Contacts of the strand formed by residues 80 - 84 (chain D) in PDB entry 1L0N


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 MET 80 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  GLN*     3.4    43.8    +      -       +      +
     72D  ASP      3.4    16.8    -      -       -      +
     73D  GLY*     4.1     9.4    -      -       -      -
     74D  PRO*     4.1    23.1    -      -       +      -
     75D  ASN*     4.8     1.6    -      -       -      +
     78D  GLY      4.8     5.8    -      -       -      +
     79D  GLU*     1.3    97.7    -      -       -      +
     81D  PHE*     1.3    61.6    +      -       -      +
     82D  MET*     6.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 81 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  GLN*     3.7     5.7    -      -       -      +
     72D  ASP*     3.1    50.1    +      -       +      +
     73D  GLY*     3.1    27.4    -      -       -      -
     74D  PRO      4.1     2.7    -      -       -      -
     75D  ASN*     3.2    42.6    -      -       -      +
     80D  MET*     1.3    75.3    -      -       -      +
     82D  MET*     1.3    78.7    -      -       -      +
     83D  ARG*     4.3    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 82 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  GLU*     3.3    37.0    -      -       +      +
     70D  VAL*     3.4    26.7    -      -       -      +
     71D  GLN*     4.5    14.6    -      -       +      +
     80D  MET      6.2     0.2    -      -       -      -
     81D  PHE*     1.3    86.0    -      -       -      +
     83D  ARG*     1.3    70.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  GLU*     3.3    21.9    -      -       -      +
     70D  VAL*     3.9    10.9    +      -       -      +
     72D  ASP*     4.9    13.6    -      -       +      +
     81D  PHE*     4.3    21.2    +      -       +      -
     82D  MET*     1.3    81.4    -      -       -      +
     84D  PRO*     1.4    80.1    -      -       +      +
     85D  GLY*     3.2     4.5    +      -       -      -
     86D  LYS*     5.1     4.9    -      -       -      -
     75E  GLU*     4.9    15.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 84 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66D  GLU*     3.3    30.9    -      -       +      +
     67D  GLU      5.0     2.0    -      -       -      +
     68D  VAL      3.9     2.7    -      -       -      +
     69D  GLU*     4.9     1.1    -      -       +      +
     83D  ARG*     1.4   100.5    -      -       +      +
     85D  GLY*     1.3    68.3    +      -       -      +
     86D  LYS*     3.5    11.7    +      -       -      +
----------------------------------------------------------
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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