Contacts of the helix formed by residues 807 - 819 (chain B) 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 807 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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805B ASP* 3.0 35.2 + - - +
806B VAL* 1.3 88.3 - - + +
808B ASN* 1.3 62.2 + - - +
809B PHE 3.3 0.7 - - - -
810B GLN* 3.3 20.3 + - + +
811B VAL* 3.3 12.4 + - - +
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Residues in contact with ASN 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B LYS* 5.2 6.0 + - - +
716B LEU* 4.0 27.6 - - + +
801B ALA* 2.9 34.9 + - + +
804B LYS* 4.1 12.1 - - - +
805B ASP* 3.0 31.5 + - - +
807B ARG* 1.3 78.8 - - - +
809B PHE* 1.3 64.3 + - - +
811B VAL* 3.0 28.8 - - + +
812B LEU* 3.0 14.2 + - - +
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Residues in contact with PHE 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802B ILE* 3.6 38.3 - - + +
805B ASP 4.4 1.0 + - - -
806B VAL 3.6 10.8 + - - +
807B ARG 3.3 0.6 - - - -
808B ASN* 1.3 78.8 - - - +
810B GLN* 1.3 63.4 + - + +
812B LEU* 3.4 0.9 + - - +
813B LYS* 3.1 44.3 + - + +
873B GLN* 3.9 49.4 - - + -
874B ILE* 4.2 11.7 - - + -
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Residues in contact with GLN 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B VAL 4.6 1.0 + - - +
807B ARG* 3.3 14.0 + - - +
808B ASN 3.2 0.4 - - - -
809B PHE* 1.3 81.0 - - + +
811B VAL* 1.3 58.5 + - - +
813B LYS* 3.6 22.9 + - + +
814B GLU* 3.0 47.4 + - + +
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Residues in contact with VAL 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712B GLU* 4.4 15.7 - - + +
713B TRP* 3.9 26.7 - - + +
716B LEU* 3.4 26.9 - - + -
807B ARG 3.3 6.7 + - - +
808B ASN* 3.0 30.2 + - - +
810B GLN* 1.3 77.3 - - - +
812B LEU* 1.3 60.0 + - - +
814B GLU* 3.3 15.0 + - - +
815B MET* 2.9 33.5 + - - +
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Residues in contact with LEU 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716B LEU* 3.5 25.4 - - + -
720B MET* 3.8 25.6 - - + -
798B PHE 4.8 0.7 - - - +
801B ALA* 4.1 15.3 - - + -
802B ILE* 3.7 26.5 - - + -
808B ASN 3.0 16.9 + - - +
809B PHE 3.9 3.1 - - - +
811B VAL* 1.3 75.1 - - - +
813B LYS* 1.3 64.7 + - - +
815B MET* 3.1 20.3 + - + +
816B TYR* 2.9 23.6 + - - +
822B PHE* 3.9 6.9 - - + -
874B ILE* 3.8 32.8 - - + +
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Residues in contact with LYS 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809B PHE* 3.1 46.5 + - + +
810B GLN* 3.7 26.3 + - + +
812B LEU* 1.3 75.9 - - - +
814B GLU* 1.3 59.2 + - + +
816B TYR* 3.3 2.9 + - - +
817B ASN* 2.7 38.4 + - - +
873B GLN 4.2 10.1 - - - +
874B ILE* 3.5 23.1 - - - +
876B GLY* 5.5 4.9 - - - +
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Residues in contact with GLU 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713B TRP* 4.8 6.9 + - + +
810B GLN* 3.0 43.2 + - + +
811B VAL* 3.6 18.6 - - - +
813B LYS* 1.3 75.7 - - + +
815B MET* 1.3 58.2 + - - +
817B ASN* 3.2 5.0 + - - +
818B GLU* 2.8 56.7 + - - +
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Residues in contact with MET 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713B TRP* 3.3 49.1 - - + +
716B LEU* 4.7 9.4 - - + -
717B MET* 4.0 16.6 - - + -
811B VAL* 2.9 20.0 + - - +
812B LEU* 3.1 24.4 + - + +
814B GLU* 1.3 76.6 - - - +
816B TYR* 1.3 57.3 + - - +
819B TRP* 2.9 49.2 + - + +
822B PHE* 3.5 45.7 - - + +
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Residues in contact with TYR 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 4.9 0.3 - - - -
812B LEU 2.9 12.5 + - - +
813B LYS 3.6 7.9 - - - +
814B GLU 3.3 0.2 - - - -
815B MET* 1.3 77.4 - - - +
817B ASN* 1.3 71.4 + - - +
819B TRP 4.7 0.5 + - - -
822B PHE* 3.6 12.7 - + + -
823B ARG* 3.3 64.7 + - + +
826B LEU* 4.3 28.0 - - + -
827B ASP* 3.0 25.3 + - - -
830B GLU* 3.9 2.2 + - - -
871B LEU* 5.9 0.2 - - + -
874B ILE* 4.0 10.5 - - + +
875B ALA* 3.5 44.4 - - + +
877B HIS* 3.4 22.8 - - - -
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Residues in contact with ASN 817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 3.3 18.1 - - - -
813B LYS* 2.7 33.0 + - - +
814B GLU* 3.9 5.3 - - - +
815B MET 3.2 0.6 - - - -
816B TYR* 1.3 92.7 - - - +
818B GLU* 1.3 65.1 + - + +
819B TRP 3.9 0.2 - - - -
823B ARG* 4.2 14.1 + - - +
874B ILE 5.2 1.2 + - - -
875B ALA 5.1 3.9 + - - +
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Residues in contact with GLU 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 3.8 12.1 - - - -
707B VAL* 4.1 15.2 - - - +
710B LYS* 5.1 4.7 - - - -
713B TRP* 3.8 25.2 - - + -
814B GLU* 2.8 37.0 + - - +
817B ASN* 1.3 86.6 - - + +
819B TRP* 1.3 58.7 + - - +
820B PRO* 3.5 9.0 - - - +
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Residues in contact with TRP 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 4.2 2.7 - - - -
615B TRP* 3.6 30.3 - + - -
618B TYR* 4.5 8.4 + + - -
706B PRO* 6.0 0.2 - - + -
707B VAL* 4.3 13.2 + - + -
709B PRO* 3.5 37.9 - - + +
713B TRP* 3.6 43.5 - + + -
717B MET* 3.8 21.5 - - + -
815B MET* 2.9 28.7 + - + +
816B TYR 4.7 0.2 - - - -
817B ASN 3.9 0.6 - - - -
818B GLU* 1.3 78.4 - - - +
820B PRO* 1.3 76.9 - - + +
821B PHE* 3.6 35.5 - + + +
822B PHE* 3.0 24.2 + - + -
823B ARG* 3.1 10.6 + - - +
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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