Contacts of the strand formed by residues 846 - 853 (chain M) in PDB entry 5X22


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 LYS 846 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445M  GLU*     4.6     5.1    +      -       -      -
    557M  ARG*     4.2    19.9    -      -       -      +
    560M  MET*     4.0    18.0    -      -       -      +
    564M  MET*     3.7    33.8    -      -       +      -
    686M  ASP*     3.8    18.5    -      -       -      +
    688M  ILE*     5.0     1.6    -      -       -      -
    838M  LYS*     4.0    13.5    -      -       -      -
    839M  LEU      3.5     5.4    -      -       -      +
    840M  ALA*     3.8     4.0    -      -       +      -
    844M  GLY      3.5     4.9    +      -       -      +
    845M  ASN*     1.3    84.3    +      -       -      +
    847M  GLY*     1.3    58.2    +      -       -      +
    741N  ASP*     4.0    24.2    -      -       +      +
   2007N  2TM      4.0    13.9    +      -       -      -
      2S    A      2.5    35.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 847 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686M  ASP      3.1    17.9    -      -       -      -
    688M  ILE*     4.0    10.7    -      -       -      +
    838M  LYS*     3.6     5.3    -      -       -      +
    839M  LEU*     2.9    34.7    +      -       -      +
    846M  LYS*     1.3    76.1    -      -       -      +
    848M  VAL*     1.3    65.7    +      -       -      -
    740N  PHE      4.1     5.2    -      -       -      -
    741N  ASP*     4.3     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 848 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686M  ASP      3.9     1.2    +      -       -      -
    687M  ALA*     3.5     5.4    -      -       -      +
    688M  ILE*     2.9    22.2    +      -       -      -
    836M  GLY*     3.5    37.2    -      -       -      +
    837M  ASP      3.3     7.4    -      -       -      +
    838M  LYS*     4.3     8.5    -      -       +      -
    847M  GLY*     1.3    76.2    -      -       -      +
    849M  VAL*     1.3    69.6    +      -       -      +
    850M  ALA*     3.1     1.4    +      -       -      -
    630N  VAL*     4.2     7.9    -      -       +      -
    631N  ILE      4.3     1.8    -      -       -      +
    632N  VAL*     3.6    14.8    -      -       +      -
    740N  PHE*     3.1    23.7    +      -       +      +
    741N  ASP      4.1     1.1    -      -       -      -
    742N  GLY*     3.5    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 849 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    688M  ILE*     3.4     8.7    -      -       +      +
    690M  ILE*     3.8    31.4    -      -       +      -
    833M  LEU*     4.4     9.0    -      -       +      -
    834M  GLN      4.1    10.8    -      -       -      +
    835M  VAL*     3.3    11.8    -      -       -      +
    836M  GLY      3.0    21.5    +      -       -      -
    837M  ASP      3.0    13.0    +      -       -      +
    839M  LEU*     3.7    31.6    -      -       +      -
    847M  GLY      4.3     0.2    +      -       -      -
    848M  VAL*     1.3    73.0    -      -       -      +
    850M  ALA*     1.3    59.5    -      -       -      +
    851M  LYS      3.7    22.7    -      -       -      +
    852M  ILE*     4.1     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 850 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682M  TYR*     3.5    26.1    -      -       +      +
    687M  ALA*     3.8    11.4    -      -       +      -
    688M  ILE      2.9     6.5    +      -       -      -
    835M  VAL*     3.9     9.6    -      -       -      +
    848M  VAL      3.1     1.8    +      -       -      +
    849M  VAL*     1.3    74.4    -      -       -      +
    851M  LYS*     1.3    66.1    +      -       +      +
    632N  VAL*     3.6    27.7    -      -       +      +
    633N  VAL*     3.5    22.8    -      -       +      +
    727N  GLN*     6.1     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 851 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183L  ASP*     6.0     2.4    +      -       -      -
    191L  ASP*     5.9     1.4    +      -       -      -
    682M  TYR*     3.5    60.0    +      -       +      -
    688M  ILE      3.8     2.2    +      -       -      -
    689M  VAL*     3.8     7.6    -      -       +      -
    690M  ILE      3.2    23.6    +      -       -      +
    835M  VAL*     4.5     3.4    -      -       -      -
    849M  VAL*     3.6     5.3    -      -       -      +
    850M  ALA*     1.3    84.0    -      -       -      +
    852M  ILE*     1.3    75.2    +      -       -      +
    853M  LEU*     3.6    33.2    -      -       +      -
    636N  GLN*     5.7     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 852 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    690M  ILE*     3.5    24.9    -      -       +      +
    691M  SER      4.1     2.7    -      -       -      +
    692M  GLU*     3.7    38.6    -      -       +      +
    695M  LEU*     3.9    13.0    -      -       +      -
    833M  LEU      3.8    22.2    -      -       -      +
    834M  GLN*     4.3     1.8    -      -       -      -
    835M  VAL*     4.0    29.1    -      -       +      +
    849M  VAL*     4.1     1.8    -      -       +      -
    851M  LYS*     1.3    86.2    -      -       -      +
    853M  LEU*     1.3    63.3    +      -       -      +
    854M  PRO*     4.1     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 853 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679M  PHE*     3.6    37.5    -      -       +      -
    682M  TYR*     5.4     3.6    -      -       +      -
    689M  VAL*     3.7    23.8    -      -       +      -
    690M  ILE      3.2     5.9    +      -       -      -
    692M  GLU*     2.9    29.4    +      -       -      +
    851M  LYS*     3.6    30.5    -      -       +      -
    852M  ILE*     1.3    73.9    -      -       -      +
    854M  PRO*     1.3    75.1    -      -       +      +
    857M  ASP*     4.3    18.8    -      -       +      +
    858M  MET*     3.4    26.3    -      -       +      +
    870M  ILE*     4.6     0.7    -      -       +      -
----------------------------------------------------------
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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