Contacts of the helix formed by residues 807 - 819 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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805A ASP* 3.0 31.6 + - - +
806A VAL* 1.3 86.3 - - + +
808A ASN* 1.3 67.1 + - - +
809A PHE 3.3 0.7 - - - -
810A GLN* 3.2 12.6 + - + +
811A VAL* 3.2 26.4 + - + +
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Residues in contact with ASN 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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715A LYS* 6.2 0.2 - - - +
716A LEU* 3.8 33.4 - - + +
719A GLU* 5.1 3.4 + - - -
801A ALA* 2.9 35.6 + - + +
802A ILE* 5.1 0.2 - - - -
804A LYS* 4.8 4.8 - - - +
805A ASP* 3.1 28.2 + - - +
807A ARG* 1.3 78.4 - - - +
809A PHE* 1.3 61.1 + - - +
811A VAL* 3.6 10.4 - - - +
812A LEU* 2.9 35.5 + - - +
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Residues in contact with PHE 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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802A ILE* 3.6 44.2 - - + +
806A VAL 3.9 9.2 + - - +
807A ARG 3.3 0.8 - - - -
808A ASN* 1.3 80.1 - - - +
810A GLN* 1.3 61.2 + - - +
812A LEU* 3.4 2.5 + - + +
813A LYS* 3.1 56.1 + - + +
873A GLN* 3.9 48.7 - - + -
874A ILE* 4.3 13.0 - - + -
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Residues in contact with GLN 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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806A VAL 4.9 0.6 + - - -
807A ARG* 3.2 12.3 + - - +
809A PHE* 1.3 76.5 - - - +
811A VAL* 1.3 61.4 + - + +
813A LYS* 3.3 25.2 + - - +
814A GLU* 2.9 53.9 + - + +
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Residues in contact with VAL 811 (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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712A GLU* 4.6 16.4 - - + +
713A TRP* 3.9 26.2 + - + +
716A LEU* 3.9 19.1 - - + -
807A ARG* 3.2 23.1 + - + +
808A ASN* 3.2 14.1 + - - +
810A GLN* 1.3 77.8 - - + +
812A LEU* 1.3 57.4 + - - +
814A GLU* 3.4 15.6 + - - +
815A MET* 2.9 28.8 + - - +
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Residues in contact with LEU 812 (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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716A LEU* 3.6 25.8 - - + -
720A MET* 4.3 13.5 - - - -
798A PHE* 4.6 4.9 - - + +
801A ALA* 4.2 22.0 - - + -
802A ILE* 4.4 11.7 - - + -
808A ASN 2.9 19.5 + - - +
809A PHE* 3.9 4.7 - - - +
811A VAL* 1.3 73.9 - - - +
813A LYS* 1.3 59.4 + - - +
815A MET* 3.1 25.9 + - + +
816A TYR* 2.9 24.6 + - - +
822A PHE* 3.9 7.0 - - + -
874A ILE* 3.6 44.5 - - + +
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Residues in contact with LYS 813 (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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809A PHE* 3.1 56.0 + - + +
810A GLN* 3.3 25.8 + - - +
812A LEU* 1.3 76.0 - - - +
814A GLU* 1.3 58.1 + - + +
816A TYR* 3.3 2.6 + - - +
817A ASN* 2.5 37.7 + - - +
873A GLN 4.1 9.4 - - - +
874A ILE* 3.7 25.1 - - - +
876A GLY* 5.6 4.5 - - - +
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Residues in contact with GLU 814 (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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710A LYS* 5.1 8.3 + - - -
713A TRP* 4.7 8.5 + - + +
810A GLN* 2.9 41.0 + - + +
811A VAL* 3.7 16.9 - - - +
812A LEU 3.3 0.2 - - - -
813A LYS* 1.3 76.8 - - + +
815A MET* 1.3 57.9 + - - +
817A ASN* 3.2 4.1 + - - +
818A GLU* 2.8 57.3 + - - +
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Residues in contact with MET 815 (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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713A TRP* 3.4 48.9 - - + +
716A LEU* 4.6 4.5 - - + -
717A MET* 4.1 13.7 - - + -
811A VAL* 2.9 24.3 + - - +
812A LEU* 3.1 26.4 + - + +
814A GLU* 1.3 77.1 - - - +
816A TYR* 1.3 59.8 + - - +
819A TRP* 2.9 52.1 + - + +
822A PHE* 3.5 45.2 - - + +
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Residues in contact with TYR 816 (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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131A PHE* 5.0 0.3 - - - -
812A LEU 2.9 12.2 + - - +
813A LYS 3.3 7.4 + - - +
815A MET* 1.3 77.4 - - - +
817A ASN* 1.3 70.6 + - - +
819A TRP 4.8 0.3 + - - -
822A PHE* 3.6 12.7 - - + -
823A ARG* 3.2 66.1 + - - +
826A LEU* 3.8 35.0 - - + -
827A ASP* 3.1 20.3 + - - -
830A GLU* 3.8 2.8 + - - -
874A ILE* 3.9 9.4 - - + +
875A ALA* 3.4 43.3 - - + +
877A HIS* 3.3 25.4 + - - -
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Residues in contact with ASN 817 (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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131A PHE* 3.5 17.1 - - - -
813A LYS* 2.5 36.6 + - - +
814A GLU* 3.2 5.2 + - - +
816A TYR* 1.3 91.6 - - - +
818A GLU* 1.3 65.1 + - + +
823A ARG* 4.2 9.5 + - - +
874A ILE 5.1 1.0 + - - -
875A ALA 5.4 2.8 + - - +
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Residues in contact with GLU 818 (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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131A PHE* 3.8 12.1 - - - -
707A VAL* 3.4 19.6 - - - +
710A LYS* 3.8 14.3 + - - -
713A TRP* 3.7 22.9 - - + -
814A GLU* 2.8 39.6 + - - +
817A ASN* 1.3 86.0 - - + +
819A TRP* 1.3 59.1 + - - +
820A PRO* 3.5 3.8 - - - +
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Residues in contact with TRP 819 (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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131A PHE* 4.2 2.4 - - - -
615A TRP* 3.6 33.0 - + - -
618A TYR* 4.5 7.7 + + - -
706A PRO* 6.0 0.9 - - + -
707A VAL* 4.3 13.2 + - + -
709A PRO* 3.5 36.4 - - + +
713A TRP* 3.5 44.4 - + + -
717A MET* 3.9 20.6 - - + -
815A MET* 2.9 28.4 + - + +
817A ASN 3.9 0.4 - - - -
818A GLU* 1.3 77.0 - - - +
820A PRO* 1.3 75.0 - - + +
821A PHE* 3.7 35.4 - + + +
822A PHE* 3.0 25.1 + - + +
823A ARG* 3.0 11.0 + - - +
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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