Contacts of the helix formed by residues 724 - 737 (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 THR 724 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717C VAL* 3.6 8.1 - - - -
718C ARG* 4.4 24.2 - - + +
723C THR* 1.3 85.4 + - - +
725C THR* 1.3 64.4 + - - +
726C GLU* 3.7 8.0 + - - +
727C ALA* 3.2 22.4 + - + +
728C MET* 3.1 25.6 + - - +
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Residues in contact with THR 725 (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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714C ALA* 4.5 0.5 - - - -
717C VAL* 3.7 25.1 - - - +
724C THR* 1.3 70.0 - - - +
726C GLU* 1.3 67.0 + - - +
728C MET* 3.3 6.1 + - - +
729C ILE* 3.0 41.1 + - + +
783C ALA* 4.4 4.5 - - + -
788C ASN 4.9 0.7 - - - +
789C GLU* 2.7 29.3 + - - +
790C ASP 3.4 22.7 - - - +
791C LEU* 3.7 21.0 + - + -
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Residues in contact with GLU 726 (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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724C THR* 3.3 7.9 + - - +
725C THR* 1.3 80.9 - - - +
727C ALA* 1.3 62.2 + - - +
729C ILE* 3.3 9.6 + - - +
730C GLU* 3.1 33.3 + - + +
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Residues in contact with ALA 727 (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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723C THR* 3.6 17.0 - - - +
724C THR* 3.2 19.7 + - - +
726C GLU* 1.3 77.4 - - - +
728C MET* 1.3 62.7 + - - +
730C GLU* 3.4 6.7 + - - +
731C VAL* 3.0 30.4 + - + +
858C ALA* 4.1 13.0 - - + +
681D LEU* 6.3 0.4 - - - -
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Residues in contact with MET 728 (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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717C VAL* 4.4 2.5 - - + -
721C LEU* 4.4 4.7 - - + -
723C THR* 3.6 12.8 - - + -
724C THR 3.1 20.6 + - - +
725C THR 3.5 7.2 - - - +
727C ALA* 1.3 76.2 - - - +
729C ILE* 1.3 58.8 + - - +
731C VAL* 3.3 4.2 + - - +
732C ASN* 2.9 29.3 + - - +
781C MET* 3.9 15.5 - - - +
791C LEU* 3.6 31.6 - - + -
851C LEU* 3.3 33.9 - - + +
854C MET* 3.6 15.9 - - + +
855C ALA* 3.3 34.3 - - + +
858C ALA* 4.3 3.3 - - - +
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Residues in contact with ILE 729 (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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725C THR* 3.0 30.1 + - + +
726C GLU* 3.7 7.9 - - - +
728C MET* 1.3 72.9 - - - +
730C GLU* 1.3 70.6 + - - +
732C ASN* 3.2 5.6 + - - +
733C ILE* 3.0 44.9 + - + +
781C MET* 4.1 11.7 - - - +
782C GLU* 3.5 11.0 - - - +
783C ALA* 3.3 40.2 - - + +
791C LEU* 4.0 13.5 - - + -
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Residues in contact with GLU 730 (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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782A GLU* 4.0 11.5 - - - +
726C GLU* 3.1 29.0 + - + +
727C ALA* 3.7 8.1 - - - +
729C ILE* 1.3 84.4 - - - +
731C VAL* 1.3 62.6 + - - +
733C ILE* 4.9 7.1 - - - +
734C ASN* 2.9 35.4 + - - +
595D ARG* 3.2 45.2 + - - +
681D LEU* 4.3 9.0 - - + -
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Residues in contact with VAL 731 (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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727C ALA* 3.0 23.5 + - + +
728C MET* 3.8 3.8 - - - +
