Contacts of the helix formed by residues 798 - 810 (chain A) in PDB entry 5OQN
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 LYS 798 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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780A TRP* 3.5 30.4 - - + +
784A GLN* 4.5 7.1 - - - +
794A GLU* 6.0 4.6 - - - +
796A MET 5.1 2.0 - - - +
797A LEU* 1.3 74.4 - - - +
799A PRO* 1.3 73.7 - - + +
800A ASN* 3.1 22.9 - - - +
801A ILE* 2.8 30.0 + - + +
802A ILE* 3.2 9.2 + - - +
850A MET* 4.6 11.9 - - + +
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Residues in contact with PRO 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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773A LEU* 4.3 4.7 - - + +
776A LEU 5.4 0.2 - - - +
777A CYS* 4.0 29.8 - - - +
780A TRP* 3.5 46.0 - - + -
796A MET* 5.6 0.2 - - + -
797A LEU 3.8 1.1 - - - +
798A LYS* 1.3 84.0 - - + +
800A ASN* 1.3 56.8 + - - +
802A ILE* 3.8 14.6 - - + +
803A PHE* 2.9 29.6 + - - +
847A ILE* 4.5 5.8 - - + -
850A MET* 3.8 15.3 - - - -
851A ILE* 4.3 9.8 - - + +
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Residues in contact with ASN 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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798A LYS* 3.1 29.8 - - - +
799A PRO* 1.3 74.4 - - - +
801A ILE* 1.3 88.0 + - - +
803A PHE* 3.3 4.6 + - - +
804A GLN* 3.0 30.6 + - - +
850A MET* 3.7 34.2 - - + +
853A THR* 5.0 0.7 - - - +
854A ASN* 3.3 21.4 - - - +
1D G 5.3 6.7 - - - -
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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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797A LEU* 4.0 27.6 - - + -
798A LYS* 2.8 24.0 + - + +
800A ASN* 1.3 93.7 + - - +
802A ILE* 1.3 67.8 + - - +
804A GLN* 3.1 17.8 + - - +
805A GLN* 2.9 21.6 + - + +
406B GLU* 4.3 16.6 - - + +
408B TRP* 3.9 25.7 - - + +
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Residues in contact with ILE 802 (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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733A PHE* 4.1 24.9 - - + -
772A ILE* 5.8 0.7 - - + -
773A LEU* 4.5 13.7 - - + -
776A LEU* 3.7 37.0 - - + -
796A MET* 4.0 11.2 - - + -
797A LEU* 3.7 37.5 - - + +
798A LYS 3.2 9.3 + - - +
799A PRO* 3.8 12.6 - - + +
801A ILE* 1.3 76.9 - - - +
803A PHE* 1.3 63.2 + - - +
805A GLN* 3.1 9.0 + - - +
806A LEU* 3.0 33.3 + - + +
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Residues in contact with PHE 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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773A LEU* 3.3 31.8 - - + +
799A PRO 2.9 19.2 + - - +
800A ASN* 3.5 6.7 - - - +
801A ILE 3.2 0.2 - - - -
802A ILE* 1.3 75.2 - - - +
804A GLN* 1.3 63.4 + - - +
806A LEU* 3.1 5.6 + - + +
807A LEU* 2.9 54.8 + - + +
831A PHE* 4.3 13.0 - + - -
832A LEU* 4.2 14.1 - - + -
835A VAL* 4.2 13.7 - - + -
851A ILE* 3.1 39.9 - - + -
854A ASN* 3.8 23.6 - - + -
855A ILE* 3.6 21.5 - - + -
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Residues in contact with GLN 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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800A ASN* 3.0 22.8 + - - +
801A ILE* 3.3 21.3 + - - +
803A PHE* 1.3 77.2 - - - +
805A GLN* 1.3 57.7 + - - +
807A LEU* 3.2 9.3 + - - +
808A PHE* 2.8 30.1 + - - +
