Contacts of the strand formed by residues 283 - 294 (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 LEU 283 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  LEU*     3.4    43.3    -      -       +      +
    263B  LEU      3.7     2.7    -      -       -      -
    264B  PRO*     3.5    31.9    -      -       +      -
    281B  TYR      3.4     4.1    -      -       -      +
    282B  PRO*     1.3    80.9    -      -       -      +
    284B  HIS*     1.3    67.1    +      -       -      +
    330B  ASN*     3.6    24.0    -      -       -      +
    352B  LYS*     3.4     2.1    -      -       -      -
    353B  PHE*     2.9    36.3    +      -       +      +
    355B  ALA*     3.8    14.8    -      -       +      -
    432B  PHE*     3.7    20.0    -      -       +      -
    436B  TRP*     5.2     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 284 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271B  PHE*     4.2     2.2    -      +       +      -
    275B  TYR*     3.5    60.2    -      +       +      +
    282B  PRO      4.6     2.2    +      -       -      -
    283B  LEU*     1.3    80.8    -      -       -      +
    285B  ILE*     1.3    65.6    +      -       -      +
    286B  GLN*     3.8    26.4    +      -       +      +
    329B  SER*     3.4     2.9    -      -       -      -
    330B  ASN*     2.8    58.5    +      -       +      +
    333B  LEU*     4.7     9.3    -      -       +      +
    351B  LEU      3.0    17.0    -      -       -      +
    353B  PHE*     4.1     2.9    -      -       -      -
    432B  PHE*     3.4     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 285 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221B  GLU      4.9     2.5    -      -       -      +
    222B  VAL*     4.1    30.1    -      -       +      +
    225B  ALA*     3.7    32.1    -      -       +      -
    271B  PHE*     4.1     1.7    -      -       -      -
    284B  HIS*     1.3    79.0    -      -       -      +
    286B  GLN*     1.3    61.7    +      -       -      +
    327B  TRP*     4.1    22.0    -      -       +      -
    328B  LEU      3.3     8.5    -      -       -      +
    329B  SER*     4.2     6.1    -      -       -      -
    350B  GLY*     3.0     5.0    -      -       -      -
    351B  LEU*     2.8    38.1    +      -       +      +
    353B  PHE*     4.1    15.3    -      -       +      -
    428B  PRO*     5.6     0.4    -      -       +      -
    431B  VAL*     4.2    10.5    -      -       +      -
    432B  PHE*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 286 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271B  PHE*     3.7     3.9    -      -       -      -
    273B  GLY      2.8    26.0    +      -       -      -
    274B  LYS*     3.7     1.2    -      -       -      +
    275B  TYR*     3.1    32.4    +      -       -      +
    284B  HIS*     3.8    14.4    +      -       +      +
    285B  ILE*     1.3    74.6    -      -       -      +
    287B  HIS*     1.3    70.9    +      -       -      +
    288B  ILE*     3.4    23.6    +      -       +      +
    326B  LEU      3.5     1.6    -      -       -      +
    327B  TRP*     3.3     2.7    -      -       -      -
    328B  LEU*     2.7    41.7    +      -       +      +
    333B  LEU*     4.7    10.4    -      -       +      +
    347B  TYR*     3.6    28.4    -      -       +      +
    349B  SER      3.6     8.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 287 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285B  ILE      4.2     0.4    +      -       -      -
    286B  GLN*     1.3    73.9    +      -       -      +
    288B  ILE*     1.3    69.7    +      -       -      +
    289B  ARG*     4.4     5.6    -      -       -      -
    325B  ASP*     2.9    35.0    +      -       -      -
    326B  LEU      3.4    11.9    -      -       -      -
    327B  TRP*     3.4    47.6    +      +       +      -
    348B  ILE*     3.0    58.9    +      -       +      +
    349B  SER*     2.7    25.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 288 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286B  GLN*     3.4    30.7    +      -       +      +
    287B  HIS*     1.3    80.3    -      -       -      +
    289B  ARG*     1.3    67.0    +      -       -      +
    290B  CYS*     4.1    13.5    -      -       +      -
    325B  ASP*     3.7     2.1    -      -       -      -
    326B  LEU*     2.7    50.8    +      -       +      +
    328B  LEU*     4.3     6.7    -      -       +      -
    333B  LEU*     4.2    18.6    -      -       +      -
    336B  MET*     4.0    27.4    -      -       +      -
    342B  LEU*     5.6     1.8    -      -       +      -
    345B  VAL*     4.9     8.7    -      -       +      -