730C GLU* 1.3 74.8 - - - +
732C ASN* 1.3 63.5 + - - +
735C LYS* 2.9 38.6 + - + +
854C MET* 3.5 19.5 - - + +
857C LEU* 4.4 9.9 - - + -
858C ALA* 3.8 21.3 - - + -
681D LEU* 3.7 36.5 - - + +
682D ALA* 4.0 21.5 - - + -
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Residues in contact with ASN 732 (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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728C MET 2.9 17.5 + - - +
729C ILE 3.2 4.5 + - - +
731C VAL* 1.3 77.2 - - - +
733C ILE* 1.3 63.3 + - + +
736C ASN* 2.8 58.6 + - - +
737C LEU* 3.3 5.1 + - - +
779C THR* 2.9 26.7 + - - +
780C LEU* 3.6 5.3 - - - +
781C MET* 3.5 49.7 + - + +
854C MET* 3.4 8.6 - - + +
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Residues in contact with ILE 733 (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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733A ILE* 3.9 28.5 - - + -
737A LEU* 4.4 13.5 - - + -
780A LEU* 6.2 0.2 - - + -
729C ILE* 3.0 38.3 + - + +
730C GLU* 4.1 8.7 - - - +
732C ASN* 1.3 79.8 - - + +
734C ASN* 1.3 72.4 + - - +
737C LEU* 3.1 24.9 + - + +
738C VAL* 2.8 34.8 + - + +
781C MET 5.2 5.2 - - - +
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Residues in contact with ASN 734 (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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780A LEU* 5.5 1.9 - - - +
730C GLU* 2.9 29.0 + - - +
733C ILE* 1.3 84.2 - - - +
735C LYS* 1.3 57.2 + - - +
738C VAL* 4.0 10.9 - - - +
739C GLY 3.0 8.2 + - - -
593D VAL* 4.4 3.8 - - + +
595D ARG* 3.5 24.8 + - - +
642D ASN* 2.8 30.1 + - - +
644D TYR* 2.6 30.7 + - - +
681D LEU* 3.4 23.9 - - + +
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Residues in contact with LYS 735 (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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731C VAL* 2.9 22.8 + - + +
734C ASN* 1.3 76.6 - - - +
736C ASN* 1.3 73.1 + - - +
737C LEU 3.4 0.9 - - - -
739C GLY* 3.2 2.8 + - - -
740C SER 3.1 26.2 + - - -
751C ALA* 3.7 13.2 - - - -
854C MET* 3.8 16.2 - - + -
857C LEU* 3.5 15.1 - - + +
202D MAH 2.8 28.8 + - - -
593D VAL* 4.9 3.8 - - + -
684D SER* 2.8 35.0 + - - +
685D GLY* 3.7 14.8 - - - -
686D ASN* 2.8 35.7 + - - +
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Residues in contact with ASN 736 (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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732C ASN* 2.8 42.3 + - - +
735C LYS* 1.3 85.2 - - - +
737C LEU* 1.3 58.6 + - - +
740C SER* 3.5 2.4 + - - -
749C TYR* 3.1 42.8 - - - +
750C ASN* 3.1 26.4 - - - +
751C ALA 3.4 10.1 + - - +
779C THR* 3.8 16.3 - - - +
850C GLU* 3.9 1.2 + - - -
854C MET* 3.7 19.3 - - - -
686D ASN* 3.2 9.9 + - - +
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Residues in contact with LEU 737 (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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733A ILE* 4.2 17.0 - - + -
737A LEU* 4.2 26.2 - - + +
738A VAL* 3.9 26.0 - - + -
741A ALA* 5.6 0.4 - - + -
749A TYR* 5.4 0.5 - - - -
732C ASN* 3.3 5.6 + - - +
733C ILE* 3.1 29.0 + - + +
736C ASN* 1.3 87.8 - - - +
738C VAL* 1.3 66.8 + - - +
740C SER* 3.7 1.6 + - - -
741C ALA* 3.1 24.0 + - - +
749C TYR* 4.0 10.9 - - + -
778C ILE* 4.1 19.7 - - + -
779C THR 4.8 2.5 - - - +
780C LEU* 4.0 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