854A ASN* 3.8 32.2 + - + +
857A ALA* 6.0 1.8 - - - -
408B TRP* 3.7 16.9 - - + -
2D A 4.4 11.7 + - - -
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Residues in contact with GLN 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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732A TYR* 4.7 4.2 + - - -
733A PHE* 4.3 12.2 - - + -
801A ILE* 2.9 13.1 + - + +
802A ILE* 3.1 15.7 + - - +
804A GLN* 1.3 76.3 - - - +
806A LEU* 1.3 63.2 + - + +
808A PHE* 3.0 24.6 + - - +
809A TRP* 2.7 69.6 + - + -
404B GLY 4.7 9.1 + - - -
406B GLU 5.8 0.2 - - - +
408B TRP* 3.4 40.7 - - + +
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Residues in contact with LEU 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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729A VAL* 5.2 0.9 - - + -
733A PHE* 4.5 14.4 - - + -
765A MET* 5.0 3.1 - - - -
769A ALA* 3.5 36.6 - - + +
772A ILE* 4.6 8.1 - - + -
773A LEU* 4.0 25.8 - - + +
802A ILE* 3.0 25.0 + - + +
803A PHE* 3.1 4.2 + - - +
805A GLN* 1.3 75.1 - - - +
807A LEU* 1.3 51.8 + - - +
809A TRP* 3.9 29.7 - - + +
810A THR* 2.6 39.9 + - - +
831A PHE* 3.8 21.5 - - + -
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Residues in contact with LEU 807 (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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803A PHE* 2.9 66.1 + - + +
804A GLN* 3.6 10.1 - - - +
806A LEU* 1.3 73.8 - - - +
808A PHE* 1.3 66.3 + - - +
810A THR* 3.3 5.3 + - - -
811A ASP* 3.1 13.8 + - - +
828A GLN* 2.7 27.4 - - + +
831A PHE* 4.0 12.3 - - + -
832A LEU* 6.0 1.1 - - + -
854A ASN 3.7 20.4 - - - +
855A ILE* 4.6 1.8 - - - +
857A ALA* 3.9 21.8 - - + -
858A ILE* 4.1 22.7 - - + +
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Residues in contact with PHE 808 (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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752A PRO* 6.2 1.8 - - + -
756A PHE* 4.1 15.9 - + - -
804A GLN 2.8 13.6 + - - +
805A GLN* 3.0 18.4 + - - +
807A LEU* 1.3 74.6 - - - +
809A TRP* 1.3 74.1 + + - +
811A ASP* 2.9 15.7 + - + +
814A ASN* 3.0 47.8 - - - +
401B ASN* 5.5 4.3 - - - -
408B TRP* 3.7 32.8 - + + -
410B VAL* 4.2 33.9 - - + -
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Residues in contact with TRP 809 (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 VAL* 4.4 4.0 - - + -
732A TYR* 4.0 8.7 - + - -
733A PHE* 3.7 17.3 - + - -
747A PHE 5.7 0.4 - - - -
748A ALA* 6.3 1.3 - - - -
751A ILE* 3.5 48.2 - - + -
752A PRO* 4.2 19.6 - - + +
755A CYS* 4.0 17.9 - - + +
756A PHE* 3.4 28.4 - + - -
762A GLN* 2.9 21.0 + - - +
765A MET* 4.0 17.7 - - + -
805A GLN* 2.7 49.4 + - + +
806A LEU* 3.9 31.4 - - + +
808A PHE* 1.3 89.0 - + - +
810A THR* 1.3 59.0 + - - +
811A ASP 3.2 0.7 + - - -
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Residues in contact with THR 810 (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 GLN* 3.1 14.0 + - - +
765A MET* 3.8 26.0 - - + -
766A SER* 4.0 24.9 - - - +
769A ALA* 4.9 1.3 - - + -
806A LEU 2.6 23.7 + - - +
807A LEU* 3.3 11.3 + - - -
809A TRP* 1.3 73.2 - - - +
811A ASP* 1.3 64.2 + - - +
812A PRO* 3.1 4.7 - - - +
827A VAL* 3.3 15.4 - - - +
828A GLN* 3.7 21.4 - - - +
831A PHE* 4.2 14.1 - - + -
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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