Contacts of the helix formed by residues 837 - 849 (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 ASP 837 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D TYR* 2.6 39.5 + - - -
72D GLU* 4.8 7.6 - - - +
785D ARG* 3.0 25.1 + - + +
836D GLY* 1.3 76.4 - - - +
838D PRO* 1.3 70.4 - - - +
839D GLY 3.0 3.7 + - - -
840D ILE* 2.9 40.1 + - + +
841D ALA* 3.1 20.8 + - - +
864D TYR* 3.9 1.4 + - - -
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Residues in contact with PRO 838 (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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786D PHE* 5.3 3.6 - - + -
836D GLY 4.5 0.9 - - - +
837D ASP* 1.3 85.3 - - - +
839D GLY* 1.3 58.0 + - - +
841D ALA* 3.3 8.0 + - + +
842D GLY* 2.7 27.4 + - - -
861D ARG* 3.7 23.4 - - + -
864D TYR* 3.5 40.4 - - + +
865D VAL* 4.9 10.8 - - + -
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Residues in contact with GLY 839 (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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71D TYR* 3.6 11.4 + - - -
77D THR* 4.4 16.2 + - - -
80D LEU* 6.0 0.7 - - - -
837D ASP* 3.0 8.8 + - - -
838D PRO* 1.3 79.8 - - - +
840D ILE* 1.3 57.2 + - - +
842D GLY* 3.1 3.4 + - - -
843D LEU* 2.9 26.7 + - - +
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Residues in contact with ILE 840 (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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71D TYR* 4.1 11.7 - - + +
80D LEU* 4.3 12.8 - - + -
784D THR 4.1 6.1 - - - +
785D ARG* 3.5 27.6 - - + +
837D ASP* 2.9 32.2 + - + +
839D GLY* 1.3 71.3 - - - +
841D ALA* 1.3 68.3 + - - +
843D LEU* 3.0 21.7 + - + +
844D TYR* 3.1 39.4 + - + -
899D THR* 3.6 24.0 - - + -
902D ASN* 3.8 20.6 - - + +
903D VAL* 5.5 2.2 - - + -
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Residues in contact with ALA 841 (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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784D THR* 3.5 21.0 + - - +
786D PHE* 3.7 36.3 - - + -
837D ASP 3.1 11.9 + - - +
838D PRO* 3.6 8.7 - - + +
840D ILE* 1.3 77.7 - - - +
842D GLY* 1.3 60.7 + - - +
844D TYR* 3.5 8.1 + - - +
845D ASP* 3.3 24.4 + - - +
861D ARG* 4.2 4.2 + - + +
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Residues in contact with GLY 842 (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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838D PRO 2.7 18.7 + - - -
839D GLY* 3.5 4.3 - - - -
840D ILE 3.1 0.4 - - - -
841D ALA* 1.3 71.1 - - - +
843D LEU* 1.3 60.5 + - - +
844D TYR 3.3 0.2 - - - -
845D ASP* 3.3 3.8 + - - +
846D GLU* 2.8 27.9 + - - +
861D ARG* 3.8 25.6 + - - +
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Residues in contact with LEU 843 (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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77D THR* 4.7 13.0 - - - +
80D LEU* 4.6 14.4 - - + -
81D GLY* 5.1 6.5 - - - +
839D GLY 2.9 11.9 + - - +
840D ILE* 3.0 14.1 + - + +
842D GLY* 1.3 75.6 - - - +
844D TYR* 1.3 66.2 + - + +
846D GLU* 3.1 12.6 + - + +
847D LEU* 3.1 51.0 + - + +
903D VAL* 3.9 36.8 - - + -
906D ALA* 4.7 4.9 - - + -
907D TYR* 4.5 15.0 - - + +
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Residues in contact with TYR 844 (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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745D ALA* 3.8 25.6 - - - +
746D THR* 5.4 0.2 - - - -
747D PRO* 5.1 1.6 - - + -
783D GLN 3.6 0.2 + - - -
784D THR* 3.9 23.6 - - + -
840D ILE* 3.1 47.6 + - + -
841D ALA* 3.6 9.2 - - - +
843D LEU* 1.3 76.5 - - + +
845D ASP* 1.3 56.7 + - - +
848D LEU* 2.9 54.3 + - + +
849D VAL* 5.0 1.1 - - - -
902D ASN* 3.1 40.2 + - - -
905D GLN* 2.6 30.7 + - - +
906D ALA* 4.1 22.2 - - + -
909D LEU* 4.5 7.0 - - + -
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Residues in contact with ASP 845 (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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741D TYR* 2.7 41.7 + - - -
745D ALA* 3.5 14.0 - - - +
841D ALA 3.3 8.4 + - - +
842D GLY 3.3 9.4 + - - +
843D LEU 3.2 0.4 - - - -
844D TYR* 1.3 74.5 - - - +
846D GLU* 1.3 66.3 + - - +
847D LEU 3.1 0.9 + - - -
849D VAL* 3.2 40.5 + - + +
854D LYS* 3.8 9.9 - - + +
857D GLY* 3.6 6.6 - - - -
861D ARG* 3.0 28.7 + - - +
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Residues in contact with GLU 846 (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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842D GLY 2.8 17.7 + - - +
843D LEU* 3.3 20.0 - - + +
845D ASP* 1.3 72.4 - - - +
847D LEU* 1.3 71.3 + - + +
849D VAL 5.1 0.2 - - - +
854D LYS* 3.1 43.1 + - - +
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Residues in contact with LEU 847 (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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843D LEU* 3.1 28.0 + - + +
846D GLU* 1.3 86.1 - - + +
848D LEU* 1.3 71.6 + - + +
849D VAL 3.9 1.3 - - - -
906D ALA* 3.8 24.9 - - + +
907D TYR* 3.6 53.8 - - + +
910D LYS* 3.2 40.8 + - + +
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Residues in contact with LEU 848 (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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744D SER* 3.3 33.1 - - - +
745D ALA 4.9 1.6 - - - -
746D THR 5.3 0.4 - - - +
844D TYR* 2.9 43.8 + - + +
847D LEU* 1.3 88.5 - - + +
849D VAL* 1.3 61.4 + - - +
850D ALA 4.1 0.9 + - - -
906D ALA* 3.8 9.4 - - - +
909D LEU* 4.1 16.6 - - + -
910D LYS* 3.6 37.0 - - + +
913D ARG* 3.8 20.9 + - - +
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Residues in contact with VAL 849 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741D TYR* 4.0 16.6 - - + -
744D SER* 3.6 26.2 - - - -
745D ALA* 3.6 28.0 - - + +
845D ASP* 3.2 35.1 + - + +
846D GLU 5.1 0.3 - - - +
847D LEU 5.2 0.7 - - - -
848D LEU* 1.3 78.7 - - + +
850D ALA* 1.3 66.3 + - - +
851D GLU 3.6 0.2 + - - -
853D LEU* 4.8 3.1 - - + -
854D LYS* 3.4 35.8 - - + +
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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