Contacts of the strand formed by residues 263 - 272 (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 263 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  GLN      4.1     3.4    -      -       -      +
    258A  MET*     3.8    24.9    -      -       -      +
    261A  ARG*     3.6    11.9    -      -       +      +
    262A  LEU*     1.3    79.4    -      -       -      +
    264A  PRO*     1.3    75.6    -      -       +      +
    283A  LEU*     3.8     3.8    -      -       -      -
    355A  ALA*     3.1     2.4    -      -       -      -
    356A  THR*     2.9    39.2    +      -       -      +
    359A  LEU*     5.2     2.9    -      -       +      -
    360A  PHE*     3.6    30.3    -      -       +      -
    429A  MET*     3.8    14.4    -      -       +      -
    432A  PHE*     4.0     5.2    -      -       +      -
    433A  ILE*     4.0    23.1    -      -       +      -
    436A  TRP*     4.0    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263A  LEU*     1.3    88.5    -      -       +      +
    265A  TYR*     1.3    63.6    +      -       -      +
    283A  LEU*     3.6    17.0    -      -       +      -
    353A  PHE*     3.9    29.6    -      -       +      -
    354A  LYS      3.3     7.9    -      -       -      +
    359A  LEU*     4.3     0.2    -      -       -      +
    426A  TYR*     3.6     3.9    -      -       -      -
    428A  PRO*     3.3    33.9    -      -       +      +
    429A  MET*     3.0    31.6    -      -       -      +
    432A  PHE*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  LYS      5.3     0.7    -      -       -      -
    210A  VAL*     3.4    43.3    -      -       +      -
    211A  PHE*     4.6     0.2    -      -       +      -
    264A  PRO*     1.3    77.6    -      -       -      +
    266A  GLY*     1.3    66.1    +      -       -      +
    353A  PHE*     4.6     1.0    -      -       -      +
    354A  LYS*     3.2    61.4    +      -       +      +
    355A  ALA*     3.7    33.8    +      -       -      -
    356A  THR*     3.7    24.9    -      -       +      -
    359A  LEU*     4.1     4.0    -      -       +      -
    426A  TYR*     3.1    14.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  LYS      4.4     4.7    -      -       -      -
    210A  VAL      2.9    19.1    +      -       -      -
    212A  PRO*     3.7    13.6    -      -       -      +
    265A  TYR*     1.3    81.0    -      -       -      +
    267A  GLU*     1.3    64.3    -      -       -      -
    268A  PRO*     3.6     4.3    -      -       -      +
    353A  PHE*     4.8     0.3    -      -       -      -
    354A  LYS*     4.2    10.3    -      -       -      -
    426A  TYR*     2.5    30.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  PRO*     3.9    19.7    -      -       +      +
    213A  THR      4.6     6.1    -      -       -      +
    214A  LEU*     3.7    23.2    -      -       -      +
    218A  LEU*     4.6     5.9    -      -       -      +
    265A  TYR      5.0     0.5    -      -       -      +
    266A  GLY*     1.3    70.9    -      -       -      -
    268A  PRO*     1.3    78.5    -      -       +      +
    269A  ILE*     3.9     1.6    +      -       -      +
    281A  TYR*     4.0    18.5    +      -       -      -
    353A  PHE*     5.2     1.7    -      -       -      -
    354A  LYS*     4.7     8.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  LEU*     3.5    25.6    -      -       +      -
    218A  LEU*     3.5    30.1    -      -       +      +
    266A  GLY      3.6     3.8    -      -       -      +
    267A  GLU*     1.3    99.9    -      -       +      +
    269A  ILE*     1.3    62.4    +      -       -      +
    270A  VAL*     4.1     3.2    +      -       +      +
    351A  LEU*     4.4    11.9    -      -       +      -
    352A  LYS      3.3    10.1    -      -       -      +
    353A  PHE*     3.6    32.1    -      -       +      -
    426A  TYR*     5.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 269 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  GLU      4.7     1.3    -      -       -      +
    268A  PRO*     1.3    74.6    -      -       -      +
    270A  VAL*     1.3    76.2    +      -       -      +
    271A  PHE*     3.7     2.9    +      -       +      -
    278A  ASP*     5.6     0.2    -      -       -      +
    281A  TYR*     3.3    47.8    -      -       +      +
    351A  LEU*     3.7     1.9    -      -       -      -
    352A  LYS*     3.0    52.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  LEU*     4.2    15.9    -      -       +      -
    221A  GLU*     5.5     1.3    -      -       -      +
    268A  PRO      4.1     3.3    +      -       -      +
    269A  ILE*     1.3    83.5    -      -       -      +
    271A  PHE*     1.3    73.3    +      -       -      +
    272A  GLU*     5.7     3.8    -      -       +      -
    349A  SER*     5.5     3.6    -      -       -      +
    350A  GLY      3.7     7.6    -      -       -      +
    351A  LEU*     3.5    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ILE*     4.1     0.9    -      -       +      +
    270A  VAL*     1.3    79.8    -      -       -      +
    272A  GLU*     1.3    69.5    +      -       -      +
    273A  GLY      3.3    24.0    -      -       -      -
    274A  LYS      4.4     0.9    -      -       -      -
    275A  TYR*     3.5    29.4    -      +       +      -
    284A  HIS*     4.1     6.1    -      +       +      -
    286A  GLN*     3.5    17.9    -      -       -      -
    349A  SER*     3.1    21.5    -      -       -      -
    350A  GLY*     3.1    32.1    +      -       -      +
    351A  LEU      3.4    26.0    -      -       -      -
    352A  LYS*     3.5    36.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 272 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  VAL*     5.7     3.8    -      -       +      -
    271A  PHE*     1.3    82.8    -      -       -      +
    273A  GLY*     1.3    66.8    +      -       -      +
    274A  LYS      3.7     3.8    +      -       -      +
    348A  ILE      4.6     1.6    -      -       -      +
    349A  SER*     4.0     8.1    -      -       -      -
----------------------------------------------------------
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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