Contacts of the helix formed by residues 807 - 819 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712D GLU* 5.7 10.1 - - - +
805D ASP* 2.9 22.3 + - + +
806D VAL* 1.3 82.2 - - + +
808D ASN* 1.3 65.8 + - - +
809D PHE 3.4 0.9 + - - -
810D GLN* 3.5 9.7 + - - +
811D VAL* 3.2 34.1 + - + +
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Residues in contact with ASN 808 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716D LEU* 3.8 32.5 - - + +
801D ALA* 2.9 36.6 + - + +
804D LYS* 4.1 11.7 - - - +
805D ASP* 2.9 27.7 + - - +
807D ARG* 1.3 81.4 - - - +
809D PHE* 1.3 67.4 + - - +
811D VAL* 2.9 13.0 + - - +
812D LEU* 2.9 27.6 + - - +
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Residues in contact with PHE 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802D ILE* 3.9 41.9 - - + +
805D ASP 4.4 0.8 + - - -
806D VAL 3.8 7.7 + - - +
807D ARG 3.4 1.2 - - - -
808D ASN* 1.3 76.9 - - - +
810D GLN* 1.3 66.6 + - - +
812D LEU* 3.2 10.5 + - - +
813D LYS* 3.0 46.9 + - + +
873D GLN* 3.6 51.8 - - + -
874D ILE* 4.6 9.9 - - + +
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Residues in contact with GLN 810 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806D VAL 4.7 1.2 + - - +
807D ARG 3.5 10.6 + - - +
808D ASN 3.3 0.2 - - - -
809D PHE* 1.3 82.7 - - - +
811D VAL* 1.3 57.7 + - + +
813D LYS* 3.5 28.9 + - - +
814D GLU* 3.0 32.3 + - + +
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Residues in contact with VAL 811 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712D GLU* 4.6 15.9 - - + +
713D TRP* 3.9 23.8 - - + -
716D LEU* 4.6 10.8 - - + -
807D ARG* 3.2 36.1 - - + +
808D ASN* 2.9 15.1 + - - +
810D GLN* 1.3 76.3 - - + +
812D LEU* 1.3 60.9 + - - +
814D GLU* 3.1 20.6 - - - +
815D MET* 2.9 34.7 + - + +
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Residues in contact with LEU 812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716D LEU* 3.6 19.1 - - + -
720D MET* 3.6 24.5 - - + -
798D PHE* 4.8 5.2 - - + +
801D ALA* 4.2 17.5 - - + -
802D ILE* 4.5 12.1 - - + -
808D ASN 2.9 20.2 + - - +
809D PHE* 3.8 11.4 - - + +
811D VAL* 1.3 72.8 - - - +
813D LYS* 1.3 66.1 + - - +
815D MET* 3.1 29.4 + - + +
816D TYR* 2.9 19.4 + - - +
822D PHE* 3.8 7.9 - - + -
874D ILE* 3.7 34.6 - - + +
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Residues in contact with LYS 813 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809D PHE* 3.0 46.3 + - + +
810D GLN* 3.7 27.1 - - - +
812D LEU* 1.3 75.7 - - - +
814D GLU* 1.3 62.4 + - - +
816D TYR* 3.3 4.5 + - - +
817D ASN* 2.9 35.9 + - - +
873D GLN 4.2 2.1 + - - +
874D ILE* 3.4 27.2 + - - +
875D ALA 5.5 0.6 - - - -
876D GLY* 4.6 17.2 - - - -
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Residues in contact with GLU 814 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710D LYS* 4.2 12.3 + - - +
712D GLU* 5.5 3.3 - - - +
713D TRP* 3.4 25.3 + - + +
810D GLN* 3.0 21.5 + - + +
811D VAL* 3.1 29.3 - - - +
813D LYS* 1.3 76.3 - - - +
815D MET* 1.3 57.3 + - - +
817D ASN* 3.3 4.6 + - - +
818D GLU* 2.9 61.1 + - - +
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Residues in contact with MET 815 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713D TRP* 3.3 57.0 - - + +
716D LEU* 4.9 6.1 - - + -
717D MET* 4.8 6.1 - - - -
720D MET* 5.4 0.2 - - - -
811D VAL* 2.9 22.1 + - - +
812D LEU* 3.1 37.9 + - + +
814D GLU* 1.3 77.1 - - - +
816D TYR* 1.3 57.6 + - - +
819D TRP* 2.9 45.7 + - + +
822D PHE* 3.5 38.4 - - + +
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Residues in contact with TYR 816 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 4.8 0.3 - - - -
812D LEU 2.9 12.9 + - - +
813D LYS 3.3 8.0 + - - +
815D MET* 1.3 78.0 - - - +
817D ASN* 1.3 72.7 + - - +
819D TRP 4.6 0.3 - - - +
822D PHE* 3.5 9.5 - - + -
823D ARG* 3.1 70.9 + - - +
826D LEU* 3.9 36.6 - - + -
827D ASP* 3.2 17.3 + - - -
830D GLU* 3.9 3.4 + - - -
871D LEU* 5.6 0.4 - - + -
874D ILE* 4.2 9.6 - - + +
875D ALA* 3.4 40.8 - - + +
877D HIS* 3.3 24.0 - - - -
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Residues in contact with ASN 817 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 3.4 16.5 - - - -
813D LYS* 2.9 30.2 + - - +
814D GLU* 4.1 5.4 - - - +
815D MET 3.2 0.4 - - - -
816D TYR* 1.3 94.2 - - - +
818D GLU* 1.3 65.9 + - + +
819D TRP 3.9 0.2 - - - -
823D ARG* 4.1 11.7 + - - +
874D ILE 5.3 1.2 - - - +
875D ALA 5.2 3.9 + - - +
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Residues in contact with GLU 818 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 3.7 12.7 - - - -
707D VAL* 3.3 20.8 - - + +
710D LYS* 4.1 10.7 + - - -
713D TRP* 3.8 20.5 - - + -
814D GLU* 2.9 43.7 + - - +
817D ASN* 1.3 86.5 - - + +
819D TRP* 1.3 58.2 + - - +
820D PRO* 3.5 4.0 - - - +
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Residues in contact with TRP 819 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 4.5 2.7 - - - -
615D TRP* 3.6 28.0 - + - -
618D TYR* 4.5 9.0 + + - -
706D PRO* 5.8 1.1 - - + +
707D VAL* 4.3 12.4 + - + -
709D PRO* 3.5 36.4 - - + +
713D TRP* 3.5 46.9 - + + -
717D MET* 3.9 22.0 - - + -
815D MET* 2.9 21.5 + - - +
817D ASN 3.9 0.6 - - - -
818D GLU* 1.3 76.5 - - - +
820D PRO* 1.3 77.8 - - + +
821D PHE* 3.6 40.2 - + + +
822D PHE* 3.1 16.4 + - + -
823D ARG* 3.0 20.4 + - - +
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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