3    59.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 570 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552B  ARG      4.0     0.5    -      -       -      +
    553B  LYS*     4.3     4.5    -      -       -      -
    555B  LYS*     2.6    43.6    +      -       +      +
    557B  LYS*     4.4    29.0    +      -       +      +
    568B  VAL      3.7     0.4    +      -       -      +
    569B  ASP*     1.3    75.2    -      -       -      +
    571B  THR*     1.3    92.4    +      -       -      +
    572B  PHE      3.2     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 571 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551B  SER*     4.0    11.9    -      -       -      +
    552B  ARG*     3.6    11.4    -      -       -      +
    553B  LYS*     2.7    39.8    -      -       +      +
    555B  LYS*     5.5     1.0    -      -       -      +
    570B  ASP*     1.3    88.6    +      -       -      +
    572B  PHE*     1.3    61.6    +      -       -      +
    573B  THR*     3.4    22.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 572 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    530B  CYS*     3.5    26.5    -      -       -      -
    531B  ALA      3.7     7.2    -      -       -      -
    532B  GLY*     3.2    33.4    -      -       -      -
    533B  MET*     3.4    32.5    -      -       +      -
    537B  ILE*     3.7    34.3    -      -       +      -
    550B  PHE*     4.7     3.1    -      +       -      -
    551B  SER*     2.9    24.9    -      -       -      -
    552B  ARG      2.9    12.0    +      -       -      +
    555B  LYS*     3.9    24.0    -      -       +      -
    570B  ASP      3.2     1.2    +      -       -      -
    571B  THR*     1.3    70.9    -      -       -      +
    573B  THR*     1.3    71.7    +      -       -      +
    574B  ILE*     4.1    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 573 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549B  GLY*     3.7    19.5    -      -       -      +
    550B  PHE      3.1    11.0    -      -       -      +
    551B  SER*     2.8    18.9    -      -       -      -
    571B  THR*     3.4    13.8    +      -       -      +
    572B  PHE*     1.3    87.0    -      -       -      +
    574B  ILE*     1.3    69.6    +      -       -      +
    575B  LYS*     3.3    27.2    +      -       +      +
----------------------------------------------------------
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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