Contacts of the helix formed by residues 783 - 797 (chain A) in PDB entry 2ONI
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 ASN 783 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A PHE* 3.4 23.7 - - + -
771A LYS* 5.0 3.6 - - - +
777A ILE* 4.3 8.3 - - - +
778A MSE 3.0 21.2 + - - -
779A VAL* 3.4 6.2 - - - +
780A THR* 2.8 33.7 + - - +
782A GLU* 1.3 79.2 - - + +
784A LYS* 1.3 66.4 + - - +
785A ARG 3.2 2.9 - - - -
786A GLU* 3.3 18.2 + - - +
787A TYR 3.0 17.0 + - - -
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Residues in contact with LYS 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A ILE* 2.7 45.5 - - + +
744A LEU* 3.5 20.2 + - - +
745A GLU 5.6 0.2 - - - -
746A ASN 3.3 12.1 - - - +
748A PRO* 3.4 24.9 - - + -
779A VAL* 4.3 4.7 - - + -
780A THR 3.0 13.1 + - - +
781A ASN* 3.3 26.8 + - - +
782A GLU 3.7 0.6 - - - -
783A ASN* 1.3 81.1 - - - +
785A ARG* 1.3 81.7 + - + +
787A TYR* 3.3 8.7 + - - +
788A ILE* 3.0 31.3 + - - +
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Residues in contact with ARG 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A LEU* 4.4 37.7 + - + +
781A ASN 5.0 5.3 + - - -
782A GLU 5.4 0.6 + - - +
783A ASN 3.2 1.0 - - - -
784A LYS* 1.3 98.8 - - + +
786A GLU* 1.3 59.0 + - - +
788A ILE* 3.4 9.1 + - + +
789A ASP* 3.0 27.9 + - - +
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Residues in contact with GLU 786 (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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755A PHE* 3.8 5.3 - - + -
771A LYS* 2.8 43.1 + - - +
783A ASN* 3.3 16.4 + - - +
785A ARG* 1.3 74.7 - - - +
787A TYR* 1.3 67.5 + - - +
789A ASP* 3.3 6.7 + - - +
790A LEU* 3.0 38.3 + - + +
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Residues in contact with TYR 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A TYR* 4.7 6.9 + - - -
740A LEU* 4.3 13.9 - - + +
743A ILE* 4.4 16.4 - - + -
753A LEU* 4.3 20.3 - - + +
754A MSE 3.4 22.8 + - - -
755A PHE* 3.4 30.2 - + + -
756A CYS 4.8 5.1 + - - -
757A ILE* 5.8 1.9 - - - +
770A LEU* 3.7 21.3 - - + -
779A VAL* 3.6 27.8 - - + -
783A ASN 3.0 8.2 + - - +
784A LYS* 3.3 13.9 - - - +
785A ARG 3.3 0.2 - - - -
786A GLU* 1.3 75.4 - - - +
788A ILE* 1.3 69.4 + - + +
790A LEU* 3.3 3.0 + - - +
791A VAL* 3.2 39.2 + - + +
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Residues in contact with ILE 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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726A LEU* 4.2 23.3 - - + -
740A LEU* 3.9 38.4 - - + +
743A ILE* 4.2 7.6 - - + -
744A LEU* 4.0 30.7 - - + +
784A LYS* 3.0 24.0 + - + +
785A ARG* 3.8 10.5 - - + +
786A GLU 3.4 0.4 - - - -
787A TYR* 1.3 77.6 - - + +
789A ASP* 1.3 66.6 + - - +
790A LEU 3.3 0.2 + - - -
791A VAL* 3.5 5.5 + - - +
792A ILE* 3.1 41.3 + - + +
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Residues in contact with ASP 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A GLN* 4.5 15.4 + - - -
724A ILE 4.9 7.1 - - - +
785A ARG 3.0 17.8 + - - +
786A GLU* 3.3 7.6 + - - +
788A ILE* 1.3 76.2 - - - +
790A LEU* 1.3 59.6 + - + +
792A ILE* 3.4 11.5 + - - +
793A GLN* 2.8 55.6 + - - +
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Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A PHE* 3.8 20.4 - - + -
770A LEU* 3.6 40.8 - - + +
771A LYS* 3.9 10.8 - - + -
786A GLU* 3.0 40.4 + - + +
787A TYR 3.7 4.0 - - - +
788A ILE 3.2 0.2 - - - -
789A ASP* 1.3 73.4 - - - +
791A VAL* 1.3 56.5 + - - +
