Contacts of the strand formed by residues 283 - 294 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  LEU*     3.3    39.3    -      -       +      +
    263A  LEU      3.8     2.9    -      -       -      -
    264A  PRO*     3.6    33.0    -      -       +      -
    275A  TYR*     4.9     0.2    -      -       -      -
    281A  TYR      3.3     4.2    -      -       -      +
    282A  PRO*     1.3    81.4    -      -       -      +
    284A  HIS*     1.3    66.2    +      -       -      +
    330A  ASN*     3.4    27.6    -      -       -      +
    352A  LYS*     3.4     2.6    -      -       -      -
    353A  PHE*     3.0    38.0    +      -       +      +
    355A  ALA*     3.8    13.7    -      -       +      -
    432A  PHE*     3.7    18.8    -      -       +      -
    436A  TRP*     5.1     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  PHE*     4.1     2.5    -      +       +      -
    275A  TYR*     3.4    62.8    -      +       +      +
    282A  PRO      4.7     1.6    +      -       -      -
    283A  LEU*     1.3    79.3    -      -       -      +
    285A  ILE*     1.3    63.9    +      -       -      +
    286A  GLN*     3.9    25.9    +      -       +      +
    329A  SER*     3.4     3.1    -      -       -      -
    330A  ASN*     2.9    61.2    +      -       +      +
    333A  LEU*     4.6    10.2    -      -       +      +
    351A  LEU      3.0    18.8    -      -       -      +
    353A  PHE*     4.1     2.9    -      -       -      -
    432A  PHE*     3.5     2.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  GLU      5.0     2.5    -      -       -      +
    222A  VAL*     3.9    31.9    -      -       +      -
    225A  ALA*     3.8    28.9    -      -       +      -
    271A  PHE*     4.2     1.6    -      -       -      -
    284A  HIS*     1.3    78.3    -      -       -      +
    286A  GLN*     1.3    61.7    +      -       -      +
    327A  TRP*     4.1    22.2    -      -       +      -
    328A  LEU      3.3     9.2    -      -       -      +
    329A  SER*     4.1     7.9    -      -       -      -
    350A  GLY*     3.0     5.4    -      -       -      -
    351A  LEU*     2.8    38.5    +      -       +      +
    353A  PHE*     4.0    19.1    -      -       +      -
    428A  PRO*     5.4     0.9    -      -       +      -
    431A  VAL*     4.4     4.3    -      -       +      -
    432A  PHE*     3.9    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  PHE*     3.5    10.7    -      -       -      -
    273A  GLY      2.7    26.4    +      -       -      -
    274A  LYS*     4.7     0.2    -      -       -      +
    275A  TYR*     3.2    24.6    +      -       -      +
    284A  HIS*     3.9    13.7    +      -       +      +
    285A  ILE*     1.3    76.3    -      -       -      +
    287A  HIS*     1.3    72.7    +      -       -      +
    288A  ILE*     3.6     8.2    +      -       +      +
    326A  LEU      3.5     1.4    -      -       -      +
    327A  TRP*     3.3     3.7    -      -       -      -
    328A  LEU*     2.8    37.7    +      -       +      +
    333A  LEU*     4.6    11.4    -      -       +      -
    347A  TYR*     3.3    41.4    -      -       +      +
    349A  SER      4.0     5.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  ILE      4.2     0.2    +      -       -      -
    286A  GLN*     1.3    75.1    +      -       -      +
    288A  ILE*     1.3    63.0    +      -       -      +
    289A  ARG*     4.4     5.4    -      -       -      -
    325A  ASP*     2.8    31.5    +      -       -      -
    326A  LEU      3.3    11.2    -      -       -      -
    327A  TRP*     3.3    51.3    +      +       +      -
    348A  ILE*     2.9    59.7    +      -       +      +
    349A  SER*     2.7    27.2    +      -       -      +
    350A  GLY*     4.3     0.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  GLN*     4.5    13.5    -      -       +      +
    287A  HIS*     1.3    79.8    -      -       -      +
    289A  ARG*     1.3    73.3    +      -       -      +
    290A  CYS*     4.4    17.9    -      -       -      -
    325A  ASP*     3.8     1.7    -      -       -      -
    326A  LEU*     2.8    53.2    +      -       +      +
    328A  LEU*     4.8    12.6    -      -       +      -
    333A  LEU*     4.6     8.7    -      -       +      -
    336A  MET*     4.5    11.7    -      -       +      -
    342A  LEU*     5.5     1.6    -      -       +      -
