Contacts of the strand formed by residues 340 - 356 (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 TYR 340 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292A  PHE*     3.5    28.3    -      +       +      -
    293A  GLU      3.5     5.8    -      -       -      +
    294A  LEU*     3.6    32.1    -      -       +      -
    295A  LYS*     3.0    21.3    -      -       -      -
    300A  PRO      3.8     0.3    -      -       -      -
    301A  THR*     2.8    29.5    +      -       +      -
    302A  ILE*     2.6    51.1    +      -       +      +
    316A  LEU      3.1    23.6    +      -       -      -
    317A  LYS      4.4     0.9    -      -       -      -
    336A  MET*     2.9    25.1    +      -       +      +
    337A  LYS*     3.2    12.8    -      -       -      +
    339A  HIS*     1.3    84.4    -      -       +      +
    341A  ASP*     1.3    67.3    +      -       -      +
    342A  LEU*     3.9     6.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292A  PHE*     3.1     6.4    -      -       -      -
    293A  GLU*     2.8    37.9    +      -       +      +
    294A  LEU      5.2     0.3    -      -       -      +
    295A  LYS*     3.3    33.7    -      -       -      +
    340A  TYR*     1.3    71.1    -      -       -      +
    342A  LEU*     1.3    63.4    +      -       -      +
    343A  TYR*     3.9    29.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ILE*     5.5     1.8    -      -       +      -
    290A  CYS*     4.1     9.0    -      -       -      -
    291A  GLU      3.5     0.9    -      -       -      +
    292A  PHE*     3.8    22.2    -      -       +      -
    333A  LEU*     5.4     0.7    -      -       +      -
    336A  MET*     3.2    39.3    -      -       +      -
    337A  LYS*     3.5    39.7    -      -       +      +
    340A  TYR*     4.0     7.4    +      -       +      +
    341A  ASP*     1.3    75.0    -      -       -      +
    343A  TYR*     1.3    70.6    +      -       -      +
    344A  ASN      4.3     0.3    +      -       -      -
    345A  VAL*     3.6    24.6    -      -       +      +
    347A  TYR*     6.1     1.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290A  CYS*     3.6     1.9    -      -       -      +
    291A  GLU*     2.7    50.7    +      -       +      +
    293A  GLU*     4.2    21.2    -      -       +      +
    341A  ASP*     3.9    37.0    +      -       +      +
    342A  LEU*     1.3    79.4    -      -       -      +
    344A  ASN*     1.3    82.7    +      -       -      +
    345A  VAL      3.3     2.0    +      -       -      -
    407B  LYS*     5.2    11.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  ARG      3.6     6.2    -      -       -      +
    290A  CYS*     4.0     2.9    -      -       -      -
    291A  GLU*     3.6    22.5    +      -       +      +
    323A  ILE*     5.9     2.3    -      -       +      +
    342A  LEU      4.3     0.2    +      -       -      -
    343A  TYR*     1.3    78.7    -      -       -      +
    345A  VAL*     1.3    63.1    +      -       -      +
    346A  GLU*     3.5     5.5    +      -       -      +
    405B  TYR*     3.5    17.2    +      -       -      +
    407B  LYS*     3.7    19.5    +      -       -      +
    412B  LEU      4.4     1.5    +      -       -      +
    413B  GLY*     3.4    17.5    -      -       -      -
    414B  PHE*     3.4    46.2    +      -       -      +
    415B  ARG*     5.8     1.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ILE*     3.2    30.7    -      -       +      -
    289A  ARG      3.6     4.3    -      -       -      -
    290A  CYS*     4.1     8.5    -      -       +      -
    342A  LEU*     3.6    41.1    -      -       +      +
    343A  TYR      4.4     0.2    -      -       -      -
    344A  ASN*     1.3    75.8    -      -       -      +
    346A  GLU*     1.3    60.1    +      -       -      +
    347A  TYR*     3.4    36.3    +      -       +      +
    405B  TYR*     5.6     0.3    +      -       -      -
    415B  ARG*     5.7     1.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ILE*     3.5     2.6    -      -       -      -
    289A  ARG*     2.8    76.9    +      -       +      +
    344A  ASN      3.5     3.3    +      -       -      +
    345A  VAL*     1.3    74.3    -      -       -      +
    347A  TYR*     1.3    68.7    +      -       -      +
    348A  ILE*     3.4     9.2    +      -       +      +
    415B  ARG*     3.2    52.5    +      -       +      +
    416B  LEU      5.0     3.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273A  GLY*     3.6     9.8    -      -       -      -
    274A  LYS*     3.6    54.7    +      -       +      +
    286A  GLN*     3.3    36.3    -      -       +      +
    287A  HIS      4.0     1.8    -      -       -      -
    288A  ILE*     4.2    12.8    -      -       +      +
    333A  LEU*     4.8    12.4    -      -       +      +
    337A  LYS*     4.8    14.9    +      -       -      +
    342A  LEU*     6.1     1.2    -      -       -      +
    345A  VAL*     3.4    33.4    -      -       +      +
    346A  GLU*     1.3    75.7    -      -       -      +
    348A  ILE*     1.3    63.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  GLU*     4.1     2.1    -      -       -      +
    273A  GLY*     2.8    23.2    +      -       -      -
    287A  HIS*     2.9    52.1    +      -       +      +
