Contacts of the strand formed by residues 53 - 57 (chain M) in PDB entry 5LXY


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 ALA 53 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  LEU      4.0     0.2    -      -       -      +
     13M  PHE*     3.9     5.0    -      -       -      +
     14M  VAL*     3.2    42.0    +      -       +      +
     17M  LEU*     4.1    17.2    -      -       +      +
     23M  GLU*     6.3     2.5    -      -       +      -
     26M  LEU*     5.4     8.7    -      -       +      -
     39M  VAL*     5.2     9.2    -      -       +      -
     52M  PHE*     1.3    75.3    -      -       -      +
     54M  PHE*     1.3    62.1    +      -       -      +
     55M  VAL*     4.4     4.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 54 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  LEU      3.8     6.7    -      -       -      +
     13M  PHE*     5.3     0.2    -      -       -      +
     39M  VAL*     3.2    32.5    -      -       -      +
     53M  ALA*     1.3    73.9    -      -       -      +
     55M  VAL*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11M  THR*     3.2     6.5    -      -       -      -
     12M  LEU*     3.0    38.6    +      -       +      +
     14M  VAL*     5.8     3.1    -      -       +      -
     26M  LEU*     5.2     3.6    -      -       +      -
     30M  PHE*     4.0    35.0    -      -       +      -
     36M  VAL*     4.5     2.2    -      -       +      -
     38M  LYS      3.7     3.4    -      -       -      +
     39M  VAL*     3.7    28.9    -      -       +      -
     53M  ALA*     5.2     5.4    -      -       +      +
     54M  PHE*     1.3    81.4    -      -       -      +
     56M  ASN*     1.3    66.8    +      -       -      +
     57M  PHE*     3.9    31.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 56 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10M  ARG      3.6    11.4    -      -       -      +
     11M  THR*     5.3     2.7    -      -       -      -
     36M  VAL*     3.2     5.4    -      -       -      +
     37M  ILE*     2.4    37.4    +      -       +      -
     38M  LYS*     2.7    28.7    +      -       +      +
     55M  VAL*     1.3    73.8    -      -       -      +
     57M  PHE*     1.3    57.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 57 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10M  ARG*     3.3    25.8    +      -       +      +
     11M  THR*     5.0     5.8    -      -       -      -
     12M  LEU*     4.5    12.3    -      -       +      -
     30M  PHE*     3.3    53.2    -      +       +      -
     34M  GLY*     3.7     6.3    -      -       -      -
     35M  PRO      3.2    20.9    -      -       -      +
     36M  VAL*     4.1     4.9    -      -       +      -
     37M  ILE*     4.1     5.7    -      -       -      +
     55M  VAL*     3.9    16.2    -      -       +      -
     56M  ASN*     1.3    75.3    -      -       -      +
     58M  LYS*     1.3    65.3    +      -       -      +
     59M  HIS      3.3     6.7    -      -       -      +
     62M  SER*     3.5    30.1    -      -       -      -
     63M  VAL*     4.3    15.0    -      -       +      -
     66M  ALA*     3.6    22.2    -      -       +      -
----------------------------------------------------------
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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