Contacts of the helix formed by residues 717 - 726 (chain K) in PDB entry 6D6Q
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.
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 THR 717 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699K TYR* 5.5 0.9 - - - -
715K THR 4.2 4.7 - - - +
716K ASP* 1.3 97.1 + - - +
718K ALA* 1.3 70.3 + - - +
719K LYS* 3.5 13.4 + - + +
720K SER* 3.3 29.0 + - - +
721K LEU* 3.6 12.3 - - - +
765K TYR* 4.0 10.2 + - - -
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Residues in contact with ALA 718 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628K GLY 4.5 9.0 - - - +
630K LEU* 4.5 8.1 - - + +
717K THR* 1.3 81.9 + - - +
719K LYS* 1.3 65.7 + - + +
721K LEU* 3.4 5.0 - - - +
722K ALA* 2.9 23.7 + - - +
765K TYR* 3.7 48.4 - - + +
766K GLY 5.5 0.4 - - - +
768K ALA* 5.6 4.9 - - + -
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Residues in contact with LYS 719 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626K GLU 4.7 7.9 + - - -
627K LYS 4.5 8.4 + - - +
628K GLY* 3.6 31.2 - - - +
717K THR* 3.5 11.2 + - + +
718K ALA* 1.3 75.1 - - + +
720K SER* 1.3 69.1 + - - +
722K ALA 2.7 12.9 + - - +
723K GLU* 2.4 35.5 + - - +
768K ALA* 5.9 2.0 - - + -
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Residues in contact with SER 720 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714K LYS* 2.5 41.6 + - - +
716K ASP* 2.5 29.0 + - - -
717K THR* 3.3 13.1 + - - +
719K LYS* 1.3 75.5 - - - +
721K LEU* 1.3 66.8 + - - +
723K GLU* 3.8 4.0 - - - +
724K SER* 2.9 25.2 + - - -
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Residues in contact with LEU 721 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630K LEU* 5.2 11.4 - - + -
632K LEU* 5.7 4.3 - - + -
699K TYR* 3.1 41.7 - - + -
702K LEU* 6.3 2.2 - - + -
713K ILE* 5.0 5.6 - - + -
714K LYS 3.5 9.6 - - - +
715K THR* 5.1 5.6 - - + -
717K THR 3.6 9.9 - - - +
718K ALA 3.4 10.3 + - - +
719K LYS 2.9 0.8 + - - -
720K SER* 1.3 81.7 + - - +
722K ALA* 1.3 69.5 + - + +
724K SER* 2.9 5.9 + - - -
725K LEU* 2.9 49.3 + - + +
744K ALA* 5.1 13.9 - - + -
748K MET* 5.3 4.5 - - + -
765K TYR* 3.8 12.6 - - - +
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Residues in contact with ALA 722 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628K GLY 4.4 7.4 - - - +
629K ALA 4.8 2.5 - - - +
630K LEU* 4.2 27.1 - - + -
718K ALA 2.9 12.5 + - - +
719K LYS 2.7 11.6 + - - +
721K LEU* 1.3 77.5 - - - +
723K GLU* 1.3 66.1 + - - +
724K SER 2.8 6.6 + - - -
725K LEU* 2.9 17.2 + - - +
726K ASP* 3.3 16.7 + - - +
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Residues in contact with GLU 723 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625K ILE* 3.7 19.4 - - - +
626K GLU* 4.4 7.6 - - - +
628K GLY* 4.2 8.2 - - - -
719K LYS* 2.4 56.5 + - - +
720K SER* 3.8 4.5 - - - +
722K ALA* 1.3 75.5 - - - +
724K SER* 1.3 57.9 + - - +
726K ASP* 4.2 12.9 + - - +
727K GLN* 3.7 24.1 + - - +
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Residues in contact with SER 724 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712K GLU 3.2 23.6 + - - -
713K ILE* 3.6 20.9 - - - +
714K LYS* 4.6 11.8 + - - -
720K SER 2.9 19.3 + - - -
721K LEU* 2.9 7.5 + - - -
722K ALA 2.8 2.2 + - - -
723K GLU* 1.3 75.7 - - - +
725K LEU* 1.3 56.8 + - - +
726K ASP 3.1 1.6 - - - -
727K GLN* 2.7 32.6 + - - +
728K ALA* 3.1 11.2 + - - +
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Residues in contact with LEU 725 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632K LEU* 6.2 2.2 - - + -
702K LEU* 5.5 6.1 - - + -
713K ILE* 5.3 10.3 - - + -
721K LEU* 2.9 56.3 + - + +
722K ALA* 2.9 9.7 + - - +
724K SER* 1.3 79.0 - - - +
726K ASP* 1.3 60.5 + - - +
727K GLN 3.3 0.9 + - - -
728K ALA* 3.5 6.0 + - + +
737K ASN* 2.9 36.8 + - + +
740K LEU* 3.5 48.5 - - + +
741K ARG* 4.4 25.4 + - + +
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Residues in contact with ASP 726 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625K ILE* 5.2 9.7 - - - +
631K THR* 5.6 2.1 - - - +
722K ALA* 3.3 12.9 + - - +
723K GLU* 4.4 12.6 - - - +
724K SER 3.0 1.0 + - - -
725K LEU* 1.3 78.5 - - - +
727K GLN* 1.3 59.1 + - + +
729K GLU* 4.8 11.1 + - - +
737K ASN* 4.9 2.0 - - - +
741K ARG* 3.2 24.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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