Contacts of the helix formed by residues 793 - 807 (chain A) in PDB entry 2P8Q
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 ARG 793 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733A GLU* 5.0 5.5 + - - +
736A LEU* 3.8 49.4 + - + +
737A ASN* 3.4 31.7 + - - +
740A GLN* 3.6 24.6 + - - +
769A TYR* 5.7 1.3 - - + -
789A LEU 4.9 0.6 + - - +
790A VAL* 2.5 33.5 + - + +
792A PRO* 1.3 79.9 - - + +
794A VAL* 1.3 63.6 + - - +
795A GLU 3.2 2.9 - - - -
796A PHE* 3.0 20.6 + - + +
797A ILE* 3.0 22.1 + - + +
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Residues in contact with VAL 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 VAL 3.5 0.9 + - - +
791A GLN* 3.0 22.6 + - - +
793A ARG* 1.3 77.9 - - - +
795A GLU* 1.3 65.2 + - - +
796A PHE 3.2 0.3 + - - -
797A ILE* 3.2 9.4 + - + +
798A LEU* 2.9 46.3 + - + +
825A LEU* 4.5 9.2 - - + -
829A PHE* 3.2 44.9 - - + -
833A VAL* 4.5 15.5 - - + -
836A LEU* 4.0 10.8 - - + -
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Residues in contact with GLU 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 GLN 4.7 0.4 + - - -
792A PRO 4.6 8.7 + - - +
793A ARG 3.2 0.8 - - - -
794A VAL* 1.3 78.9 - - - +
796A PHE* 1.3 57.9 + - - +
798A LEU* 3.7 3.3 - - - +
799A SER* 3.1 30.7 + - - +
836A LEU* 3.5 35.3 - - + +
840A ARG* 2.6 33.9 + - - -
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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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740A GLN* 2.9 53.8 - - - +
743A SER* 3.4 27.1 - - - -
744A GLN* 4.4 12.8 - - + -
769A TYR* 3.5 25.8 - + - -
793A ARG* 3.0 15.9 + - + +
795A GLU* 1.3 77.8 - - - +
797A ILE* 1.3 64.1 + - + +
798A LEU 3.1 2.0 - - - -
799A SER* 3.0 11.2 + - - -
800A PHE* 2.8 34.6 + - + +
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Residues in contact with ILE 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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769A TYR* 3.9 46.2 - - + +
773A VAL* 5.5 2.0 - - + -
790A VAL* 4.4 10.8 - - + -
793A ARG* 3.0 29.6 + - + +
794A VAL* 3.8 9.0 - - - +
796A PHE* 1.3 78.4 - - + +
798A LEU* 1.3 57.7 + - - +
800A PHE* 3.2 10.2 + - + +
801A ILE* 3.0 32.9 + - + +
821A LEU* 3.2 34.1 - - + -
825A LEU* 4.4 22.7 - - + -
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Residues in contact with LEU 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 VAL* 2.9 26.7 + - + +
795A GLU* 3.7 4.7 - - - +
797A ILE* 1.3 78.9 - - - +
799A SER* 1.3 56.6 + - - +
801A ILE* 3.1 5.8 + - - +
802A ASP* 2.8 28.8 + - - +
822A ILE* 3.7 28.3 - - + -
825A LEU* 3.9 14.6 - - + -
833A VAL* 4.4 6.1 - - + +
836A LEU* 3.4 45.5 - - + -
837A VAL* 4.2 22.2 - - + -
840A ARG* 3.4 12.8 + - - +
843A ILE* 4.4 8.3 - - + +
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Residues in contact with SER 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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795A GLU* 3.1 17.9 + - - +
796A PHE* 3.0 18.6 + - - -
798A LEU* 1.3 76.3 - - - +
800A PHE* 1.3 57.5 + - - +
802A ASP* 3.5 3.8 - - - +
803A HIS* 2.9 30.5 + - - +
840A ARG* 3.1 23.7 + - - +
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Residues in contact with PHE 800 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743A SER* 3.6 54.7 - - - -
762A ARG* 3.9 34.5 - - + -
765A CYS* 3.9 13.2 - - + -
766A LEU* 3.6 31.9 - - + -
769A TYR* 4.5 9.9 - + - -
