Contacts of the strand formed by residues 121 - 124 (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 GLY 121 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  LEU      3.8     2.8    +      -       -      -
     64B  ILE*     3.6     1.6    -      -       -      +
     65B  GLY      3.1    23.1    +      -       -      +
    119B  VAL*     3.7     0.6    -      -       -      +
    120B  SER*     1.3    80.7    -      -       -      +
    122B  LEU*     1.3    64.5    +      -       -      -
    123B  ILE      3.8     0.2    +      -       -      -
    143B  VAL*     3.5     5.1    -      -       -      +
    144B  PRO*     3.2    12.8    -      -       -      -
    304B  LEU*     3.6    28.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  GLY*     3.6     2.7    -      -       -      +
    111B  VAL*     4.6     3.8    -      -       +      -
    114B  LEU*     3.6    33.9    -      -       +      -
    115B  LEU*     3.2    37.0    -      -       +      -
    119B  VAL*     3.7     9.0    -      -       +      -
    121B  GLY*     1.3    72.5    -      -       -      +
    123B  ILE*     1.3    56.0    +      -       -      +
    124B  ILE*     3.6    19.9    +      -       +      -
    140B  CYS*     3.5    23.8    -      -       +      -
    143B  VAL*     3.5    22.9    -      -       +      +
    144B  PRO      2.8     9.2    +      -       -      +
    145B  ALA*     3.0     6.3    -      -       +      +
    146B  LEU      2.7    32.4    +      -       -      -
    304B  LEU*     3.6     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  ILE*     5.1     4.7    -      -       +      -
     65B  GLY      3.0    13.8    +      -       -      +
     66B  VAL*     3.3    11.1    -      -       +      +
     67B  ALA      3.1    22.3    +      -       -      -
     83B  ILE*     3.8    33.2    -      -       +      -
    121B  GLY      4.3     0.2    -      -       -      +
    122B  LEU*     1.3    73.7    -      -       -      +
    124B  ILE*     1.3    60.6    +      -       -      +
    125B  ASN*     3.1     5.0    +      -       +      +
    146B  LEU*     3.5     4.9    -      -       +      +
    148B  LEU*     3.5    42.2    -      -       +      -
    300B  SER*     4.7     4.5    -      -       -      +
    301B  VAL*     4.4    21.3    -      -       +      +
    304B  LEU*     4.1    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  ALA*     4.0    12.8    -      -       +      +
    107B  CYS*     3.3    30.1    -      -       -      -
    111B  VAL*     3.6    25.4    -      -       +      -
    114B  LEU*     5.8     0.7    -      -       +      -
    122B  LEU*     3.6    29.6    -      -       +      +
    123B  ILE*     1.3    69.8    -      -       -      +
    125B  ASN*     1.3    57.1    +      -       -      +
    126B  TYR*     3.1    10.9    +      -       +      +
    128B  LEU*     4.0    17.0    -      -       +      -
    136B  VAL*     4.6     2.9    -      -       +      -
    140B  CYS*     4.7     0.9    -      -       -      -
    145B  ALA*     4.5     4.7    -      -       +      -
    146B  LEU      3.0    10.0    +      -       -      +
    147B  PHE*     3.9    30.7    -      -       +      +
    148B  LEU*     3.3    21.8    +      -       -      +
    149B  ASP      4.1     2.8    +      -       -      -
----------------------------------------------------------
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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