Contacts of the strand formed by residues 162 - 167 (chain E) in PDB entry 1LNU


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 TYR 162 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106E  LEU*     4.1    17.5    -      -       +      -
    122E  TRP*     5.3     2.5    -      -       +      -
    123E  LEU      3.0     6.7    -      -       -      +
    124E  ARG*     3.5    47.2    +      -       +      -
    125E  ASN      4.6     0.9    -      -       -      +
    152E  LEU*     4.1    22.0    -      -       +      -
    154E  PHE*     3.2    42.1    -      +       +      +
    155E  ILE      3.6     9.6    +      -       -      -
    156E  PRO*     5.8     0.7    -      -       +      -
    157E  SER      6.2     0.2    -      -       -      -
    160E  ASP*     4.2    22.0    +      -       -      -
    161E  ILE*     1.3    83.7    -      -       -      +
    163E  ASP*     1.3    62.9    +      -       -      +
    178E  HIS*     3.0    24.4    -      -       -      -
    179E  TRP*     3.1    45.2    +      +       +      +
    181E  PRO*     5.6     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 163 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122E  TRP*     4.4     2.0    -      -       -      -
    123E  LEU*     2.6    54.5    +      -       +      +
    126E  SER      6.0     1.3    -      -       -      +
    161E  ILE*     5.5     0.3    -      -       -      +
    162E  TYR*     1.3    75.5    -      -       -      +
    164E  CYS*     1.3    61.4    +      -       -      +
    176E  LEU*     3.0    37.7    -      -       +      +
    177E  LYS      3.2    19.7    -      -       -      +
    178E  HIS*     2.7    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 164 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  VAL*     3.8    12.1    -      -       +      +
    108E  CYS*     2.0    49.8    -      -       -      -
    120E  ILE*     3.6    21.3    -      -       -      -
    121E  THR      3.8     1.1    -      -       -      -
    122E  TRP*     3.3    26.8    -      -       +      -
    163E  ASP*     1.3    69.8    -      -       -      +
    165E  LYS*     1.3    58.3    +      -       -      +
    166E  VAL*     3.9     7.1    +      -       -      +
    175E  VAL      3.5     5.7    -      -       -      +
    176E  LEU*     3.8     1.8    -      -       -      -
    177E  LYS*     3.0    31.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 165 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119E  ASN      3.4     1.2    -      -       -      +
    120E  ILE*     3.2     6.4    -      -       -      +
    121E  THR*     2.6    62.2    +      -       -      +
    123E  LEU*     3.8    29.3    -      -       +      +
    128E  SER*     5.8     1.1    -      -       -      +
    163E  ASP      3.4     0.8    +      -       -      -
    164E  CYS*     1.3    71.7    -      -       -      +
    166E  VAL*     1.3    62.6    +      -       -      +
    167E  GLU*     4.6    12.7    -      -       -      +
    174E  PRO*     4.1    29.7    -      -       +      +
    175E  VAL      3.8     2.0    -      -       -      -
    176E  LEU*     4.0    17.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 166 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88E  PRO*     4.4     7.4    -      -       +      -
     89E  GLN      5.2     1.3    -      -       -      +
     90E  ALA*     4.7    13.7    -      -       +      -
    110E  VAL*     4.4    16.6    -      -       +      -
    118E  ILE*     3.4    28.7    -      -       +      -
    119E  ASN      3.3     1.6    -      -       -      -
    120E  ILE*     4.3    10.1    -      -       +      -
    164E  CYS*     4.2    19.5    -      -       -      +
    165E  LYS*     1.3    78.3    -      -       -      +
    167E  GLU*     1.3    65.8    +      -       -      +
    171E  LEU*     3.5    15.4    -      -       +      +
    174E  PRO*     3.1     5.5    -      -       -      +
    175E  VAL*     2.8    48.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 167 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118E  ILE*     3.2     6.3    -      -       -      +
    119E  ASN*     3.0    49.4    +      -       +      +
    121E  THR*     4.1    17.0    +      -       -      +
    165E  LYS*     4.6    10.8    -      -       +      +
    166E  VAL*     1.3    78.0    -      -       -      +
    168E  HIS*     1.3    61.2    +      -       -      +
    171E  LEU*     3.8     6.3    -      -       +      -
    174E  PRO*     3.6    25.4    -      -       +      +
    308E  NAG      2.8    30.4    -      -       -      +
----------------------------------------------------------
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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