Contacts of the strand formed by residues 116 - 122 (chain A) in PDB entry 5LPN


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 116 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  MET      3.5     8.2    +      -       -      +
     85A  ILE*     2.9    26.3    +      -       -      -
    114A  ASP      3.7     0.2    +      -       -      -
    115A  VAL*     1.3    82.5    -      -       -      +
    117A  ARG*     1.3    63.1    +      -       -      +
    147A  ARG*     6.1     0.5    -      -       -      +
    166A  LEU*     3.8    20.6    -      -       +      -
    169A  ASP*     4.0    24.7    -      -       +      +
    170A  ILE*     4.3    11.9    -      -       +      -
    173A  LYS*     2.8    40.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  ILE*     3.4     5.4    -      -       +      -
     87A  LEU*     3.8    16.4    -      -       +      -
    104A  LEU*     3.8    30.1    +      -       -      +
    107A  ILE*     3.3    42.9    -      -       +      +
    108A  ASP*     3.1    30.9    +      -       -      +
    112A  ASN      5.2     1.6    +      -       -      -
    113A  GLU*     4.8    13.3    +      -       -      +
    115A  VAL*     4.0    15.1    +      -       +      +
    116A  GLU*     1.3    80.7    -      -       -      +
    118A  MET*     1.3    61.3    +      -       -      +
    144A  HIS*     6.2     2.1    -      -       -      -
    146A  ILE*     3.1    43.2    -      -       +      +
    147A  ARG*     4.1     3.1    +      -       -      +
    166A  LEU*     5.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  ILE      2.9     7.7    +      -       -      +
     86A  MET*     3.2    31.7    -      -       -      +
     87A  LEU*     2.9    27.8    +      -       -      +
    117A  ARG*     1.3    74.3    -      -       -      +
    119A  LEU*     1.3    63.4    +      -       -      +
    120A  LEU*     4.0     8.7    -      -       +      -
    146A  ILE*     4.6     0.4    -      -       -      -
    147A  ARG*     3.7    31.0    -      -       +      +
    149A  PHE*     3.9    16.6    -      -       +      -
    162A  ALA*     3.3    20.9    -      -       -      +
    165A  THR*     3.6    31.6    -      -       +      -
    166A  LEU*     3.6    24.4    -      -       +      +
    169A  ASP*     4.4     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  LEU*     3.5    11.0    -      -       +      +
     89A  TYR*     3.9    19.1    -      -       +      -
    100A  ILE*     3.7    40.8    -      -       +      -
    104A  LEU*     6.5     0.2    -      -       +      -
    118A  MET*     1.3    73.0    -      -       -      +
    120A  LEU*     1.3    65.9    +      -       -      +
    137A  GLY      3.6    17.0    -      -       -      +
    140A  ILE*     3.7    17.5    -      -       +      -
    141A  ALA*     4.4     4.7    -      -       +      -
    146A  ILE*     4.1    14.0    -      -       +      +
    147A  ARG      2.9    14.8    +      -       -      +
    148A  PHE*     3.4    26.2    -      -       +      -
    149A  PHE      2.9    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     5.8     0.4    -      -       +      -
     25A  VAL*     4.6    20.6    -      -       +      -
     86A  MET*     3.9    34.8    -      -       +      -
     87A  LEU      2.8    15.3    +      -       -      +
     88A  VAL*     3.3    17.5    -      -       +      +
     89A  TYR*     2.9    32.9    +      -       -      +
    118A  MET*     4.0    15.3    -      -       +      -
    119A  LEU*     1.3    85.6    -      -       -      +
    121A  GLY*     1.3    60.0    +      -       -      +
    122A  ASN      3.7     0.2    -      -       -      -
    149A  PHE*     3.4    23.8    -      -       +      +
    151A  THR*     4.1    19.3    -      -       +      +
    162A  ALA*     4.0    12.6    -      -       +      -
    163A  PHE*     5.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  TYR*     3.6    33.7    -      -       -      -
     91A  ILE*     3.7    10.6    -      -       -      +
    120A  LEU*     1.3    69.4    -      -       -      +
    122A  ASN*     1.3    65.3    +      -       -      +
    124A  CYS      4.5     0.3    +      -       -      -
    148A  PHE*     3.9     2.1    -      -       -      -
    149A  PHE      2.9    13.0    +      -       -      -
    150A  GLU*     3.3     7.4    -      -       -      +
    151A  THR      2.9    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  VAL      2.9    29.1    +      -       -      +
     21A  GLY*     3.5     7.9    -      -       -      -
     25A  VAL*     3.7    17.4    -      -       -      +
     88A  VAL*     4.1     9.2    -      -       +      -
     89A  TYR      2.9    14.1    +      -       -      +
     90A  ASP*     3.8     0.7    -      -       -      +
     91A  ILE*     3.2    25.5    +      -       -      +
    120A  LEU      3.7     1.2    +      -       -      -
    121A  GLY*     1.3    71.1    -      -       -      +
    123A  LYS*     1.3    77.7    +      -       -      +
    151A  THR*     3.1    24.0    +      -       -      +
    153A  ALA      3.4     9.2    +      -       -      -
    202A  GNP      3.2    31.7    +      -       -      +
----------------------------------------------------------
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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