Contacts of the helix formed by residues 806 - 819 (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 VAL 806 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802F ILE* 4.0 19.5 - - + +
803F ASP 5.8 0.7 - - - +
805F ASP* 1.3 72.7 + - - +
807F ARG* 1.3 67.8 + - + +
808F ASN 3.1 1.2 + - - -
809F PHE* 3.8 11.6 + - - +
810F GLN* 3.8 12.0 - - - +
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Residues in contact with ARG 807 (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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805F ASP* 2.9 28.8 + - - +
806F VAL* 1.3 80.7 - - + +
808F ASN* 1.3 62.6 + - - +
809F PHE 3.3 0.2 - - - -
810F GLN* 3.3 12.1 + - - +
811F VAL* 3.1 26.6 + - + +
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Residues in contact with ASN 808 (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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716F LEU* 3.7 27.7 - - + +
801F ALA* 2.9 33.7 + - + +
802F ILE* 4.6 0.4 - - - -
804F LYS* 3.7 21.9 + - - +
805F ASP* 3.1 30.8 + - - +
807F ARG* 1.3 77.2 - - - +
809F PHE* 1.3 59.1 + - - +
811F VAL* 3.2 11.5 + - - +
812F LEU* 2.9 33.6 + - - +
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Residues in contact with PHE 809 (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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802F ILE* 3.8 39.4 - - + +
805F ASP 4.3 0.8 + - - -
806F VAL 3.8 11.7 + - - +
807F ARG 3.3 0.6 - - - -
808F ASN* 1.3 78.1 - - - +
810F GLN* 1.3 69.2 + - - +
812F LEU* 3.3 3.8 + - - +
813F LYS* 3.1 49.3 + - + +
870F LEU* 6.6 0.2 - - + -
873F GLN* 3.9 44.6 - - + -
874F ILE* 4.3 12.1 - - + -
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Residues in contact with GLN 810 (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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806F VAL 3.8 14.0 - - - +
807F ARG* 3.3 10.1 + - - +
809F PHE* 1.3 86.1 - - - +
811F VAL* 1.3 58.4 + - + +
813F LYS* 3.2 30.9 + - - +
814F GLU* 2.9 48.0 + - + +
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Residues in contact with VAL 811 (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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712F GLU* 4.6 14.6 - - + +
713F TRP* 4.0 25.3 + - + +
716F LEU* 4.0 17.9 - - + -
807F ARG* 3.1 23.3 - - + +
808F ASN* 3.2 15.4 + - - +
810F GLN* 1.3 77.7 - - + +
812F LEU* 1.3 57.2 + - - +
814F GLU* 3.4 15.3 + - - +
815F MET* 2.9 28.0 + - - +
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Residues in contact with LEU 812 (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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716F LEU* 3.9 15.3 - - + -
720F MET* 3.7 29.8 - - + -
798F PHE* 4.5 6.3 - - + +
801F ALA* 4.2 12.8 - - + -
802F ILE* 3.5 31.9 - - + -
808F ASN 2.9 14.0 + - - +
809F PHE 3.6 5.6 - - - +
810F GLN 3.2 0.2 - - - -
811F VAL* 1.3 73.3 - - - +
813F LYS* 1.3 64.9 + - - +
815F MET* 3.2 16.6 + - + +
816F TYR* 3.0 23.7 + - - +
822F PHE* 3.9 8.7 - - + -
874F ILE* 3.7 34.4 - - + +
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Residues in contact with LYS 813 (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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809F PHE* 3.1 48.2 + - + +
810F GLN* 3.6 33.2 - - + +
812F LEU* 1.3 75.0 - - - +
814F GLU* 1.3 63.5 + - + +
816F TYR* 3.3 3.8 + - - +
817F ASN* 3.1 31.8 + - - +
873F GLN 4.0 15.3 - - - +
874F ILE* 3.5 25.5 - - - +
876F GLY* 5.6 4.7 - - - +
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Residues in contact with GLU 814 (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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713F TRP* 4.8 6.7 + - + +
810F GLN* 2.9 35.8 + - + +
811F VAL* 3.8 16.6 - - - +
813F LYS* 1.3 73.5 - - + +
815F MET* 1.3 61.5 + - - +
817F ASN* 3.2 5.9 + - - +
818F GLU* 2.8 54.3 + - - +
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Residues in contact with MET 815 (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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713F TRP* 3.4 52.5 - - + +
716F LEU* 4.5 4.7 - - + -
717F MET* 4.0 15.9 - - + -
720F MET* 4.6 1.1 - - + -
811F VAL* 2.9 25.7 + - - +
812F LEU* 3.2 20.4 + - + +
814F GLU* 1.3 76.1 - - - +
816F TYR* 1.3 56.8 + - - +
819F TRP* 2.9 48.2 + - + +
822F PHE* 3.4 45.7 - - + +
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Residues in contact with TYR 816 (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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131F PHE* 5.0 0.2 - - - -
812F LEU 3.0 12.7 + - - +
813F LYS 3.6 7.0 - - - +
814F GLU 3.3 0.4 - - - -
815F MET* 1.3 76.9 - - - +
817F ASN* 1.3 71.9 + - - +
818F GLU 3.8 0.2 + - - -
819F TRP 4.5 0.5 - - - +
822F PHE* 3.6 13.2 - - + -
823F ARG* 3.3 70.5 + - + +
826F LEU* 4.3 25.4 - - + -
827F ASP* 3.4 24.3 + - - -
830F GLU* 4.2 1.2 + - - -
874F ILE* 4.0 10.5 - - + +
875F ALA* 3.3 45.3 - - + -
877F HIS* 3.1 26.2 + - - -
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Residues in contact with ASN 817 (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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131F PHE* 3.3 19.4 - - - -
813F LYS* 3.1 20.6 + - - +
814F GLU* 3.2 7.1 + - - +
816F TYR* 1.3 89.4 - - - +
818F GLU* 1.3 65.4 + - + +
819F TRP 3.8 0.2 - - - -
823F ARG* 3.7 22.1 + - - +
875F ALA 5.2 2.0 + - - -
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Residues in contact with GLU 818 (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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131F PHE* 4.0 10.2 - - - -
707F VAL* 3.5 22.2 - - - +
710F LYS* 5.4 5.6 + - - -
713F TRP* 3.8 22.2 - - + -
814F GLU* 2.8 38.6 + - - +
817F ASN* 1.3 85.9 - - + +
819F TRP* 1.3 61.7 + - - +
820F PRO* 3.5 5.0 - - - +
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Residues in contact with TRP 819 (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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131F PHE* 4.6 2.7 - - - -
615F TRP* 3.6 30.7 - + - -
618F TYR* 4.3 10.0 + + - -
658F SER 5.8 0.2 + - - -
706F PRO* 6.0 0.7 - - + -
707F VAL* 4.3 11.6 + - + -
709F PRO* 3.5 35.6 - - + +
713F TRP* 3.5 44.2 - + + -
717F MET* 3.9 20.4 - - + -
815F MET* 2.9 28.9 + - + +
817F ASN 3.8 0.6 - - - -
818F GLU* 1.3 76.8 - - - +
820F PRO* 1.3 77.7 - - + +
821F PHE* 3.6 37.4 - + + +
822F PHE* 3.1 15.5 + - + -
823F ARG* 3.1 19.2 + - - +
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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