Contacts of the strand formed by residues 243 - 251 (chain A) in PDB entry 3LX7


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 CYS 243 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  GLN*     5.7     6.3    -      -       +      -
    175A  TRP      3.6     7.0    -      -       -      +
    176A  ILE*     4.7    11.2    -      -       -      -
    237A  LEU*     3.6     4.9    -      -       -      +
    238A  TYR*     2.9    28.8    +      -       -      +
    241A  THR*     3.2    10.4    +      -       -      +
    242A  THR*     1.3    89.0    -      -       -      +
    244A  PHE*     1.3    59.8    +      -       -      +
    245A  TYR*     3.6    32.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  ALA*     3.7    23.3    -      -       +      -
    174A  GLN*     6.0     0.2    -      -       -      +
    175A  TRP*     2.9    38.0    +      -       +      +
    176A  ILE      3.8    14.6    -      -       -      -
    177A  LEU*     3.7    31.9    -      -       +      -
    213A  LEU*     3.8    31.0    -      -       +      -
    235A  LEU*     4.1    17.1    -      -       +      +
    236A  ALA*     3.3    12.1    -      -       -      -
    237A  LEU*     3.5    33.4    -      -       +      -
    243A  CYS*     1.3    73.0    -      -       -      +
    245A  TYR*     1.3    71.6    +      -       -      +
    283A  TYR*     3.5    22.7    -      +       -      -
    285A  VAL*     5.0     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  LEU*     3.5     8.0    -      -       -      -
    236A  ALA      2.9    29.2    +      -       -      +
    238A  TYR*     3.7    37.7    -      +       +      -
    241A  THR*     5.0     1.1    -      -       +      -
    243A  CYS*     3.6    33.0    -      -       +      +
    244A  PHE*     1.3    79.7    -      -       -      +
    246A  ARG*     1.3    66.4    +      -       -      +
    247A  ALA      3.5     0.3    +      -       -      -
    264A  PHE*     3.8    18.0    -      -       +      -
    265A  GLU      5.7     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  LEU*     3.5    32.0    -      -       +      +
    234A  VAL      3.3     6.1    -      -       -      -
    235A  LEU*     3.8     7.7    -      -       +      +
    245A  TYR*     1.3    75.3    -      -       -      +
    247A  ALA*     1.3    58.8    +      -       -      +
    264A  PHE*     3.7     4.9    -      -       -      +
    265A  GLU*     3.0    65.5    +      -       +      +
    287A  CYS*     3.7    27.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  LEU*     3.4     7.5    -      -       -      +
    234A  VAL*     2.8    42.5    +      -       +      +
    236A  ALA*     4.4     1.6    -      -       +      -
    245A  TYR      4.2     1.3    -      -       -      +
    246A  ARG*     1.3    76.0    -      -       -      +
    248A  LEU*     1.3    62.9    +      -       -      +
    262A  VAL*     4.1    15.9    -      -       +      -
    263A  LEU      3.3    17.0    -      -       -      +
    264A  PHE*     3.8    22.0    -      -       +      -
    265A  GLU*     4.2     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  GLU*     3.4    37.5    -      -       -      +
    232A  GLN      3.4     8.7    -      -       -      +
    233A  LEU*     4.0    17.3    -      -       +      +
    247A  ALA*     1.3    75.1    -      -       -      +
    249A  ILE*     1.3    69.2    +      -       -      +
    262A  VAL*     3.3     4.1    -      -       -      -
    263A  LEU*     2.8    48.0    +      -       +      +
    265A  GLU*     5.8     0.9    -      -       -      +
    273A  TYR*     3.3    44.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  PHE*     3.7    17.3    -      -       +      +
    229A  GLN      3.2    32.1    -      -       -      +
    230A  LYS*     3.5     2.6    -      -       -      +
    231A  GLU*     2.8    26.3    +      -       -      -
    232A  GLN*     3.0    15.0    +      -       +      +
    234A  VAL*     3.7    28.9    -      -       +      -
    248A  LEU*     1.3    74.4    -      -       -      +
    250A  HIS*     1.3    60.8    +      -       -      +
    251A  ALA      3.6    26.9    -      -       -      +
    252A  PRO      3.9     3.1    -      -       -      -
    260A  TYR*     3.9    18.8    -      -       +      -
    261A  SER      4.0     2.0    -      -       -      +
    262A  VAL*     3.8    15.5    -      -       +      -
    263A  LEU*     5.2     1.7    -      -       -      +
    284A  VAL*     4.3     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  LYS*     3.3    27.0    -      -       +      +
    248A  LEU      3.4     2.6    +      -       -      -
    249A  ILE*     1.3    76.3    -      -       -      +
    251A  ALA*     1.3    68.5    +      -       +      +
    261A  SER*     2.8    37.1    +      -       -      +
    263A  LEU*     4.0    30.7    -      -       +      -
    276A  PRO*     4.7     7.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  ILE*     3.6     5.1    -      -       -      +
    250A  HIS*     1.3    96.9    -      -       +      +
    252A  PRO*     1.4    75.4    -      -       +      +
    259A  ASP      4.5     0.2    -      -       -      +
    260A  TYR*     3.5     3.1    -      -       -      -
    261A  SER*     2.9    38.3    +      -       -      +
----------------------------------------------------------
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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