Contacts of the strand formed by residues 90 - 96 (chain L) in PDB entry 4WEB


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 90 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43L  GLN*     3.6    20.9    -      -       +      -
     44L  GLN      3.4    17.0    -      -       -      +
     45L  LYS*     4.0     4.0    -      -       +      +
     46L  PRO*     4.4     4.0    -      -       -      -
     88L  ASP      3.3    10.6    +      -       -      +
     89L  LEU*     1.3    79.3    -      -       -      +
     91L  ASP*     1.3    68.7    +      -       -      +
     92L  TYR*     3.6    12.6    -      -       +      -
    109L  LYS*     4.5     1.1    -      -       -      +
    110L  LEU*     2.9    32.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 91 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  GLN*     5.5     1.4    +      -       -      -
     42L  TYR      3.9     0.3    -      -       -      +
     43L  GLN*     3.7     1.2    -      -       -      -
     44L  GLN*     2.8    46.8    +      -       +      +
     90L  ALA*     1.3    75.1    -      -       -      +
     92L  TYR*     1.3    61.8    +      -       -      +
     93L  PHE*     3.7    26.1    -      -       +      -
    107L  GLY*     5.7     0.7    -      -       -      -
    108L  THR      3.4     7.4    -      -       -      +
    109L  LYS*     3.5    30.0    +      -       -      +
    301L  ARF      3.4    29.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 92 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  GLN*     2.9     7.0    +      -       -      +
     21L  MET*     3.5    33.2    -      -       +      -
     41L  TRP*     5.0     1.8    -      -       +      -
     42L  TYR      3.2     7.4    -      -       -      -
     43L  GLN*     2.9    26.7    +      -       +      -
     53L  LEU*     3.6    32.5    -      -       +      -
     68L  PHE*     3.7    16.1    -      +       -      -
     79L  LEU*     3.9    14.6    -      -       +      -
     81L  ILE*     3.8    10.4    -      -       +      +
     88L  ASP*     2.8    29.9    +      -       -      +
     90L  ALA*     3.6    13.5    -      -       +      -
     91L  ASP*     1.3    75.3    -      -       -      +
     93L  PHE*     1.3    62.1    +      -       -      +
    107L  GLY*     3.1     3.5    -      -       -      -
    108L  THR      2.8    36.5    +      -       -      +
    110L  LEU*     3.7    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 93 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  GLN*     4.3     4.7    -      -       -      -
     43H  GLN      4.7     2.0    -      -       -      -
     44H  GLY*     3.9    25.4    -      -       -      -
     45H  LEU*     3.7    30.3    -      -       +      -
      6L  GLN*     3.5     1.3    -      -       -      -
     41L  TRP*     3.4     7.6    -      -       -      -
     42L  TYR*     2.7    48.2    +      -       +      +
     44L  GLN*     3.5    28.9    -      -       +      -
     50L  PRO*     5.7     0.2    -      -       +      -
     91L  ASP*     3.7    31.9    -      -       +      -
     92L  TYR*     1.3    74.7    -      -       -      +
     94L  CYS*     1.3    65.8    +      -       -      +
    104L  PHE*     4.4     5.8    -      -       +      -
    105L  GLY      3.5    17.3    -      -       -      -
    106L  GLY      3.8     9.0    -      -       -      -
    107L  GLY*     3.6    18.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 94 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  MET*     4.0     7.4    -      -       -      -
      6L  GLN*     3.1    25.3    +      -       -      +
     23L  CYS*     2.1    48.0    -      -       +      -
     39L  LEU*     4.2     4.9    -      -       +      -
     40L  ALA      3.2     9.2    -      -       -      +
     41L  TRP*     3.6    17.3    -      -       +      -
     93L  PHE*     1.3    75.9    -      -       -      +
     95L  GLN*     1.3    59.1    +      -       -      +
    104L  PHE*     3.2     7.2    -      -       -      +
    105L  GLY*     2.6    37.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 95 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47H  TRP*     4.7     3.2    -      -       -      -
    103H  TYR      4.4     2.9    +      -       -      +
    105H  LEU*     4.3    12.1    -      -       -      +
      4L  MET*     4.7     0.7    -      -       -      -
     39L  LEU*     3.6     5.8    -      -       -      -
     40L  ALA*     2.8    36.2    +      -       -      +
     42L  TYR*     2.6    35.3    +      -       +      -
     94L  CYS*     1.3    74.8    -      -       -      +
     96L  GLN*     1.3    69.7    +      -       -      +
     97L  HIS*     3.4    13.5    +      -       -      +
    102L  TYR*     3.2    32.1    +      -       -      +
    103L  THR      3.3    17.3    -      -       -      +
    104L  PHE*     3.4    38.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 96 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2L  ILE*     3.8    24.4    -      -       +      +
      4L  MET*     3.8    18.0    -      -       -      +
     29L  LEU*     3.6    31.2    -      -       +      -
     38L  TYR      3.5     6.5    -      -       -      +
     95L  GLN*     1.3    74.7    -      -       -      +
     97L  HIS*     1.3    57.3    +      -       -      +
     98L  TYR*     2.8    27.0    +      -       -      +
     99L  SER*     3.0    19.1    +      -       -      -
    101L  PRO*     3.0    19.4    +      -       -      +
    102L  TYR*     3.4    17.0    -      -       -      +
    103L  THR*     2.9    38.6    +      -       -      +
----------------------------------------------------------
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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