Contacts of the strand formed by residues 670 - 676 (chain M) in PDB entry 5D4E


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 GLN 670 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    571M  LEU*     3.2    15.0    -      -       -      +
    573M  ARG*     2.9    48.5    +      -       -      +
    574M  ALA*     3.5     4.9    -      -       -      +
    575M  GLN*     3.5    15.3    -      -       -      +
    669M  GLY*     1.3    73.4    -      -       -      -
    671M  ASN*     1.3    62.7    +      -       -      +
    672M  VAL*     3.7     1.7    +      -       +      -
    699M  PHE*     3.4    35.1    -      -       +      -
    700M  TYR*     2.7    51.8    +      -       +      +
    993M  PHE*     3.7     2.7    -      -       -      -
    994M  ILE      3.0    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 671 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575M  GLN*     2.8    24.1    +      -       -      +
    576M  ALA      2.6    26.5    +      -       -      -
    577M  PRO*     3.4     0.3    -      -       -      +
    578M  VAL*     3.3    41.1    +      -       +      +
    670M  GLN*     1.3    70.3    -      -       -      +
    672M  VAL*     1.3    63.4    +      -       -      +
    699M  PHE*     4.1     9.9    -      -       -      -
    868M  ASP*     5.0     0.5    -      -       -      +
    900M  ARG*     4.0    12.1    -      -       -      +
    991M  GLN*     4.4    14.9    +      -       +      +
    992M  MET      3.5     5.4    -      -       -      +
    993M  PHE*     3.3    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 672 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    670M  GLN*     4.4     0.9    -      -       +      -
    671M  ASN*     1.3    79.1    -      -       -      +
    673M  LEU*     1.3    61.3    +      -       -      +
    674M  VAL*     3.5     8.4    +      -       +      +
    694M  LEU*     4.0    20.2    -      -       +      -
    699M  PHE*     4.2     7.2    -      -       +      -
    700M  TYR*     3.7    39.5    -      -       +      +
    868M  ASP*     3.8    13.7    -      -       +      +
    869M  VAL*     4.1     7.2    -      -       +      -
    991M  GLN*     3.4     5.6    -      -       -      -
    992M  MET      2.9    36.9    +      -       -      +
    994M  ILE*     3.8    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 673 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    672M  VAL*     1.3    70.7    -      -       -      +
    674M  VAL*     1.3    60.0    +      -       -      +
    861M  LEU*     4.7     8.3    -      -       +      -
    865M  THR*     4.2    16.6    -      -       +      -
    866M  PRO      4.4     7.2    -      -       -      +
    867M  VAL*     3.7     8.0    -      -       +      +
    868M  ASP*     2.7    48.7    +      -       -      +
    869M  VAL      3.2     3.9    +      -       -      -
    892M  LEU*     5.6     2.7    -      -       +      -
    895M  TYR*     3.9    49.6    -      -       +      +
    989M  VAL*     4.0    19.1    -      -       +      -
    990M  GLY*     3.5    31.4    -      -       -      +
    991M  GLN*     4.0     4.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 674 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    672M  VAL*     3.9    17.9    -      -       +      +
    673M  LEU*     1.3    76.8    -      -       -      +
    675M  ALA*     1.3    64.1    +      -       -      +
    676M  ILE*     4.7     7.0    -      -       +      -
    867M  VAL*     4.6     0.7    -      -       -      -
    869M  VAL*     3.1    28.9    -      -       +      +
    871M  LEU*     4.6     9.0    -      -       +      -
    888M  THR*     3.9    17.0    -      -       +      -
    988M  VAL      4.0     0.2    -      -       -      +
    989M  VAL*     3.2     7.2    -      -       -      +
    990M  GLY      2.9    40.5    +      -       -      +
    992M  MET*     3.9    29.4    -      -       +      -
    994M  ILE*     4.2     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 675 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673M  LEU      4.3     0.2    +      -       -      -
    674M  VAL*     1.3    75.3    -      -       -      +
    676M  ILE*     1.3    64.0    +      -       -      +
    677M  MET*     3.6     8.4    +      -       +      -
    859M  PRO*     5.3     0.2    -      -       +      -
    867M  VAL*     3.8    21.9    -      -       +      +
    869M  VAL      2.9     6.2    +      -       -      +
    870M  ILE*     3.3     6.4    -      -       +      +
    871M  LEU*     2.9    23.4    +      -       -      +
    974M  LEU*     3.9    15.7    -      -       +      -
    987M  ILE*     4.3     2.7    -      -       +      -
    988M  VAL      3.3     4.7    -      -       -      -
    989M  VAL*     3.8    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 676 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    674M  VAL*     4.7     9.0    -      -       +      -
    675M  ALA*     1.3    74.8    -      -       -      +
    677M  MET*     1.3    59.1    -      -       -      +
    871M  LEU*     3.2    26.5    -      -       +      +
    872M  ASN      4.1     0.7    -      -       -      -
    873M  PRO*     3.6    31.0    -      -       +      -
    876M  VAL*     5.4     4.5    -      -       +      -
    884M  GLN*     6.4     0.9    -      -       +      -
    885M  ILE*     3.7    28.3    -      -       +      -
    888M  THR*     4.6    11.9    -      -       +      +
    987M  ILE*     3.4     5.5    -      -       -      +
    988M  VAL*     2.9    24.3    +      -       +      +
    992M  MET*     5.2     5.4    -      -       +      -
    948N  THR*     2.9    33.6    +      -       -      +
    949N  ILE*     4.1    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