    288A  ILE      4.6     0.2    -      -       -      -
    289A  ARG*     3.2    52.3    -      -       +      +
    346A  GLU*     3.8    17.9    -      -       +      +
    347A  TYR*     1.3    73.4    -      -       -      +
    349A  SER*     1.3    62.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  VAL*     5.5     4.5    -      -       -      +
    271A  PHE      3.1    17.5    -      -       -      -
    272A  GLU*     4.0     8.3    -      -       -      -
    273A  GLY      3.6    12.8    +      -       -      +
    286A  GLN*     4.1     1.8    -      -       -      -
    287A  HIS*     2.7    43.6    +      -       -      +
    327A  TRP*     4.8     7.3    -      -       -      -
    348A  ILE*     1.3    89.3    -      -       -      +
    350A  GLY*     1.3    55.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  VAL*     3.7     2.4    -      -       -      +
    271A  PHE*     3.1    42.3    +      -       -      +
    285A  ILE      3.0    14.8    -      -       -      -
    286A  GLN*     4.2     0.4    -      -       -      -
    287A  HIS      4.3     0.4    -      -       -      -
    327A  TRP*     5.0     5.8    -      -       -      -
    349A  SER*     1.3    78.7    +      -       -      +
    351A  LEU*     1.3    75.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  LEU*     4.1    23.1    -      -       +      +
    221A  GLU*     4.4    18.8    -      -       +      +
    222A  VAL*     3.7    31.4    -      -       +      +
    268A  PRO*     4.4     7.6    -      -       +      -
    269A  ILE      3.7     3.8    -      -       -      +
    270A  VAL*     3.5    30.1    -      -       +      +
    271A  PHE*     3.4     4.2    -      -       -      -
    284A  HIS*     3.0     7.3    -      -       -      +
    285A  ILE*     2.8    38.3    +      -       +      +
    327A  TRP*     5.1     6.3    -      -       +      -
    350A  GLY*     1.3    84.7    -      -       -      +
    352A  LYS*     1.3    60.3    +      -       -      +
    353A  PHE*     3.3    20.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  PRO*     3.3     7.8    -      -       -      +
    269A  ILE*     3.0    56.5    +      -       +      +
    271A  PHE*     3.5    24.4    -      -       +      +
    275A  TYR*     3.4    35.2    -      -       +      -
    276A  VAL      4.7     2.2    +      -       -      +
    278A  ASP*     2.5    32.6    +      -       +      +
    281A  TYR*     3.6    23.3    -      -       +      -
    283A  LEU      3.4     4.7    -      -       -      +
    351A  LEU*     1.3    71.5    -      -       -      +
    353A  PHE*     1.3    64.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  VAL*     4.6     1.1    -      -       +      -
    264A  PRO*     3.9    13.7    -      -       +      -
    265A  TYR      4.6     2.0    -      -       -      +
    266A  GLY      4.8     0.9    -      -       -      -
    267A  GLU      5.2     0.4    -      -       -      -
    268A  PRO*     3.6    23.8    -      -       +      -
    281A  TYR*     3.0    28.9    -      -       -      -
    282A  PRO*     3.4     1.6    -      -       -      +
    283A  LEU*     3.0    23.5    +      -       +      +
    284A  HIS*     4.1     3.8    -      -       -      -
    285A  ILE*     4.0    28.3    -      -       +      -
    351A  LEU*     3.3    44.9    -      -       +      -
    352A  LYS*     1.3    77.1    -      -       -      +
    354A  LYS*     1.3    71.4    +      -       -      +
    426A  TYR*     3.9    16.6    -      -       -      -
    428A  PRO*     3.6    31.9    -      -       +      -
    432A  PHE*     4.8     5.4    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  LYS      6.0     0.2    +      -       -      -
    264A  PRO*     3.3     4.5    -      -       -      +
    265A  TYR*     3.2    75.5    +      -       +      +
    266A  GLY*     4.2    10.7    -      -       -      -
    267A  GLU*     4.7     6.5    +      -       -      +
    280A  ASP*     3.5    21.5    -      -       +      +
    281A  TYR*     3.6    29.8    +      -       +      +
    353A  PHE*     1.3    78.0    -      -       -      +
    355A  ALA*     1.3    60.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  LEU*     3.6    29.4    -      -       +      +
    263A  LEU      3.1    14.1    -      -       -      +
    265A  TYR*     3.7     9.7    +      -       -      -
    280A  ASP      4.5     0.4    +      -       -      -
    282A  PRO*     3.9    18.3    -      -       +      +
    283A  LEU*     3.8    18.2    -      -       +      -
    353A  PHE      3.9     0.2    +      -       -      -
    354A  LYS*     1.3    77.8    -      -       -      +
    356A  THR*     1.3    64.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  ARG      3.7     0.9    -      -       -      +
    262A  LEU*     4.1     4.9    -      -       -      +
    263A  LEU*     2.9    32.1    +      -       -      +
    265A  TYR*     3.7    16.8    -      -       +      -
    355A  ALA*     1.3    75.1    -      -       -      +
    357A  THR*     1.3    69.8    +      -       -      +
    358A  GLY*     3.2    11.8    +      -       -      +
    359A  LEU*     3.3    40.4    +      -       +      +
----------------------------------------------------------
 Back to top of page


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