793A GLN* 3.2 25.3 + - + +
794A TRP* 2.8 34.0 + - - +
798A ASN* 5.9 1.3 - - - +
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Residues in contact with VAL 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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729A MSE 4.6 4.0 - - + -
736A TYR* 3.7 34.3 - - + +
740A LEU* 4.2 14.8 - - + -
757A ILE* 5.0 6.3 - - + -
770A LEU* 3.7 21.7 - - + +
787A TYR* 3.2 38.3 + - + +
788A ILE* 3.7 6.7 - - - +
790A LEU* 1.3 73.7 - - - +
792A ILE* 1.3 56.1 + - - +
794A TRP* 3.1 13.8 + - + +
795A ARG* 2.8 34.3 + - + +
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Residues in contact with ILE 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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724A ILE* 3.7 41.1 - - + +
725A THR* 3.5 5.8 - - - +
726A LEU* 3.2 38.6 - - + +
729A MSE 4.9 13.9 - - + -
740A LEU* 5.0 2.0 - - + -
788A ILE* 3.1 31.4 + - + +
789A ASP* 3.5 13.2 - - - +
791A VAL* 1.3 72.0 - - - +
793A GLN* 1.3 68.9 + - + +
795A ARG* 3.2 5.1 + - - -
796A PHE* 3.0 29.7 + - + +
797A VAL* 4.5 0.3 - - - +
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Residues in contact with GLN 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A ASP* 2.8 43.7 + - - +
790A LEU* 3.4 26.1 - - + +
792A ILE* 1.3 77.2 - - + +
794A TRP* 1.3 63.6 + - - +
797A VAL* 3.0 31.9 + - + -
798A ASN* 2.9 51.8 + - - +
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Residues in contact with TRP 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A TYR* 5.6 5.6 - + - -
757A ILE* 3.7 38.4 - - + +
758A ASP 3.6 24.9 - - - -
759A GLU* 2.9 40.5 + - + -
768A VAL* 4.1 8.0 - - + +
770A LEU* 4.3 9.0 - - + -
790A LEU 2.8 16.7 + - - +
791A VAL* 3.1 12.8 + - + +
793A GLN* 1.3 79.6 - - - +
795A ARG* 1.3 99.8 + - + +
796A PHE 3.5 0.2 + - - -
797A VAL 4.6 1.0 + - - -
798A ASN* 4.9 7.2 - - + +
799A ARG* 3.5 37.3 - - + +
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Residues in contact with ARG 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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666A SER 3.3 20.2 + - - -
674A GLN* 2.9 40.7 + - - +
729A MSE 3.8 20.6 - - + -
732A VAL* 3.7 16.2 - - - +
733A ASP* 6.2 0.8 - - - +
736A TYR* 5.8 3.6 - - + -
791A VAL* 2.8 17.2 + - + +
792A ILE 3.2 3.6 + - - +
794A TRP* 1.3 106.4 - - + +
796A PHE* 1.3 89.3 + - + +
799A ARG* 5.9 0.2 - - - -
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Residues in contact with PHE 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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712A ILE* 3.5 32.0 - - + +
714A PRO* 3.8 23.2 - - + +
718A MSE 3.3 18.9 - - - +
724A ILE* 3.8 23.1 - - + -
725A THR 5.3 0.9 - - - -
728A ASP* 5.3 0.2 - - + -
729A MSE 3.9 37.0 - - + -
732A VAL* 4.1 17.5 - - + -
792A ILE* 3.0 21.1 + - + +
795A ARG* 1.3 121.4 - - + +
797A VAL* 1.3 61.2 + - + +
799A ARG* 6.4 0.4 - - - -
800A VAL* 3.6 12.6 - - - +
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Residues in contact with VAL 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A MSE 4.3 8.0 - - + +
724A ILE* 3.6 33.2 - - + -
792A ILE* 4.5 0.7 - - + +
793A GLN* 3.0 23.4 + - + +
794A TRP 4.6 1.0 + - - -
795A ARG 4.0 0.2 - - - -
796A PHE* 1.3 86.1 - - + +
798A ASN* 1.3 77.3 + - - +
799A ARG 3.2 3.9 + - - +
800A VAL* 3.3 13.9 + - - +
801A GLN* 3.5 34.6 + - + +
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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