Contacts of the strand formed by residues 45 - 51 (chain M) in PDB entry 5X6E


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 ILE 45 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44M  GLY*     1.3    80.9    -      -       -      +
     46M  THR*     1.3    66.8    +      -       -      +
     62M  TYR*     4.3    13.2    -      -       +      -
     63M  TYR      3.4     6.7    -      -       -      +
     64M  LYS*     3.7    29.8    -      -       +      -
     87M  VAL      3.8     0.2    -      -       -      -
     88M  ILE*     2.8    40.4    +      -       +      -
     89M  SER*     3.0    31.8    +      -       -      +
     92M  ALA*     4.3     0.4    -      -       -      +
    154M  TYR*     4.1    19.5    -      -       +      +
    166M  LEU*     4.5    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 46 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28M  ILE*     4.4    10.3    -      -       +      -
     41M  LEU*     3.4    27.0    -      -       +      +
     45M  ILE*     1.3    78.9    -      -       -      +
     47M  LYS*     1.3    57.5    +      -       -      +
     62M  TYR*     3.4     6.9    -      -       -      +
     63M  TYR*     2.6    63.4    +      -       -      +
     85M  LEU*     3.7    18.0    -      -       +      +
     86M  GLU      3.2    13.0    -      -       -      +
     87M  VAL*     4.1    20.9    -      -       +      -
     88M  ILE*     4.0     3.1    -      -       -      +
     92M  ALA*     4.7     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 47 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46M  THR*     1.3    74.1    -      -       -      +
     48M  LEU*     1.3    60.3    +      -       -      +
     49M  THR*     3.6    18.6    +      -       +      +
     57M  ILE*     5.6     1.4    -      -       -      +
     59M  ASN*     3.3    30.2    +      -       -      +
     61M  GLN      3.6    11.9    -      -       -      +
     62M  TYR*     4.3    11.7    -      -       +      +
     63M  TYR*     4.6     0.4    -      -       -      +
     84M  ASN      3.6     0.2    -      -       -      +
     85M  LEU*     3.4     7.7    -      -       -      +
     86M  GLU*     2.7    66.1    +      -       +      +
     88M  ILE*     3.6    28.0    -      -       +      +
    173M  GLU*     3.1    26.7    +      -       -      +
    176M  TYR*     4.9     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 48 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29M  PHE*     4.2    12.8    -      -       +      -
     47M  LYS*     1.3    71.8    -      -       -      +
     49M  THR*     1.3    60.2    +      -       -      +
     59M  ASN*     3.9     1.1    -      -       -      -
     60M  LEU*     3.0    54.1    +      -       +      +
     61M  GLN*     3.0    26.9    +      -       -      +
     62M  TYR*     5.0     0.2    -      -       -      +
     63M  TYR*     4.1    20.6    -      -       +      +
     69M  ILE*     4.9     5.8    -      -       +      -
     83M  TYR*     3.8    21.1    -      -       +      -
     84M  ASN      3.2    18.8    -      -       -      +
     85M  LEU*     4.2    12.6    -      -       +      -
    128N  LEU*     4.0    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 49 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27M  LEU*     5.4     0.2    -      -       -      +
     47M  LYS*     3.6    28.7    -      -       +      +
     48M  LEU*     1.3    75.5    -      -       -      +
     50M  SER*     1.3    66.2    +      -       -      +
     51M  ILE*     4.9     4.6    -      -       -      +
     57M  ILE*     5.5     4.9    -      -       +      -
     58M  MET      3.3     9.0    -      -       -      -
     59M  ASN*     3.5    20.9    -      -       -      +
     60M  LEU*     4.8     0.7    -      -       -      -
     83M  TYR*     3.4     9.5    -      -       -      +
     84M  ASN*     2.8    56.7    +      -       -      +
     86M  GLU*     4.5    10.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 50 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31M  GLN*     4.0     5.6    -      -       -      -
     49M  THR*     1.3    77.8    -      -       -      +
     51M  ILE*     1.3    65.5    +      -       -      +
     52M  SER      4.2     0.7    +      -       -      -
     56M  THR      4.1     0.5    -      -       -      +
     57M  ILE*     3.2     4.0    -      -       -      +
     58M  MET*     2.8    40.8    +      -       -      +
     60M  LEU*     4.7     4.7    -      -       -      -
     82M  TYR      4.5     1.6    -      -       -      -
     83M  TYR*     3.7    22.2    -      -       -      -
    132N  ASN*     4.3     7.9    +      -       -      -
    220N  LYS*     3.1    27.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D    T      3.7    25.1    -      -       +      +
     31M  GLN*     3.1    37.3    +      -       -      +
     32M  TRP*     4.5    14.1    -      -       +      -
     49M  THR*     4.9     4.0    -      -       -      +
     50M  SER*     1.3    82.5    +      -       -      +
     52M  SER*     1.3    74.5    +      -       -      +
     55M  GLY*     3.9    25.6    -      -       -      +
     56M  THR      4.0     2.0    -      -       -      -
     57M  ILE*     3.6    19.5    -      -       +      -
     84M  ASN*     4.1    10.5    -      -       -      +
    220N  LYS*     5.6     2.0    -      -       -      -
----------------------------------------------------------
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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