    346B  GLU      3.4     7.9    -      -       -      +
    347B  TYR*     3.8    20.2    -      -       +      -
    348B  ILE*     4.7     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 289 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416A  LEU*     3.8    44.1    +      -       +      +
    287B  HIS*     4.4     5.1    -      -       -      -
    288B  ILE*     1.3    72.9    -      -       -      +
    290B  CYS*     1.3    63.4    +      -       -      +
    323B  ILE*     3.9    11.2    -      -       +      -
    324B  ALA      3.3    15.3    -      -       -      +
    325B  ASP*     3.2    25.9    +      -       +      +
    344B  ASN      3.5     2.6    -      -       -      +
    345B  VAL*     3.5     0.9    -      -       -      +
    346B  GLU*     2.7    71.4    +      -       +      +
    348B  ILE*     3.1    27.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 290 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  ILE*     4.1    13.0    -      -       +      +
    289B  ARG*     1.3    76.6    -      -       -      +
    291B  GLU*     1.3    72.0    +      -       -      +
    292B  PHE*     3.9    11.4    -      -       -      -
    323B  ILE*     3.6     6.6    -      -       -      +
    324B  ALA*     2.7    42.7    +      -       -      +
    326B  LEU*     4.9     4.3    -      -       -      -
    336B  MET*     3.8    29.2    -      -       -      -
    342B  LEU*     3.8     4.9    -      -       -      -
    343B  TYR      3.6    14.4    -      -       -      +
    344B  ASN      4.0     2.9    -      -       -      -
    345B  VAL*     4.1    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 291 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  LYS*     3.9     8.5    +      -       -      -
    414A  PHE*     5.5     5.0    -      -       -      +
    290B  CYS*     1.3    81.9    -      -       -      +
    292B  PHE*     1.3    64.7    +      -       -      +
    319B  SER*     3.3    14.3    +      -       -      +
    321B  GLY*     3.2    35.0    +      -       -      +
    322B  GLU      4.0     5.6    -      -       -      +
    323B  ILE*     4.0    18.7    -      -       +      +
    342B  LEU*     3.4     2.6    -      -       -      -
    343B  TYR*     2.7    45.7    +      -       +      +
    344B  ASN*     3.1    22.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 292 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309A  PHE*     4.4     2.5    -      +       -      -
    290B  CYS*     3.9    14.1    -      -       -      -
    291B  GLU*     1.3    80.5    -      -       -      +
    293B  GLU*     1.3    70.6    +      -       -      +
    302B  ILE*     3.8    26.2    -      -       +      -
    316B  LEU*     4.1    28.3    -      -       +      -
    318B  SER*     3.1    30.2    +      -       -      -
    319B  SER*     3.1    39.7    +      -       -      -
    324B  ALA*     3.6    25.1    -      -       +      -
    326B  LEU*     4.5     6.3    -      -       +      -
    336B  MET*     4.9     0.2    -      -       +      -
    340B  TYR*     3.7    22.9    -      +       +      -
    341B  ASP      3.2    10.8    -      -       -      +
    342B  LEU*     3.7    13.7    -      -       +      -
    343B  TYR*     4.7     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 293 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292B  PHE*     1.3    76.8    -      -       -      +
    294B  LEU*     1.3    68.2    +      -       -      +
    295B  LYS*     3.1     0.5    +      -       -      -
    317B  LYS      3.5     2.9    -      -       -      +
    318B  SER*     2.4    38.2    +      -       -      -
    319B  SER*     5.3     0.2    +      -       -      -
    320B  GLY*     4.5     3.8    +      -       -      -
    340B  TYR*     3.8     2.7    -      -       -      -
    341B  ASP*     3.0    38.9    +      -       +      +
    343B  TYR*     4.3    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 294 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293B  GLU*     1.3    75.3    +      -       -      +
    295B  LYS*     1.3    67.7    +      -       -      +
    296B  GLU*     3.8     1.7    +      -       -      +
    298B  TYR      3.5    20.6    -      -       -      +
    299B  ILE      3.5    21.8    -      -       -      +
    300B  PRO*     3.5    32.3    -      -       +      -
    317B  LYS*     2.6    42.1    +      -       +      +
    339B  HIS      3.4    15.9    -      -       -      +
    340B  TYR*     3.6    21.7    -      -       +      -
    341B  ASP*     5.3     0.2    -      -       -      +
----------------------------------------------------------
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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