    345A  VAL*     3.2    33.2    -      -       +      -
    346A  GLU      3.5    13.7    -      -       -      +
    347A  TYR*     4.2    13.2    -      -       +      +
    348A  ILE*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  HIS*     4.4     4.8    -      -       -      -
    288A  ILE*     1.3    77.4    -      -       -      +
    290A  CYS*     1.3    63.2    +      -       -      +
    323A  ILE*     4.0    10.3    -      -       +      -
    324A  ALA      3.2    16.4    -      -       -      +
    325A  ASP*     3.3    26.5    +      -       +      +
    344A  ASN      3.6     2.9    -      -       -      +
    345A  VAL*     3.6     0.3    -      -       -      -
    346A  GLU*     2.8    65.8    +      -       +      +
    348A  ILE*     3.2    27.2    -      -       +      +
    416B  LEU*     3.7    44.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ILE*     4.4    17.0    -      -       +      -
    289A  ARG*     1.3    76.9    -      -       -      +
    291A  GLU*     1.3    66.8    +      -       -      +
    292A  PHE*     4.1    11.9    -      -       -      -
    323A  ILE*     3.4     6.3    -      -       -      +
    324A  ALA*     2.5    44.1    +      -       -      +
    326A  LEU*     4.9     7.9    -      -       -      -
    336A  MET*     4.4     5.6    -      -       -      -
    342A  LEU*     4.1    22.0    -      -       -      -
    343A  TYR      3.6    13.7    -      -       -      +
    344A  ASN      4.0     3.4    -      -       -      -
    345A  VAL*     4.1    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290A  CYS*     1.3    81.9    -      -       -      +
    292A  PHE*     1.3    64.7    -      -       -      +
    319A  SER*     3.4    14.6    -      -       -      +
    321A  GLY*     3.1    34.3    +      -       -      +
    322A  GLU      4.0     0.5    -      -       -      +
    323A  ILE*     3.9    25.5    -      -       +      +
    342A  LEU*     3.5     2.6    -      -       -      -
    343A  TYR*     2.7    44.0    +      -       +      +
    344A  ASN*     3.6    22.0    +      -       +      +
    402B  LYS*     3.7     9.2    +      -       -      -
    414B  PHE*     5.6     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290A  CYS*     4.1    13.5    -      -       -      -
    291A  GLU*     1.3    80.7    -      -       -      +
    293A  GLU*     1.3    71.1    +      -       -      +
    302A  ILE*     3.6    26.5    -      -       +      -
    316A  LEU*     4.1    29.8    -      -       +      -
    318A  SER*     3.1    41.2    -      -       -      -
    319A  SER*     3.1    22.5    +      -       -      -
    324A  ALA*     3.5    26.2    -      -       +      -
    326A  LEU*     4.5     6.7    -      -       +      -
    340A  TYR*     3.5    24.5    -      +       +      -
    341A  ASP      3.1    10.3    -      -       -      +
    342A  LEU*     3.8    14.1    -      -       +      -
    343A  TYR*     4.7     1.8    -      -       -      -
    309B  PHE*     4.3     2.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292A  PHE*     1.3    77.7    -      -       -      +
    294A  LEU*     1.3    70.4    +      -       -      +
    295A  LYS      3.2     0.2    +      -       -      -
    317A  LYS      3.5     3.0    -      -       -      +
    318A  SER*     3.0    32.8    +      -       -      -
    319A  SER*     5.1     0.7    +      -       -      -
    320A  GLY*     4.3     6.6    +      -       -      -
    340A  TYR*     3.9     3.4    -      -       -      -
    341A  ASP*     2.8    42.9    +      -       +      +
    343A  TYR*     4.2    17.0    -      -       +      -
    557B  LYS*     4.4    15.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  GLU*     1.3    76.4    +      -       -      +
    295A  LYS*     1.3    67.3    +      -       -      +
    296A  GLU      3.9     0.2    +      -       -      -
    298A  TYR      3.4    22.9    -      -       -      +
    299A  ILE      3.4    23.3    -      -       -      +
    300A  PRO*     3.6    31.0    -      -       +      -
    317A  LYS*     2.6    41.4    +      -       +      +
    339A  HIS      3.3    17.0    -      -       -      +
    340A  TYR*     3.6    20.6    -      -       +      -
    341A  ASP*     5.2     0.5    -      -       -      +
----------------------------------------------------------
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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