Contacts of the helix formed by residues 786 - 800 (chain A) in PDB entry 1QXP
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 PHE 786 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A ILE* 5.5 12.6 - - + -
731A VAL* 5.6 12.6 - - + -
733A LEU* 6.2 1.8 - - + -
737A ASP 5.7 5.6 - - - +
738A MET* 4.8 4.7 - - + +
785A GLY* 1.4 67.7 - - - +
787A GLU* 1.3 71.2 + - + +
788A GLU* 3.8 2.2 + - - -
789A PHE* 2.9 7.3 + - - +
790A LYS* 2.9 23.5 + - - +
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Residues in contact with GLU 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A ILE* 4.4 22.1 - - + +
786A PHE* 1.3 81.1 - - + +
788A GLU* 1.3 65.2 + - - +
789A PHE 3.1 0.2 - - - -
790A LYS* 3.4 13.7 + - - +
791A TYR* 3.0 27.5 + - - +
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Residues in contact with GLU 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776A MET* 3.7 32.9 - - + +
777A ASP* 5.9 1.1 - - - -
778A SER* 5.5 4.7 + - - -
784A LEU* 3.9 12.8 - - + +
785A GLY* 3.0 43.6 - - - +
786A PHE 3.2 2.8 + - - -
787A GLU* 1.3 78.2 + - - +
789A PHE* 1.3 56.9 + - - +
791A TYR* 3.9 8.7 - - - -
792A LEU* 3.6 15.9 + - - +
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Residues in contact with PHE 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A VAL* 4.7 22.0 - - + -
733A LEU* 6.1 0.2 - - + -
740A VAL* 4.9 16.4 - - + -
745A LEU* 4.6 20.2 - - + -
748A ILE* 5.6 8.5 - - + -
749A LEU* 5.1 3.4 - - + -
784A LEU* 4.2 18.8 - - + -
785A GLY 3.3 20.1 + - - +
786A PHE* 2.9 6.9 + - - +
788A GLU* 1.3 69.9 - - - +
790A LYS* 1.4 62.8 + - - +
792A LEU* 3.3 7.4 + - + +
793A TRP* 3.1 67.7 + + + +
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Residues in contact with LYS 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786A PHE 2.9 10.3 + - - +
787A GLU* 3.4 21.8 - - - +
789A PHE* 1.4 80.2 - - - +
791A TYR* 1.3 63.4 + - - +
793A TRP* 3.8 7.6 - - - +
794A ASN* 3.2 32.9 + - - +
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Residues in contact with TYR 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 5.5 4.7 - - + -
776A MET* 3.2 31.2 - - + -
787A GLU 3.0 17.3 + - - +
788A GLU* 4.3 7.2 - - - +
789A PHE 3.3 0.4 - - - -
790A LYS* 1.3 74.8 - - - +
792A LEU* 1.3 65.9 + - - +
793A TRP 3.1 0.7 + - - -
794A ASN* 3.3 13.0 + - - +
795A ASN* 3.5 23.3 + - - -
862A ASP* 3.4 31.0 + - - -
866A ARG* 5.8 1.7 - - - +
869A ARG* 5.3 5.0 + - - -
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Residues in contact with LEU 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745A LEU* 4.2 21.1 - - + -
749A LEU* 6.3 1.1 - - + -
772A MET* 3.7 31.6 - - + +
776A MET* 4.3 22.2 - - + -
784A LEU* 4.3 13.7 - - + -
788A GLU 3.6 10.7 + - - +
789A PHE* 3.3 13.3 + - + +
791A TYR* 1.3 86.4 - - - +
793A TRP* 1.3 58.6 + - + +
794A ASN 3.5 0.2 - - - -
795A ASN* 3.4 6.7 + - - +
796A ILE* 3.2 23.2 + - + +
799A TRP* 5.0 2.2 - - + -
859A VAL* 3.5 35.0 - - + -
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Residues in contact with TRP 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748A ILE* 5.0 17.9 - - + -
749A LEU* 4.1 30.5 - - + -
789A PHE* 3.1 46.2 + + + +
790A LYS* 3.8 7.4 - - - +
792A LEU* 1.3 78.6 - - + +
794A ASN* 1.4 73.4 + - - +
795A ASN 2.9 1.8 - - - -
796A ILE* 3.8 8.3 - - + -
797A LYS* 3.1 62.3 + - + +
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Residues in contact with ASN 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A LYS* 3.2 23.6 + - - +
791A TYR* 3.3 5.8 + - - +
793A TRP* 1.4 70.5 - - - +
795A ASN* 1.3 69.7 + - - +
797A LYS* 4.7 4.5 - - - +
798A LYS* 3.4 19.3 + - - +
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Residues in contact with ASN 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A TYR* 3.5 25.4 + - - +
792A LEU* 3.4 8.8 + - + +
793A TRP 2.9 1.4 - - - -
794A ASN* 1.3 87.3 + - - +
796A ILE* 1.3 60.0 + - - +
798A LYS* 4.0 12.6 - - - +
799A TRP* 2.5 80.3 + - + +
862A ASP* 4.0 9.7 - - - +
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Residues in contact with ILE 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A LEU* 4.2 24.2 - - + -
772A MET* 5.7 0.4 - - + -
792A LEU* 3.2 18.1 + - + +
793A TRP* 3.6 10.7 + - + +
795A ASN* 1.3 82.9 - - - +
797A LYS* 1.3 58.6 + - + +
799A TRP* 2.9 18.2 + - + +
800A GLN* 3.1 16.1 + - - +
851A PHE* 5.7 4.0 - - + -
855A ILE* 4.1 27.3 - - + +
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Residues in contact with LYS 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A TRP* 3.1 55.0 + - + +
794A ASN* 4.7 4.5 - - - +
796A ILE* 1.3 78.8 - - + +
798A LYS* 1.3 59.5 + - - +
800A GLN* 3.2 46.8 + - - +
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Residues in contact with LYS 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794A ASN 3.4 14.9 + - - +
795A ASN* 3.0 20.8 + - - +
797A LYS* 1.3 73.8 - - - +
799A TRP* 1.3 72.9 + - + +
800A GLN 2.8 8.8 + - - -
801A GLY 3.8 10.9 + - - +
826A ALA* 3.9 23.9 + - - +
827A GLY* 5.7 0.2 - - - -
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Residues in contact with TRP 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A LEU* 5.0 0.7 - - + -
795A ASN* 2.5 68.0 + - + +
796A ILE* 2.9 7.8 + - - +
798A LYS* 1.3 81.9 - - + +
800A GLN* 1.3 66.7 + - - +
801A GLY 3.6 0.2 - - - -
802A ILE* 3.1 19.3 - - + +
826A ALA* 3.7 35.8 + - + +
828A PHE* 4.1 17.2 - + - -
854A PHE* 3.8 12.3 - + + -
855A ILE* 3.9 18.2 - - + -
858A LEU* 2.3 48.3 - - + +
859A VAL* 3.2 28.5 - - + -
862A ASP* 4.0 13.9 - - + -
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Residues in contact with GLN 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760A LYS 5.2 8.8 - - - -
796A ILE 3.1 12.5 + - - +
797A LYS* 3.2 43.9 + - - +
798A LYS 2.8 6.5 + - - -
799A TRP* 1.3 76.4 - - - +
801A GLY* 1.4 60.4 + - - +
802A ILE* 2.8 7.6 + - - -
851A PHE* 3.2 45.9 - - + -
854A PHE* 4.7 4.2 - - - -
855A ILE* 4.4 0.2 - - - -
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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