Contacts of the helix formed by residues 773 - 784 (chain F) in PDB entry 6V3O
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 773 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294F ASP* 2.6 54.3 + - - -
295F GLY* 4.0 5.6 - - - -
456F ARG* 3.8 13.5 - - - +
606F LYS* 4.4 2.0 - - - -
759F ARG* 3.3 45.6 - - - +
760F PRO 4.3 6.7 - - - -
761F ALA 3.2 23.1 + - - +
762F LYS* 4.5 1.8 - - - -
763F ARG* 3.4 25.1 - - + +
771F THR 4.3 5.8 - - - +
772F LEU* 1.3 80.1 - - - +
774F ALA* 1.3 65.8 + - - +
775F ILE 3.5 0.2 - - - -
776F PRO* 3.1 10.9 - - + +
777F TRP* 3.1 17.0 + - - +
1001F SO4 3.9 5.1 + - - -
1002F SO4 2.8 34.1 + - - +
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Residues in contact with ALA 774 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602F SER* 4.1 33.4 - - - +
603F ASP* 4.4 5.4 - - - +
606F LYS* 4.4 4.9 - - + -
641F ARG* 5.1 2.0 - - - -
773F ARG* 1.3 71.2 - - - +
775F ILE* 1.3 67.6 + - - +
777F TRP* 3.1 10.3 + - - +
778F ILE* 3.0 28.1 + - - +
1001F SO4 3.8 14.8 + - - +
1002F SO4 3.1 21.2 + - - +
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Residues in contact with ILE 775 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F PRO* 4.9 15.3 - - + -
641F ARG* 3.2 45.3 - - - +
751F TYR* 4.3 17.3 - - + +
759F ARG* 3.6 19.1 - - - +
774F ALA* 1.3 74.4 - - - +
776F PRO* 1.3 66.6 - - + +
778F ILE* 3.6 8.1 - - + +
779F PHE* 2.8 34.8 + - + +
1001F SO4 3.4 20.6 - - - +
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Residues in contact with PRO 776 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742F PHE* 4.7 0.3 - - - -
748F GLU* 3.4 26.5 - - - +
751F TYR* 4.4 16.6 - - + -
759F ARG* 3.9 3.8 - - - +
761F ALA* 3.8 33.2 - - + +
772F LEU* 4.4 5.6 - - + -
773F ARG* 3.1 21.8 - - + +
775F ILE* 1.3 94.7 - - + +
777F TRP* 1.3 60.3 + - - +
779F PHE* 4.1 6.5 - - + -
780F SER* 2.6 31.1 + - - +
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Residues in contact with TRP 777 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602F SER 5.3 1.3 - - - -
605F GLY 5.5 0.2 - - - -
606F LYS* 3.4 39.4 - - + +
728F TYR* 3.5 23.4 + + - -
732F VAL* 4.2 9.6 - - + -
738F PHE* 3.8 25.8 - + - -
742F PHE* 4.1 7.2 - + - -
769F ILE* 3.9 28.5 - - + -
772F LEU* 3.6 19.5 - - + +
773F ARG 3.1 15.6 + - - +
774F ALA* 3.1 11.3 + - - +
776F PRO* 1.3 79.1 - - - +
778F ILE* 1.3 66.4 + - + +
780F SER* 4.6 0.3 - - - -
781F TRP* 3.3 55.9 + - - -
788F LEU* 4.9 3.6 - - + -
789F PRO* 3.4 35.1 - - + +
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Residues in contact with ILE 778 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602F SER* 4.2 12.1 - - - +
641F ARG* 3.4 29.6 - - - +
675F GLU* 5.3 2.5 - - - +
774F ALA* 3.0 17.9 + - - +
775F ILE* 3.6 6.3 - - - +
777F TRP* 1.3 81.9 - - + +
779F PHE* 1.3 66.0 + - + +
781F TRP* 4.0 0.4 - - - -
782F THR* 2.6 36.6 + - - +
789F PRO* 4.2 23.6 - - + -
790F VAL* 5.6 2.7 - - + -
969F THR* 4.6 9.0 - - - +
970F GLY* 3.5 37.0 - - - +
