Contacts of the helix formed by residues 811 - 822 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A PRO* 4.3 10.5 - - + -
558A THR* 3.8 29.8 - - + -
517B TYR* 3.7 18.6 - - - +
518B ASN 5.6 0.2 - - - +
521B LEU* 3.7 40.6 - - + +
522B VAL* 4.0 7.9 - - + -
526B CYS* 4.2 9.9 - - - -
808B GLY* 3.1 13.3 + - - +
809B THR 4.1 0.2 - - - +
810B ASN* 1.3 80.3 - - + +
812B LEU* 1.3 60.0 + - - +
813B PRO* 3.4 3.6 - - + -
814B GLN* 3.2 26.2 + - - +
815B GLN* 2.9 29.4 + - - +
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Residues in contact with LEU 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A TYR* 3.8 51.3 - - + +
518B ASN* 5.0 12.3 - - + +
521B LEU* 4.2 22.4 - - + +
810B ASN 3.7 1.5 + - - +
811B LEU* 1.3 68.7 - - - +
813B PRO* 1.3 74.6 - - + +
815B GLN* 3.1 22.3 + - + +
816B ALA* 2.9 22.3 + - - +
819B GLN* 5.5 0.2 + - - -
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Residues in contact with PRO 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A TYR 3.5 21.8 - - - +
512A LEU* 4.5 1.2 - - - +
513A PRO* 4.1 9.0 - - + -
534A MET* 3.6 21.7 - - + +
535A PRO* 3.7 24.5 - - + -
517B TYR* 4.5 13.9 - - + -
811B LEU* 3.6 4.0 - - + -
812B LEU* 1.3 92.1 - - + +
814B GLN* 1.3 75.1 + - - +
816B ALA* 2.9 24.8 + - - +
817B CYS* 3.3 4.5 + - - -
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Residues in contact with GLN 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A MET* 3.4 20.1 - - - +
535A PRO 3.7 14.8 + - - +
536A ILE* 4.0 10.5 - - - +
558A THR* 4.4 5.9 - - - +
517B TYR* 4.8 0.3 + - - -
762B ILE 4.5 3.0 + - - -
763B ALA 3.7 11.2 - - - +
764B CYS* 3.8 1.7 - - - +
765B GLY* 3.4 28.6 - - - +
808B GLY 2.8 28.0 - - - +
809B THR* 4.8 1.1 - - - -
811B LEU* 3.2 31.8 - - + +
813B PRO* 1.3 87.3 - - - +
815B GLN* 1.3 60.7 + - - +
817B CYS* 3.3 4.7 + - - +
818B LEU* 3.1 27.5 + - - +
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Residues in contact with GLN 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809B THR 3.0 24.8 + - - +
810B ASN* 3.0 31.2 + - - +
811B LEU 2.9 14.7 + - - +
812B LEU* 3.1 21.8 + - + +
814B GLN* 1.3 73.4 - - - +
816B ALA* 1.3 60.8 + - - +
818B LEU* 3.1 4.5 + - + +
819B GLN* 2.8 45.2 + - - +
824B GLN* 3.4 37.0 + - + +
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Residues in contact with ALA 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508A SER* 3.2 26.4 - - - +
509A LEU* 4.7 0.4 - - - -
511A TYR* 4.2 3.8 - - + -
512A LEU* 3.8 30.7 - - + +
812B LEU 2.9 12.2 + - - +
813B PRO 3.1 10.8 - - - +
815B GLN* 1.3 77.3 - - - +
817B CYS* 1.3 62.9 + - - +
819B GLN* 3.2 9.7 + - - +
820B MET* 3.0 25.3 + - - +
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Residues in contact with CYS 817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A LEU* 4.2 12.1 - - - -
534A MET* 3.6 17.9 - - - -
538B VAL* 4.4 5.6 - - - -
554B PRO* 3.7 37.6 - - + +
763B ALA* 3.3 33.4 - - - +
764B CYS* 4.2 2.7 - - - -
813B PRO 3.3 0.8 + - - -
814B GLN 3.3 3.3 + - - +
815B GLN 3.3 0.4 - - - -
816B ALA* 1.3 79.5 - - - +
818B LEU* 1.3 62.5 + - - +
820B MET* 3.1 29.6 - - - +
821B LEU* 3.5 6.6 + - - +
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Residues in contact with LEU 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764B CYS* 3.6 38.4 - - + +
766B GLN* 4.4 1.1 - - - +
804B THR* 4.2 17.0 - - + +
809B THR* 3.7 29.2 - - + +
814B GLN 3.1 16.1 + - - +
815B GLN* 3.1 11.9 + - - +
817B CYS* 1.3 73.5 - - - +
819B GLN* 1.3 65.3 + - - +
821B LEU* 3.1 4.8 + - - -
822B GLY 3.0 15.8 + - - -
823B VAL* 3.2 31.2 + - + +
824B GLN* 3.8 18.6 - - + -
838B LEU* 3.9 15.5 - - + -
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Residues in contact with GLN 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A LEU* 6.0 0.3 - - - +
504A SER* 5.3 2.3 + - - -
505A GLU* 3.4 38.0 + - - +
507A SER* 4.8 1.7 + - - +
508A SER* 3.3 32.7 + - - -
511A TYR* 5.6 8.3 - - - -
812B LEU 5.5 0.2 + - - -
815B GLN* 2.8 42.9 + - - +
816B ALA* 3.5 4.0 - - - +
818B LEU* 1.3 69.8 - - - +
820B MET* 1.3 60.0 + - - +
822B GLY* 2.8 24.1 + - - +
824B GLN* 3.6 27.1 + - + +
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Residues in contact with MET 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A LEU* 4.3 7.4 - - - -
503A LEU* 3.8 39.5 - - + +
504A SER* 5.6 2.6 + - - -
508A SER* 3.7 11.2 + - - +
509A LEU* 3.3 29.2 - - + -
512A LEU* 5.1 1.3 - - + -
531A ILE* 4.0 19.1 - - + -
540B VAL* 5.1 1.6 - - - -
551B PHE* 5.7 0.5 - - - -
552B GLN* 4.0 17.0 + - + +
554B PRO* 3.8 23.8 - - - -
816B ALA 3.0 8.2 + - - +
817B CYS* 3.1 36.1 - - - +
819B GLN* 1.3 76.9 - - - +
821B LEU* 1.3 60.2 + - - +
822B GLY 3.7 0.2 + - - -
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Residues in contact with LEU 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B PHE* 3.7 36.5 - - + -
552B GLN 3.3 28.5 - - - +
553B VAL* 4.1 5.6 - - + -
554B PRO* 3.9 20.9 - - + -
760B ILE* 5.2 1.8 - - + -
764B CYS* 4.2 13.2 - - - -
817B CYS 3.5 2.9 + - - +
818B LEU 3.1 8.1 + - - +
819B GLN 3.1 0.6 - - - -
820B MET* 1.3 78.1 - - - +
822B GLY* 1.3 59.4 + - - +
823B VAL* 3.6 13.5 + - + +
837B GLN* 5.2 0.3 - - - +
838B LEU* 3.5 30.3 - - + -
841B ILE* 4.0 27.6 - - + -
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Residues in contact with GLY 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A SER* 5.1 10.3 + - - -
505A GLU* 6.1 0.4 - - - -
818B LEU 3.0 0.8 + - - -
819B GLN* 2.8 17.6 + - - -
820B MET 3.3 0.4 + - - -
821B LEU* 1.3 78.9 - - - +
823B VAL* 1.3 60.5 + - - +
824B GLN 3.7 2.0 - - - -
834B ASN* 3.9 7.8 + - - +
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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