Contacts of the helix formed by residues 811 - 821 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517C TYR* 3.7 18.6 - - - +
518C ASN 5.4 0.4 - - - +
521C LEU* 3.9 27.8 - - + +
522C VAL* 3.7 26.0 - - + -
526C CYS* 4.3 10.5 - - - -
808C GLY* 3.2 14.7 + - - +
810C ASN* 1.3 81.7 - - + +
812C LEU* 1.3 61.2 - - - +
813C PRO* 3.5 3.8 - - + -
814C GLN* 3.3 32.1 + - - +
815C GLN* 2.8 28.6 + - - +
537D PRO* 4.3 4.9 - - + -
558D THR* 4.0 20.2 - - + -
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Residues in contact with LEU 812 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518C ASN* 5.0 15.3 - - + +
521C LEU* 4.2 23.6 - - + +
810C ASN 3.8 1.1 + - - +
811C LEU* 1.3 67.9 - - - +
813C PRO* 1.3 74.4 - - + +
815C GLN* 3.1 21.8 + - + +
816C ALA* 2.9 21.8 + - - +
819C GLN* 5.3 0.2 - - - +
511D TYR* 3.8 47.9 - - + +
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Residues in contact with PRO 813 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C TYR* 4.6 13.9 - - + -
811C LEU* 3.6 4.0 - - + -
812C LEU* 1.3 92.3 - - + +
814C GLN* 1.3 77.6 + - - +
816C ALA* 3.0 17.8 + - - +
817C CYS* 3.3 5.4 + - - -
511D TYR 3.4 22.9 - - - +
512D LEU* 4.6 1.7 - - - +
513D PRO* 4.1 9.6 - - + -
534D MET* 3.5 22.7 - - + +
535D PRO* 3.8 24.9 - - + -
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Residues in contact with GLN 814 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C TYR* 4.9 0.5 + - - -
762C ILE 4.6 1.0 + - - -
763C ALA 3.6 11.7 - - - +
764C CYS 3.8 0.7 - - - -
765C GLY* 3.5 29.5 - - - +
808C GLY 2.8 28.0 + - - +
809C THR* 4.8 1.3 - - - -
811C LEU* 3.3 24.9 - - + +
813C PRO* 1.3 94.2 - - - +
815C GLN* 1.3 64.7 + - - +
817C CYS* 3.2 4.9 + - - +
818C LEU* 3.0 26.9 + - - +
534D MET* 3.4 19.0 - - - +
535D PRO 3.7 15.7 + - - +
536D ILE* 4.1 9.1 - - - +
558D THR* 4.4 6.5 - - - +
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Residues in contact with GLN 815 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809C THR 2.9 28.5 + - - +
810C ASN* 3.4 28.6 + - - +
811C LEU 2.8 14.5 + - - +
812C LEU* 3.1 22.8 + - + +
814C GLN* 1.3 75.4 - - - +
816C ALA* 1.3 56.7 + - - +
818C LEU* 3.3 5.1 + - + +
819C GLN* 2.8 43.4 + - - +
824C GLN* 3.6 37.6 + - + +
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Residues in contact with ALA 816 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812C LEU 2.9 12.3 + - - +
813C PRO 3.0 11.4 + - - +
815C GLN* 1.3 79.1 - - - +
817C CYS* 1.3 61.4 + - - +
819C GLN* 3.4 6.2 + - - +
820C MET* 3.1 25.5 + - - +
508D SER 3.0 29.2 - - - +
509D LEU* 4.4 0.7 - - + -
511D TYR* 4.3 4.7 - - + +
512D LEU* 4.0 28.9 - - + +
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Residues in contact with CYS 817 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C VAL* 4.4 6.5 - - - -
554C PRO* 3.8 30.1 - - + +
763C ALA* 3.2 25.4 - - - +
764C CYS* 4.1 3.6 - - - -
813C PRO 3.3 1.7 + - - -
814C GLN 3.2 3.4 + - - +
816C ALA* 1.3 77.9 - - - +
818C LEU* 1.3 62.8 - - - +
820C MET* 3.3 27.8 + - - +
821C LEU* 3.5 13.3 + - - +
512D LEU* 4.3 11.7 - - - -
534D MET* 3.5 27.8 - - - -
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Residues in contact with LEU 818 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764C CYS* 3.6 33.9 - - + +
766C GLN* 4.5 0.7 - - - +
804C THR* 4.2 15.9 - - + +
809C THR* 3.6 37.9 - - + +
814C GLN 3.0 16.3 + - - +
815C GLN* 3.6 7.2 - - - +
816C ALA 3.3 0.2 - - - -
817C CYS* 1.3 76.4 - - - +
819C GLN* 1.3 61.5 + - - +
821C LEU* 3.0 14.0 + - - +
822C GLY 3.1 7.6 + - - -
823C VAL* 3.1 29.5 + - + +
824C GLN* 3.7 20.6 - - + -
838C LEU* 3.8 15.5 - - + -
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Residues in contact with GLN 819 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812C LEU 5.3 0.2 - - - +
815C GLN* 2.8 39.0 + - - +
816C ALA* 3.7 6.1 + - - +
818C LEU* 1.3 68.5 - - - +
820C MET* 1.3 58.5 + - - +
822C GLY* 2.7 25.3 + - - +
824C GLN* 3.5 28.4 - - + +
503D LEU* 6.0 0.7 - - - +
504D SER* 4.7 5.2 + - - -
505D GLU* 2.7 49.1 + - - +
507D SER 5.4 0.6 + - - -
508D SER* 3.4 21.5 + - - +
511D TYR* 5.6 5.5 - - - -
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Residues in contact with MET 820 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C VAL* 4.6 4.5 - - - -
551C PHE* 5.6 1.0 - - - -
552C GLN* 3.6 25.6 + - + +
554C PRO* 3.9 20.9 - - + -
816C ALA 3.1 8.3 + - - +
817C CYS* 3.3 28.7 - - - +
819C GLN* 1.3 76.5 - - - +
821C LEU* 1.3 61.0 + - - +
822C GLY 3.7 0.3 + - - -
499D LEU* 4.1 21.1 - - - -
503D LEU* 3.9 32.9 - - + +
504D SER* 5.5 2.8 + - - -
508D SER* 3.8 13.4 - - - +
509D LEU* 3.3 26.0 - - + -
512D LEU* 4.9 0.2 - - + -
531D ILE* 3.9 12.1 - - + -
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Residues in contact with LEU 821 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C PHE* 3.7 36.7 - - + -
552C GLN 3.3 29.2 - - - +
553C VAL* 4.1 4.7 - - + -
554C PRO* 3.9 17.7 - - + -
760C ILE* 5.3 1.8 - - + -
764C CYS* 4.2 13.2 - - - -
817C CYS 3.8 8.1 - - - +
818C LEU 3.0 10.1 + - - +
820C MET* 1.3 76.5 - - - +
822C GLY* 1.3 62.4 + - - +
823C VAL* 3.5 14.6 + - + +
837C GLN* 5.2 0.2 - - - +
838C LEU* 3.6 29.4 - - + -
841C ILE* 4.0 25.8 - - + -
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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