Contacts of the strand formed by residues 240 - 244 (chain B) in PDB entry 1LBI


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 THR 240 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179B  HIS*     2.7    47.1    +      -       -      +
    180B  GLN      4.4     0.2    +      -       -      -
    181B  GLN*     2.7    31.8    +      -       +      -
    238B  VAL      4.9     2.2    -      -       -      +
    239B  PRO*     1.3    76.5    -      -       -      +
    241B  ALA*     1.3    53.5    +      -       -      +
    267B  ASP      3.6    13.4    -      -       -      +
    268B  ILE*     3.6     1.1    -      -       -      -
    269B  SER      2.7    29.4    +      -       -      -
    332B  PRO*     3.8    19.9    -      -       +      +
    333B  ASN*     4.2    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 241 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  LEU*     3.6    33.7    -      -       +      -
    179B  HIS*     3.4    19.7    -      -       +      +
    181B  GLN      3.4     1.2    +      -       -      -
    182B  ILE*     3.0    13.1    -      -       +      -
    183B  ALA      2.7    30.5    +      -       -      -
    239B  PRO*     3.2     4.0    -      -       -      +
    240B  THR*     1.3    84.8    +      -       -      +
    242B  MET*     1.3    58.6    +      -       -      +
    269B  SER*     3.5     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 242 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  LEU*     4.3     4.3    -      -       -      +
    183B  ALA*     3.3    10.8    -      -       +      +
    184B  LEU      5.8     0.7    -      -       -      -
    185B  LEU*     4.5    19.1    -      -       +      +
    216B  ARG*     6.4     0.7    -      -       -      -
    229B  THR*     3.2    43.5    -      -       +      +
    232B  MET*     4.2    20.2    -      -       +      -
    239B  PRO*     4.1     7.0    -      -       +      -
    241B  ALA*     1.3    78.1    -      -       -      +
    243B  LEU*     1.3    66.4    +      -       -      +
    244B  VAL*     3.9    11.0    -      -       +      -
    253B  ALA*     4.2     9.9    -      -       +      -
    257B  ILE*     3.9    15.5    -      -       -      -
    268B  ILE*     3.7    10.3    -      -       +      -
    269B  SER      3.0    18.0    +      -       -      +
    270B  VAL*     3.7     4.7    -      -       +      -
    271B  VAL      3.3    22.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 243 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170B  GLY*     3.9    17.5    -      -       -      -
    171B  VAL*     3.8    24.9    -      -       +      -
    174B  LEU*     3.6    27.4    -      -       +      -
    182B  ILE*     3.6    15.0    -      -       +      -
    183B  ALA      2.8     8.5    +      -       -      -
    184B  LEU*     3.3    32.3    -      -       +      -
    185B  LEU      2.9    23.7    +      -       -      +
    201B  TRP*     3.8    34.1    +      -       +      -
    205B  LEU*     3.8     4.7    -      -       +      -
    242B  MET*     1.3    73.4    -      -       -      +
    244B  VAL*     1.3    60.3    +      -       -      +
    271B  VAL*     4.1    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 244 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  LEU*     3.4    29.4    -      -       +      +
    201B  TRP*     3.9    10.0    -      -       -      -
    242B  MET*     4.3    17.3    -      -       +      -
    243B  LEU*     1.3    75.5    -      -       -      +
    245B  ALA*     1.3    64.2    +      -       -      +
    246B  ASN      3.2    26.3    +      -       -      +
    249B  MET*     3.8    21.5    -      -       +      -
    250B  ALA*     3.9    11.0    -      -       +      +
    253B  ALA*     4.4    11.7    -      -       +      -
    270B  VAL*     4.4     9.6    -      -       +      -
    271B  VAL      3.1    19.7    +      -       -      +
    272B  GLY*     3.8     2.3    -      -       -      -
    273B  TYR*     3.7    12.3    -      -       -      +
----------------------------------------------------------
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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