Contacts of the strand formed by residues 228 - 233 (chain B) in PDB entry 4LXZ


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 ALA 228 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  GLU*     4.3     6.3    -      -       +      +
    193B  TYR*     3.8    22.2    -      -       +      +
    200B  THR*     3.5    15.9    -      -       -      +
    218B  ASP      3.8     6.1    -      -       -      +
    219B  ILE*     3.3    42.4    +      -       -      +
    220B  GLY*     3.7     6.5    -      -       -      +
    226B  TYR      4.5     2.4    -      -       -      -
    227B  TYR*     1.3    78.7    -      -       -      +
    229B  VAL*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 229 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  GLU*     5.0     0.7    +      -       -      +
    199B  MET*     4.1    24.2    -      -       +      -
    200B  THR*     2.7    17.0    +      -       -      +
    201B  VAL*     3.4    23.1    -      -       +      -
    202B  SER      2.9    25.6    +      -       -      -
    219B  ILE*     6.2     0.4    -      -       -      -
    226B  TYR      4.6     6.3    -      -       -      +
    228B  ALA*     1.3    78.1    -      -       -      +
    230B  ASN*     1.3    69.5    +      -       -      +
    231B  PHE*     5.3     0.4    -      -       +      +
    249B  ILE*     4.8     6.3    -      -       +      -
    253B  VAL*     5.0     2.2    -      -       +      -
    371B  LEU*     4.0    33.4    -      -       +      +
    374B  ASN*     6.3     2.9    -      -       +      -
    375B  LEU*     4.3    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 230 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  HIS*     2.9    28.5    +      -       -      -
    189B  GLU*     2.8    23.6    +      -       -      +
    202B  SER*     3.4     5.2    -      -       -      -
    204B  HIS*     3.3     4.1    -      -       +      -
    214B  GLY*     3.6    17.7    -      -       -      +
    215B  ASP      3.5    20.4    +      -       -      +
    216B  LEU*     3.8     7.7    +      -       -      -
    218B  ASP*     3.0    30.1    +      -       -      +
    228B  ALA      4.5     0.2    +      -       -      -
    229B  VAL*     1.3    80.4    -      -       -      +
    231B  PHE*     1.3    59.9    +      -       -      +
    232B  PRO*     3.4     9.6    -      -       -      +
    371B  LEU*     3.6    20.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 231 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201B  VAL*     6.4     0.2    -      -       +      -
    202B  SER      2.8    10.0    +      -       -      +
    203B  PHE*     3.6    27.0    -      +       +      -
    204B  HIS*     3.2    24.0    +      -       -      -
    229B  VAL*     5.3     0.6    -      -       +      +
    230B  ASN*     1.3    71.5    -      -       -      +
    232B  PRO*     1.3    78.9    -      -       -      +
    233B  MET*     3.6    12.9    +      -       +      +
    245B  ILE*     3.6    24.5    -      -       +      -
    249B  ILE*     4.4     4.3    -      -       +      -
    363B  TYR*     4.7     0.4    -      +       -      -
    364B  MET*     3.6    51.8    -      -       +      -
    367B  ILE*     3.7    22.9    -      -       +      -
    368B  LYS*     3.9    15.9    -      -       +      -
    371B  LEU*     3.5    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 232 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  HIS*     3.5     8.7    -      -       -      +
    206B  TYR*     3.4    33.9    -      -       +      -
    214B  GLY      4.3     3.1    -      -       -      +
    216B  LEU*     3.9    28.7    -      -       +      +
    230B  ASN      3.4    12.6    -      -       -      +
    231B  PHE*     1.3    91.4    -      -       -      +
    233B  MET*     1.3    55.4    +      -       -      +
    234B  ARG*     4.6     3.1    -      -       -      +
    363B  TYR*     2.6    33.1    +      -       -      +
    367B  ILE*     4.1    17.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 233 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203B  PHE*     3.9    20.6    -      -       +      -
    204B  HIS      2.7    15.9    +      -       -      +
    205B  LYS*     3.2     8.2    -      -       -      +
    206B  TYR      3.2    24.8    +      -       -      +
    231B  PHE*     3.8    14.6    -      -       +      +
    232B  PRO*     1.3    78.9    -      -       -      +
    234B  ARG*     1.3    66.2    +      -       -      +
    237B  ILE*     3.7    22.7    -      -       +      -
    242B  TYR*     3.7    34.5    -      -       +      -
    245B  ILE*     3.6    30.7    -      -       +      -
    279B  PHE*     3.7    23.3    -      -       +      -
    359B  ASN*     3.7     8.3    -      -       -      +
    363B  TYR*     4.2     0.2    -      -       -      -
    364B  MET*     4.2     0.4    -      -       +      -
----------------------------------------------------------
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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