Contacts of the strand formed by residues 85 - 91 (chain B) in PDB entry 1SL2


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 GLU 85 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  PHE*     3.0     9.8    -      -       -      -
     82B  LYS*     2.7    39.5    +      -       -      +
     83B  ASN      5.0     3.0    -      -       -      +
     84B  GLY*     1.3    85.8    -      -       -      +
     86B  VAL*     1.3    65.1    +      -       -      +
     87B  ALA      3.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  TYR*     4.0    15.0    -      -       +      -
     79B  LEU*     3.8    23.3    -      -       +      -
     80B  LEU      3.2     6.5    -      -       -      +
     81B  PHE*     3.5    30.1    -      -       +      -
     85B  GLU*     1.3    74.9    -      -       -      +
     87B  ALA*     1.3    62.2    +      -       -      +
     88B  ALA      3.5    24.0    -      -       -      +
     89B  THR*     4.7     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  LEU*     2.7    24.3    +      -       +      +
     82B  LYS*     4.3    20.9    -      -       +      -
     85B  GLU      3.4     1.2    +      -       -      -
     86B  VAL*     1.3    75.4    -      -       -      +
     88B  ALA*     1.3    61.2    +      -       +      +
    106B  ASN*     5.5     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  LEU*     6.1     2.2    -      -       +      -
     78B  LEU      4.2     0.2    -      -       -      +
     80B  LEU*     3.0    30.6    +      -       +      +
     86B  VAL*     3.5     7.2    -      -       -      +
     87B  ALA*     1.3    80.9    -      -       +      +
     89B  THR*     1.3    68.3    +      -       -      +
    102B  PHE*     3.5    22.9    -      -       +      -
    106B  ASN*     3.5    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  THR      4.7     7.6    +      -       -      +
    318A  ARG      3.9     2.6    -      -       -      +
    319A  GLU*     3.3    40.1    +      -       +      +
     77B  THR*     4.6     2.6    -      -       -      +
     78B  LEU      3.4     5.9    +      -       -      -
     79B  LEU*     3.5    24.8    -      -       +      +
     86B  VAL*     4.7     6.3    -      -       +      -
     88B  ALA*     1.3    80.6    -      -       -      +
     90B  LYS*     1.3    73.9    +      -       -      +
     91B  VAL*     4.6     4.0    -      -       -      +
    102B  PHE*     4.1     3.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  GLY      3.0    23.5    +      -       -      -
    297A  ILE*     4.0    10.2    -      -       +      +
    315A  LEU*     5.7     0.4    -      -       -      +
    316A  ASP*     3.2    12.9    +      -       -      +
    318A  ARG      2.7    24.5    +      -       -      +
    319A  GLU      3.4     4.7    -      -       -      +
    320A  TYR      3.8     6.0    +      -       -      -
    321A  VAL*     3.4    28.9    -      -       +      -
     77B  THR*     3.9     0.3    -      -       -      -
     78B  LEU*     2.7    46.0    +      -       +      +
     89B  THR*     1.3    81.8    +      -       -      +
     91B  VAL*     1.3    62.9    +      -       -      +
     94B  LEU*     3.8    29.6    -      -       +      -
    102B  PHE*     3.7    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  GLU*     2.6    48.9    +      -       +      +
    320A  TYR*     4.0    23.1    -      -       +      +
    321A  VAL      4.5     2.8    +      -       -      -
    324A  ALA*     4.5     5.2    -      -       -      +
    326A  TYR*     3.9    19.7    -      -       +      +
     74B  GLY*     3.7    27.1    -      -       -      +
     76B  PRO      3.5    11.0    -      -       -      +
     77B  THR*     4.1    16.8    -      -       +      +
     89B  THR*     4.6     2.0    -      -       -      +
     90B  LYS*     1.3    81.0    -      -       -      +
     92B  GLY*     1.3    63.4    +      -       -      +
     94B  LEU*     5.1     2.0    -      -       -      +
----------------------------------------------------------
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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