Contacts of the helix formed by residues 811 - 821 (chain D) in PDB entry 1DQ8
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 LEU 811 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537C PRO* 4.4 5.2 - - + -
558C THR* 3.8 28.0 - - + -
517D TYR* 3.8 18.8 - - - +
521D LEU* 3.8 38.6 - - + +
522D VAL* 4.1 15.5 - - + -
526D CYS* 4.1 11.0 - - - -
808D GLY* 3.1 14.1 + - - +
810D ASN* 1.3 82.6 - - + +
812D LEU* 1.3 60.3 + - - +
813D PRO* 3.5 4.3 - - + -
814D GLN* 3.1 25.9 + - - +
815D GLN* 2.9 29.7 + - - +
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Residues in contact with LEU 812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511C TYR* 3.8 49.1 - - + +
518D ASN* 5.4 11.0 - - + +
521D LEU* 4.2 21.3 - - + +
810D ASN 4.9 1.1 - - - +
811D LEU* 1.3 69.1 - - - +
813D PRO* 1.3 75.7 - - + +
815D GLN* 3.1 20.9 + - - +
816D ALA* 3.0 22.5 + - - +
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Residues in contact with PRO 813 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511C TYR 3.4 22.9 - - - +
512C LEU* 4.4 3.8 - - + +
513C PRO* 4.1 8.5 - - + -
534C MET* 3.1 24.6 - - + +
535C PRO* 3.7 22.2 - - + -
517D TYR* 4.7 13.7 - - + +
811D LEU* 3.6 3.1 - - + -
812D LEU* 1.3 93.8 - - + +
814D GLN* 1.3 70.2 + - - +
816D ALA* 3.1 17.8 + - - +
817D CYS* 3.4 10.7 + - - -
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Residues in contact with GLN 814 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C MET* 2.8 30.8 - - - +
535C PRO 3.6 9.5 + - - +
536C ILE* 3.9 13.3 - - - +
558C THR* 4.4 4.8 - - - +
517D TYR* 5.0 0.5 + - - -
762D ILE 4.6 2.0 + - - -
763D ALA 3.4 13.1 - - - +
764D CYS 3.7 1.1 - - - +
765D GLY* 3.3 31.0 - - - +
808D GLY 2.8 28.3 - - - +
809D THR* 5.1 0.4 - - - -
811D LEU* 3.1 31.1 - - + +
812D LEU 3.3 0.2 - - - -
813D PRO* 1.3 79.1 - - - +
815D GLN* 1.3 61.0 + - - +
817D CYS* 3.3 3.7 + - - +
818D LEU* 3.1 27.3 + - - +
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Residues in contact with GLN 815 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809D THR 3.0 27.7 + - - +
810D ASN* 3.5 22.9 + - - +
811D LEU 2.9 20.7 + - - +
812D LEU* 3.6 20.3 - - + +
813D PRO 3.1 0.6 - - - -
814D GLN* 1.3 73.6 - - - +
816D ALA* 1.3 60.5 + - - +
818D LEU* 3.2 4.9 + - + +
819D GLN* 2.8 39.8 + - - +
824D GLN* 3.7 36.0 + - + +
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Residues in contact with ALA 816 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508C SER* 3.1 28.7 - - - +
509C LEU* 4.6 0.7 - - - -
511C TYR* 4.3 3.1 - - + +
512C LEU* 4.0 28.0 - - + +
812D LEU 3.0 11.9 + - - +
813D PRO 3.1 10.7 + - - +
815D GLN* 1.3 77.6 - - - +
817D CYS* 1.3 61.0 + - - +
819D GLN* 3.2 10.2 + - - +
820D MET* 3.0 26.8 + - - +
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Residues in contact with CYS 817 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C LEU* 4.2 15.9 - - - -
534C MET* 5.1 1.1 - - - -
538D VAL* 4.4 7.4 - - - -
554D PRO* 3.7 29.6 - - + +
763D ALA* 3.4 35.0 - - - +
764D CYS* 4.2 4.3 - - - -
813D PRO 3.4 8.4 + - - -
814D GLN 3.3 3.0 + - - +
815D GLN 3.3 0.4 - - - -
816D ALA* 1.3 76.6 - - - +
818D LEU* 1.3 66.9 + - - +
820D MET* 3.3 39.9 - - - +
821D LEU* 3.6 7.1 + - - +
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Residues in contact with LEU 818 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764D CYS* 3.7 30.1 - - + +
766D GLN* 4.5 0.9 - - - +
804D THR* 4.2 18.2 - - + +
809D THR* 3.5 31.2 - - + +
814D GLN 3.1 17.0 + - - +
815D GLN* 3.2 10.1 + - - +
817D CYS* 1.3 78.3 - - - +
819D GLN* 1.3 62.2 + - - +
821D LEU* 3.2 3.6 + - - -
822D GLY 3.1 3.6 + - - -
823D VAL* 3.0 46.2 + - + +
824D GLN* 3.6 22.9 - - + +
838D LEU* 3.8 16.2 - - + -
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Residues in contact with GLN 819 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503C LEU* 6.1 0.2 - - - +
504C SER* 4.8 2.3 + - - -
505C GLU* 2.8 40.5 + - - +
508C SER* 3.3 37.5 + - - +
511C TYR* 5.6 6.5 - - - -
815D GLN* 2.8 25.7 + - - +
816D ALA* 3.2 5.2 + - - +
818D LEU* 1.3 73.6 - - - +
820D MET* 1.3 59.0 + - - +
822D GLY* 2.7 25.2 + - - +
824D GLN* 3.6 26.9 - - + +
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Residues in contact with MET 820 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C LEU* 4.5 8.3 - - - -
503C LEU* 4.0 28.4 - - + +
504C SER* 5.2 4.5 + - - -
508C SER* 3.8 15.2 + - - +
509C LEU* 3.4 32.5 - - + -
512C LEU* 3.8 4.9 - - + -
531C ILE* 3.7 19.5 - - + -
540D VAL* 5.6 1.3 - - - -
551D PHE* 5.6 0.7 - - - -
552D GLN* 4.3 17.6 + - - +
554D PRO* 3.8 17.7 - - + -
816D ALA 3.0 13.5 + - - +
817D CYS* 3.3 44.4 - - - +
819D GLN* 1.3 76.8 - - - +
821D LEU* 1.3 60.0 - - - +
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Residues in contact with LEU 821 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D PHE* 3.8 41.7 - - + -
552D GLN 3.3 28.7 - - - +
553D VAL* 4.2 2.7 - - - -
554D PRO* 4.0 21.5 - - + -
760D ILE* 5.1 2.5 - - + -
764D CYS* 4.2 13.2 - - - -
817D CYS 3.6 6.9 + - - +
818D LEU 3.2 7.7 + - - +
819D GLN 3.1 0.6 - - - -
820D MET* 1.3 75.4 - - - +
822D GLY* 1.3 62.4 + - - +
823D VAL* 3.5 12.1 + - + +
837D GLN* 5.2 2.1 - - - +
838D LEU* 3.7 28.7 - - + -
841D ILE* 4.0 22.8 - - + +
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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