Contacts of the strand formed by residues 84 - 89 (chain A) in PDB entry 1LPB


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 PHE 84 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  CYS      3.5    15.0    -      -       -      +
     50A  SER*     4.2     9.9    -      -       -      -
     59A  TYR*     3.8    26.7    -      +       +      -
     60A  LYS*     3.6    43.3    -      -       +      +
     69A  CYS*     4.6     0.7    -      -       -      -
     71A  GLY*     3.5    16.3    -      -       -      -
     72A  ASP      3.8     9.1    +      -       -      +
     81A  ASN      4.0     7.4    -      -       -      -
     82A  THR*     2.8    47.3    +      -       +      +
     83A  ASN*     1.3    79.3    -      -       -      +
     85A  GLY*     1.3    58.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  GLU*     3.5     9.0    -      -       -      +
     49A  CYS*     3.0    29.9    +      -       -      +
     69A  CYS*     3.7     5.6    -      -       -      -
     70A  GLU      2.9    20.2    -      -       -      -
     71A  GLY*     3.8     2.5    -      -       -      -
     84A  PHE*     1.3    76.6    -      -       -      +
     86A  ILE*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  ASN*     3.3    37.5    -      -       -      +
     47A  SER      3.3     9.0    -      -       -      +
     48A  GLU*     4.7     9.4    -      -       +      -
     49A  CYS*     3.4     5.4    -      -       -      -
     70A  GLU*     2.8    28.8    +      -       -      +
     85A  GLY*     1.3    77.4    -      -       -      +
     87A  CYS*     1.3    66.7    +      -       -      +
     88A  HIS*     3.3    31.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ALA*     3.4    28.9    -      -       -      -
     44A  ARG      3.3    20.4    -      -       -      +
     45A  GLU*     3.7     9.7    -      -       -      +
     46A  ASN*     2.7    26.0    +      -       -      +
     47A  SER      3.0     9.9    +      -       -      +
     49A  CYS*     3.5     5.2    -      -       -      -
     63A  CYS*     2.0    53.8    -      -       +      -
     67A  LEU*     4.1     4.3    -      -       +      -
     68A  THR      3.6     0.2    -      -       -      -
     86A  ILE*     1.3    71.7    -      -       -      +
     88A  HIS*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLU*     4.8     0.7    -      -       +      -
     46A  ASN*     3.7    16.5    +      -       -      -
     67A  LEU*     3.7     5.6    -      -       -      -
     68A  THR*     2.8    37.2    +      -       -      +
     70A  GLU*     2.9    43.2    +      -       +      +
     86A  ILE*     3.8    34.0    +      -       +      +
     87A  CYS*     1.3    83.0    -      -       -      +
     89A  ASN*     1.3    64.3    +      -       -      +
     90A  VAL      3.1     5.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLU*     3.9    11.9    +      -       -      +
     66A  GLY      4.1     2.8    +      -       -      -
     67A  LEU*     4.1     7.9    -      -       -      +
     88A  HIS*     1.3    71.8    -      -       -      +
     90A  VAL*     1.3    82.6    +      -       -      +
    399B  LYS*     3.0    34.3    +      -       -      +
    442B  VAL*     6.1     0.8    -      -       -      +
    443B  LEU*     3.5    41.5    +      -       -      +
    445B  THR*     3.7     7.4    +      -       -      -
----------------------------------------------------------
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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