Contacts of the strand formed by residues 551 - 560 (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 SER 551 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549B  GLY      3.2     9.1    +      -       -      -
    550B  PHE*     1.3    79.1    -      -       -      +
    552B  ARG*     1.3    86.2    +      -       -      +
    571B  THR*     4.0     7.5    -      -       -      +
    572B  PHE      2.9     7.0    -      -       -      -
    573B  THR*     2.8    30.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 552 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537B  ILE*     4.3    12.0    -      -       +      +
    540B  GLU*     2.9    46.4    +      -       -      +
    545B  ASN*     3.9    15.8    +      -       -      +
    550B  PHE*     3.0    44.2    -      -       +      +
    551B  SER*     1.3    87.0    +      -       -      +
    553B  LYS*     1.3    63.6    +      -       -      +
    554B  MET*     3.1    22.0    +      -       +      +
    571B  THR*     4.2     2.8    -      -       -      +
    572B  PHE*     2.9    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 553 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  GLU*     5.1     8.7    +      -       -      -
    552B  ARG*     1.3    70.8    -      -       -      +
    554B  MET*     1.3    65.7    +      -       -      +
    555B  LYS      3.7     0.7    -      -       -      -
    569B  ASP*     3.9    24.0    -      -       +      +
    570B  ASP      4.2     2.2    -      -       -      -
    571B  THR*     2.7    37.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 554 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534B  THR*     4.5     6.6    -      -       -      +
    536B  LYS*     3.7    49.7    -      -       +      +
    537B  ILE*     4.1    20.2    -      -       +      -
    540B  GLU*     3.4    29.6    -      -       -      +
    552B  ARG*     3.1    17.9    +      -       +      -
    553B  LYS*     1.3    81.5    -      -       -      +
    555B  LYS*     1.3    60.9    +      -       -      +
    556B  PRO*     2.9    16.3    -      -       -      +
    569B  ASP*     3.8    10.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 555 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    532B  GLY*     3.5    36.7    +      -       -      +
    534B  THR*     5.2     6.1    -      -       +      -
    537B  ILE*     4.3     6.8    -      -       +      +
    554B  MET*     1.3    77.7    -      -       -      +
    556B  PRO*     1.3    71.3    -      -       +      +
    557B  LYS*     3.6     7.7    +      -       +      +
    569B  ASP*     4.1     0.4    -      -       -      -
    570B  ASP*     2.6    48.7    +      -       +      +
    571B  THR      5.5     0.7    -      -       -      +
    572B  PHE*     3.9    29.1    -      -       +      -
      3D    T      5.4     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 556 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534B  THR*     5.4     7.0    -      -       +      -
    536B  LYS*     6.4     0.9    -      -       +      -
    554B  MET      2.9    18.2    -      -       -      +
    555B  LYS*     1.3    90.1    -      -       +      +
    557B  LYS*     1.3    60.2    +      -       -      +
    558B  PRO*     4.7     0.4    -      -       -      +
    567B  LEU*     4.3    26.2    -      -       +      -
    568B  VAL      2.9    11.2    -      -       -      +
    569B  ASP*     3.8    10.1    -      -       -      +
      3D    T      4.6     6.2    -      -       -      +
      4D    T      4.5    20.6    -      -       +      +
      5D    T      5.6     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 557 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  GLU*     4.4    16.0    +      -       -      -
    318A  SER*     5.7     1.0    +      -       -      -
    320A  GLY*     5.2     9.9    -      -       -      -
    321A  GLY      5.7     1.7    -      -       -      +
    310B  TYR*     5.8     0.6    +      -       -      -
    555B  LYS*     4.4    11.7    -      -       +      +
    556B  PRO*     1.3    76.4    -      -       -      +
    558B  PRO*     1.3    85.2    -      -       +      +
    559B  VAL*     3.7     7.0    -      -       +      +
    567B  LEU*     3.6     3.8    -      -       -      -
    568B  VAL*     2.6    33.8    +      -       +      +
    570B  ASP*     4.4    25.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 558 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  LYS*     5.1    17.0    -      -       -      -
     65B  PHE*     6.0     0.4    -      -       +      -
    556B  PRO      4.7     0.9    -      -       -      +
    557B  LYS*     1.3   104.4    -      -       +      +
    559B  VAL*     1.3    65.1    +      -       -      +
    565B  VAL*     3.7    16.4    -      -       +      -
    566B  VAL      3.6     7.2    -      -       -      +
    567B  LEU*     3.9    14.6    -      -       +      -
      3D    T      5.6     7.2    -      -       -      +
      4D    T      4.6    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 559 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     5.7     2.7    -      -       +      -
    557B  LYS*     3.7     6.5    -      -       +      +
    558B  PRO*     1.3    81.5    -      -       -      +
    560B  GLN*     1.3    68.6    +      -       -      +
    561B  VAL*     3.3    22.1    +      -       +      +
    565B  VAL*     3.5     6.2    -      -       -      +
    566B  VAL      2.9    30.3    +      -       -      +
    568B  VAL*     3.6    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 560 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  LYS      5.3     1.4    +      -       -      -
     68B  ALA*     4.0     8.7    -      -       -      +
     72B  ASN*     4.7     0.5    -      -       -      +
    100B  TRP*     5.0     3.6    -      -       -      -
    407B  LYS*     5.9     0.3    +      -       -      -
    411B  ALA*     4.1     6.9    -      -       +      +
    412B  LEU*     3.4    42.2    +      -       -      +
    414B  PHE*     3.9    33.7    -      -       +      -
    559B  VAL*     1.3    75.0    -      -       -      +
    561B  VAL*     1.3    62.9    +      -       -      +
    564B  GLY      3.5     9.4    -      -       -      +
    565B  VAL*     3.5    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