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Residues in contact with PHE 779 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F PRO* 4.5 16.2 - - + -
179F THR* 3.6 32.1 - - + -
747F PRO* 5.6 1.8 - - + -
751F TYR* 3.4 43.3 - + + -
756F ILE* 5.4 0.2 - - + -
775F ILE* 2.8 25.5 + - + +
776F PRO* 4.0 4.5 - - + +
778F ILE* 1.3 79.7 - - + +
780F SER* 1.3 64.4 + - - +
782F THR* 3.1 7.7 + - + -
783F GLN* 3.0 70.1 + - + +
959F MET* 4.3 13.5 - - + -
963F ALA* 4.1 6.7 - - + -
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Residues in contact with SER 780 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742F PHE* 4.0 7.0 - - - -
746F THR* 3.5 15.2 - - - -
747F PRO* 3.8 5.7 - - - +
748F GLU* 2.6 43.6 + - - +
751F TYR* 5.2 0.5 - - - +
776F PRO* 2.6 24.3 + - - +
779F PHE* 1.3 85.7 - - - +
781F TRP* 1.3 60.1 + - - +
783F GLN* 3.6 6.3 + - - -
784F THR* 3.4 21.5 - - - +
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Residues in contact with TRP 781 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738F PHE* 4.2 6.3 - + - -
741F TYR* 3.8 29.6 - + - -
742F PHE* 3.3 43.4 - + + -
745F ALA* 4.6 5.8 - - + -
746F THR* 3.6 23.3 - - + -
777F TRP* 3.3 40.1 + + - +
778F ILE 4.5 0.9 - - - +
779F PHE 3.3 0.4 - - - -
780F SER* 1.3 76.9 - - - +
782F THR* 1.3 63.8 + - - +
784F THR* 3.4 20.0 + - - -
786F PHE* 3.4 34.7 + + + -
787F HIS* 3.2 18.9 + - - +
788F LEU* 3.7 24.6 - - + +
789F PRO* 3.5 34.1 - - + -
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Residues in contact with THR 782 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778F ILE* 2.6 24.9 + - - +
779F PHE* 3.1 7.1 + - + -
781F TRP* 1.3 75.4 - - - +
783F GLN* 1.3 69.5 + - - +
785F ARG* 3.3 12.0 + - - -
787F HIS* 3.7 24.7 + - + -
790F VAL* 5.9 0.7 - - - +
962F ILE* 4.3 1.4 - - + +
963F ALA* 6.0 1.6 - - - -
966F MET* 3.8 36.5 - - + +
967F GLN 5.3 2.5 - - - +
969F THR* 3.1 25.5 + - + +
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Residues in contact with GLN 783 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747F PRO* 4.0 11.7 - - + -
779F PHE* 3.0 56.6 + - + +
780F SER 3.9 7.0 - - - +
781F TRP 3.3 0.8 - - - -
782F THR* 1.3 82.1 - - - +
784F THR* 1.3 51.9 + - - +
785F ARG* 3.3 1.1 + - - +
844F TYR* 3.6 2.4 + - - -
902F ASN* 2.8 31.4 + - - -
905F GLN* 3.0 36.1 + - - +
959F MET* 3.1 30.7 + - - +
962F ILE* 3.8 14.1 - - - +
963F ALA* 3.6 14.8 - - - +
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Residues in contact with THR 784 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745F ALA 3.4 24.9 - - - +
746F THR* 3.8 11.4 - - + -
747F PRO* 3.9 6.3 - - + -
780F SER 3.4 16.8 - - - +
781F TRP* 3.4 18.1 + - - -
782F THR 3.3 0.4 - - - -
783F GLN* 1.3 76.1 - - - +
785F ARG* 1.3 68.8 + - - +
786F PHE* 3.3 15.8 + - - +
840F ILE* 3.9 2.6 - - - +
841F ALA* 3.5 22.7 + - - +
844F TYR* 3.8 26.7 - - + -
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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