Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 1LEI


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 LYS 92 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ALA*     1.3    76.5    -      -       -      +
     93B  VAL*     1.3    62.9    +      -       -      +
     94B  ILE*     4.0    13.4    +      -       +      -
    122B  THR*     3.7    24.7    -      -       +      -
    123B  VAL      3.7    12.8    -      -       -      +
    124B  THR*     5.8     0.7    -      -       +      -
    161B  ARG*     4.9     5.3    -      -       -      +
    163B  TYR*     4.0    26.8    -      -       -      +
    215B  THR      4.0     0.3    -      -       -      +
    216B  ALA*     3.4     1.9    -      -       -      +
    217B  PHE*     2.7    51.7    +      -       +      +
    225B  PHE*     3.7    43.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  LEU*     4.7    10.3    -      -       +      -
     82B  VAL*     4.9    11.0    -      -       +      -
     84B  ILE*     3.7    22.2    -      -       +      -
     92B  LYS*     1.3    78.8    -      -       -      +
     94B  ILE*     1.3    72.7    +      -       -      +
    121B  CYS      4.5     0.2    -      -       -      +
    123B  VAL*     2.9    48.0    +      -       +      +
    124B  THR*     5.1     0.6    -      -       -      +
    125B  ALA*     5.0     1.1    -      -       +      -
    132B  VAL*     4.8    13.9    -      -       +      -
    134B  PHE*     4.4    15.7    -      -       +      -
    214B  PHE*     5.3     0.9    -      -       +      -
    215B  THR      3.3    13.5    -      -       -      +
    216B  ALA*     3.7    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  LYS*     4.0    24.0    -      -       -      -
     93B  VAL*     1.3    84.8    -      -       -      +
     95B  VAL*     1.3    69.7    +      -       -      +
     96B  GLN*     4.7     6.7    -      -       -      +
    120B  VAL*     4.4     5.8    -      -       +      -
    121B  CYS      3.3    11.2    -      -       -      +
    122B  THR*     3.8    17.9    -      -       +      +
    134B  PHE*     5.2     0.7    -      -       -      -
    163B  TYR*     2.8    51.4    -      -       +      +
    164B  ASN*     4.3     5.2    -      -       -      +
    213B  MET      5.4     0.4    -      -       -      +
    214B  PHE*     3.7     2.9    -      -       -      -
    215B  THR*     2.8    44.5    +      -       -      +
    217B  PHE*     3.6    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  ILE*     1.3    82.2    -      -       -      +
     96B  GLN*     1.3    64.8    +      -       -      +
    111B  LEU*     3.5    20.5    -      -       +      +
    120B  VAL*     2.9    21.5    -      -       -      +
    121B  CYS*     3.0    35.6    +      -       +      +
    134B  PHE*     3.8    17.9    -      -       +      -
    137B  LEU*     5.3     0.7    -      -       +      -
    212B  LEU*     4.1    15.7    -      -       +      -
    213B  MET      3.4    12.6    -      -       -      +
    214B  PHE*     3.7    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  ILE*     4.7     6.2    -      -       +      +
     95B  VAL*     1.3    77.8    -      -       -      +
     97B  LEU*     1.3    67.2    +      -       -      +
     98B  VAL*     4.5     0.2    -      -       +      -
    106B  LEU*     3.1    23.1    -      -       +      +
    111B  LEU*     4.7     1.1    -      -       -      -
    119B  GLY      4.8     1.8    -      -       -      +
    120B  VAL*     4.1    18.1    -      -       +      +
    158B  ALA*     5.3     0.2    -      -       -      +
    163B  TYR      4.4     2.4    +      -       -      -
    164B  ASN*     3.5    26.2    +      -       -      +
    165B  PRO*     3.1    32.9    -      -       -      +
    168B  LEU*     3.4    15.9    -      -       +      +
    213B  MET*     3.1    45.8    +      -       +      +
    215B  THR*     5.1     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  GLN*     1.3    75.2    -      -       -      +
     98B  VAL*     1.3    64.5    -      -       -      +
    106B  LEU*     4.2     7.3    -      -       -      +
    107B  HIS*     3.5    21.7    +      -       +      +
    109B  HIS*     3.3    41.7    -      -       +      +
    110B  SER*     3.4    15.7    -      -       -      +
    111B  LEU*     3.4    35.4    -      -       +      +
    119B  GLY      4.8     2.9    +      -       -      +
    139B  ILE*     3.8    23.3    -      -       +      -
    210B  VAL*     4.7    11.0    -      -       +      -
    211B  ARG      3.1     5.8    -      -       -      +
    212B  LEU*     3.9    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  GLN*     3.8     1.6    -      -       +      +
     97B  LEU*     1.3    82.7    -      -       -      +
     99B  THR*     1.3    63.3    +      -       -      +
    104B  ILE*     4.2    13.2    -      -       +      -
    105B  HIS      3.0    18.8    -      -       -      +
    106B  LEU*     4.6     0.4    -      -       +      -
    107B  HIS*     3.8     8.7    -      -       -      +
    168B  LEU*     4.2    18.8    -      -       +      -
    210B  VAL*     3.5     5.2    -      -       -      -
    211B  ARG*     2.7    62.7    +      -       +      +
    212B  LEU      4.4     2.5    -      -       -      +
    213B  MET*     3.6    32.1    -      -       +      -
    233B  VAL*     4.6     7.0    -      -       +      -
----------------------------------------------------------
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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