Contacts of the strand formed by residues 53 - 57 (chain A) in PDB entry 1L0Z


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 53 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LEU*     3.9    26.5    -      -       +      -
     19A  GLN      3.2    14.4    -      -       -      +
     20A  TYR*     4.2     8.5    -      -       +      -
     26A  TRP*     4.1     2.1    -      -       -      -
     29A  THR*     4.2    11.2    -      -       +      -
     46A  CYS      3.5    25.8    -      -       -      -
     47A  VAL*     3.8    16.6    -      -       +      -
     49A  ARG      3.5    26.0    -      -       -      -
     50A  GLU*     5.3     0.2    -      -       -      -
     51A  LEU*     3.5    44.2    +      -       +      -
     52A  THR*     1.3    80.6    -      -       -      +
     54A  ARG*     1.3    60.9    +      -       -      +
     73A  GLY*     4.0     2.1    -      -       -      -
     74A  VAL*     3.1    35.1    +      -       +      +
     77A  ILE*     4.1    19.5    -      -       +      -
     97A  LEU*     6.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  SER      3.7     0.7    -      -       -      +
     18A  LEU*     3.6     4.9    -      -       -      +
     19A  GLN*     2.9    62.6    +      -       +      +
     26A  TRP*     3.5    63.7    -      -       +      +
     53A  PHE*     1.3    74.8    -      -       -      +
     55A  VAL*     1.3    69.1    +      -       -      +
     56A  VAL*     3.9     5.0    -      -       +      +
     71A  TYR*     3.2    49.6    -      -       -      +
     72A  VAL      3.4    16.4    -      -       -      +
     73A  GLY*     4.2     3.8    -      -       -      -
     74A  VAL*     4.3     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     4.0    35.4    -      -       +      -
     17A  SER      3.5     2.5    -      -       -      -
     18A  LEU*     4.1     7.6    -      -       +      -
     40A  VAL*     4.1    14.6    -      -       +      -
     54A  ARG*     1.3    79.3    -      -       -      +
     56A  VAL*     1.3    63.3    +      -       -      +
     57A  VAL*     4.1    12.3    -      -       +      -
     71A  TYR*     3.7     1.7    -      -       -      -
     72A  VAL*     2.7    56.0    +      -       +      +
     74A  VAL*     3.9    11.9    -      -       +      +
     97A  LEU*     4.2     6.5    -      -       +      -
     99A  LEU*     3.9    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     3.4     6.1    -      -       -      -
     17A  SER*     2.9    32.8    +      -       -      +
     19A  GLN*     3.6    36.6    -      -       +      +
     54A  ARG*     3.9     4.9    -      -       -      +
     55A  VAL*     1.3    77.0    -      -       -      +
     57A  VAL*     1.3    68.0    +      -       -      +
     59A  GLU*     3.7    31.7    -      -       +      +
     69A  GLU*     3.9     7.6    -      -       +      -
     70A  GLN      3.4     6.5    -      -       -      +
     71A  TYR*     3.7    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  GLN      4.8     0.9    -      -       -      -
     16A  ILE*     3.6    27.1    -      -       +      -
     34A  LEU*     4.4    12.8    -      -       +      -
     55A  VAL*     4.1    12.1    -      -       +      -
     56A  VAL*     1.3    72.9    -      -       -      +
     58A  GLY*     1.3    67.2    +      -       -      +
     59A  GLU      3.1     2.8    +      -       -      -
     69A  GLU*     3.3     2.3    -      -       -      -
     70A  GLN*     2.9    61.3    +      -       +      +
    103A  VAL*     3.9    18.8    -      -       +      -
    109A  VAL*     3.7    28.3    -      -       +      -
----------------------------------------------------------
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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