Contacts of the strand formed by residues 5 - 9 (chain B) in PDB entry 4L57


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 VAL 5 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  SER*     1.3    73.9    -      -       -      +
      6B  ARG*     1.3    62.5    +      -       -      +
      7B  VAL*     4.2    17.0    -      -       +      -
     92B  ASP      2.9     7.7    +      -       -      -
     93B  THR*     3.3     7.3    -      -       +      +
     94B  GLN*     2.9    24.3    +      -       -      +
    140B  ASP*     3.4    21.8    -      -       +      +
    141B  LEU*     4.5     7.2    -      -       +      -
    191B  LEU*     4.2     7.2    -      -       +      +
    194B  LYS*     3.7    33.4    -      -       +      +
    195B  ARG*     3.7    38.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 6 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  SER*     4.0     2.6    +      -       -      +
      5B  VAL*     1.3    71.9    -      -       -      +
      7B  VAL*     1.3    62.9    +      -       -      +
      8B  LEU*     4.3     8.7    -      -       +      -
     94B  GLN*     3.3    18.4    -      -       +      +
     96B  PHE*     3.7    37.3    -      -       +      -
    137B  VAL*     6.0     0.4    -      -       -      -
    138B  LEU*     2.8    60.5    +      -       -      +
    139B  GLY*     3.8     5.2    -      -       -      +
    140B  ASP*     2.8    42.8    +      -       -      +
    141B  LEU      3.3     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 7 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  VAL*     4.2    13.0    -      -       +      +
      6B  ARG*     1.3    76.8    -      -       -      +
      8B  LEU*     1.3    65.2    +      -       -      +
      9B  VAL*     3.8     7.3    +      -       +      -
     87B  MET*     3.8    21.1    -      -       -      -
     93B  THR*     4.6     2.2    -      -       +      -
     94B  GLN      2.8    12.9    +      -       -      +
     95B  VAL*     3.4     4.9    -      -       -      +
     96B  PHE      3.0    25.8    +      -       -      +
    141B  LEU*     3.7    12.1    -      -       +      -
    143B  ILE*     3.8    31.9    -      -       +      -
    191B  LEU*     3.8    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  ARG*     4.3    17.9    -      -       +      -
      7B  VAL*     1.3    75.2    -      -       -      +
      9B  VAL*     1.3    62.2    +      -       -      +
     10B  ASP      4.0     0.2    -      -       -      -
     96B  PHE*     3.5    24.5    -      -       +      -
     98B  CYS*     4.1    14.1    -      -       +      -
    134B  LYS*     4.7     0.7    -      -       +      +
    137B  VAL*     3.7    36.8    -      -       +      +
    138B  LEU      4.6     0.7    -      -       -      +
    139B  GLY*     4.6     6.1    -      -       -      +
    141B  LEU      2.9    15.4    +      -       -      +
    142B  LEU*     3.3    18.8    -      -       +      +
    143B  ILE      2.9    26.9    +      -       -      -
    158B  TRP*     3.5    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  VAL*     3.8    20.0    -      -       +      -
      8B  LEU*     1.3    76.1    -      -       -      +
     10B  ASP*     1.3    73.6    +      -       -      +
     14B  VAL*     3.9    16.6    -      -       +      -
     15B  LEU*     3.9    20.9    -      -       +      -
     84B  VAL*     4.2     7.0    -      -       +      -
     87B  MET*     4.2    12.1    -      -       +      -
     95B  VAL*     4.0    22.9    -      -       +      -
     96B  PHE      2.8    13.4    +      -       -      +
     97B  ILE*     3.2     9.3    -      -       +      +
     98B  CYS*     2.9    22.6    +      -       -      +
    143B  ILE*     4.0     7.0    -      -       +      +
    183B  TRP*     4.1     8.1    -      -       +      -
----------------------------------------------------------
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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