Contacts of the strand formed by residues 91 - 94 (chain G) 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 THR 91 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89G  GLN*     5.5     4.5    +      -       -      +
     90G  ALA*     1.3    79.7    +      -       -      +
     92G  VAL*     1.3    65.4    +      -       -      +
     93G  PHE*     3.7    21.1    -      -       +      -
    107G  ILE      3.5     1.0    -      -       -      +
    108G  CYS*     3.4     0.7    -      -       -      -
    109G  PHE*     2.6    58.8    +      -       +      +
    177G  LYS*     4.6     1.3    -      -       -      -
    175H  ILE*     6.4     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 92 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  THR*     1.3    80.1    -      -       -      +
     93G  PHE*     1.3    82.1    +      -       -      +
    106G  LEU*     3.5    34.1    -      -       +      -
    107G  ILE      2.9     9.6    -      -       -      +
    108G  CYS*     3.9     7.2    -      -       +      -
    122G  TRP*     4.1     2.5    -      -       +      -
    164G  CYS*     3.6    30.7    -      -       +      -
    177G  LYS*     3.6    27.1    -      -       +      +
    179G  TRP*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 93 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  THR*     3.7    17.7    -      -       +      -
     92G  VAL*     1.3    85.9    -      -       -      +
     94G  PRO*     1.3    68.3    -      -       +      +
    106G  LEU*     4.0     3.1    -      -       -      -
    107G  ILE*     2.7    64.2    +      -       +      +
    109G  PHE*     3.7    28.9    -      +       +      -
    149G  LEU*     5.1     1.3    -      -       +      -
    179G  TRP*     4.8     2.0    -      -       -      -
    175H  ILE*     4.1    14.4    -      -       +      -
    176H  ARG      3.7    17.0    -      -       -      -
    177H  ASN*     3.1    24.9    -      -       -      -
    183H  GLN*     3.6    16.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 94 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93G  PHE*     1.3    88.8    -      -       +      +
     95G  LYS*     1.3    68.9    +      -       -      +
     96G  SER*     3.2    21.5    -      -       -      +
     97G  PRO*     5.2     1.3    -      -       +      -
     98G  VAL*     4.6    14.6    -      -       +      +
    104G  ASN*     4.0     7.6    -      -       -      +
    105G  THR      3.4     6.3    -      -       -      +
    106G  LEU*     4.0    11.4    -      -       +      -
    154G  PHE*     5.4     1.6    -      -       +      -
    179G  TRP*     3.8    26.7    -      -       +      +
    183H  GLN*     3.1    16.5    +      -       -      +
----------------------------------------------------------
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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