796A PHE* 2.8 20.3 + - + +
797A ILE* 3.4 13.5 - - + +
799A SER* 1.3 76.2 - - - +
801A ILE* 1.3 60.2 + - + +
803A HIS* 3.6 5.8 + + + +
804A ILE* 2.9 54.3 + - + +
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Residues in contact with ILE 801 (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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766A LEU* 3.4 34.8 - - + -
797A ILE* 3.0 22.4 + - + +
798A LEU* 3.1 7.8 + - - +
800A PHE* 1.3 77.1 - - + +
802A ASP* 1.3 62.0 + - - +
804A ILE* 2.9 22.1 + - + +
805A ALA* 2.9 12.0 + - - +
818A ALA* 3.9 20.6 - - + +
821A LEU* 4.1 10.3 - - + -
822A ILE* 3.9 28.5 - - + -
843A ILE* 4.5 13.7 - - + -
846A LEU* 4.0 21.5 - - + +
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Residues in contact with ASP 802 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798A LEU 2.8 15.5 + - - +
799A SER* 3.5 6.3 - - - +
801A ILE* 1.3 77.7 - - - +
803A HIS* 1.3 60.8 + - - +
805A ALA* 3.3 11.3 + - - +
806A GLY* 3.3 10.2 + - - -
840A ARG* 3.1 40.7 + - + +
842A MET* 3.3 24.6 - - - +
843A ILE* 4.3 8.7 - - + +
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Residues in contact with HIS 803 (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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743A SER 6.1 0.7 - - - -
746A GLN* 4.9 21.5 + - + +
762A ARG* 4.4 16.2 - - - -
799A SER 2.9 17.2 + - - +
800A PHE* 3.8 9.6 - + + +
802A ASP* 1.3 76.0 - - - +
804A ILE* 1.3 65.7 + - + +
806A GLY* 3.5 6.2 + - - +
807A ASP* 3.4 30.2 + - - +
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Residues in contact with ILE 804 (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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762A ARG* 2.9 57.2 - - + +
766A LEU* 5.7 2.0 - - + -
800A PHE* 2.9 41.5 + - + +
801A ILE* 2.9 15.8 + - + +
803A HIS* 1.3 79.6 - - + +
805A ALA* 1.3 52.8 + - - +
806A GLY 3.6 0.2 + - - -
807A ASP* 3.6 6.2 + - - +
809A ASP 5.7 0.4 - - - +
810A HIS* 2.6 36.9 + - + -
814A VAL* 3.6 30.7 - - + -
818A ALA* 5.2 3.4 - - + -
846A LEU* 5.0 11.0 - - + -
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Residues in contact with ALA 805 (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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801A ILE 2.9 10.5 + - - +
802A ASP* 3.4 11.7 - - - +
804A ILE* 1.3 76.6 - - - +
806A GLY* 1.3 64.7 + - - +
808A GLU* 5.5 0.9 - - - +
810A HIS* 3.2 23.3 + - - -
842A MET* 3.3 45.7 - - + +
843A ILE* 4.4 1.1 - - - +
846A LEU* 4.0 16.6 - - + +
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Residues in contact with GLY 806 (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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802A ASP 3.3 9.7 + - - -
803A HIS* 3.5 4.2 + - - -
804A ILE 3.4 0.2 - - - -
805A ALA* 1.3 81.2 - - - +
807A ASP* 1.3 57.9 + - - +
808A GLU* 3.0 20.1 + - - +
842A MET* 3.3 21.5 - - - +
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Residues in contact with ASP 807 (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 LYS* 5.7 0.7 - - - +
758A LEU* 5.1 1.4 - - - +
762A ARG* 2.9 31.6 + - - +
803A HIS* 3.4 22.3 + - - +
804A ILE 3.9 7.6 - - - +
805A ALA 3.4 0.8 - - - -
806A GLY* 1.3 75.9 - - - +
808A GLU* 1.3 54.0 + - - +
809A ASP* 2.6 28.9 + - - +
810A HIS* 2.6 36.8 + - - -
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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