Contacts of the helix formed by residues 793 - 805 (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 GLY 793 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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724D ALA* 3.4 33.2 - - - +
727D GLU* 3.8 22.8 - - - +
728D TYR 4.5 0.9 - - - -
791D TRP* 3.2 1.2 + - - -
792D LEU* 1.3 77.2 - - - +
794D VAL* 1.3 60.1 + - - +
795D GLY 3.4 2.8 - - - +
796D ALA* 3.6 5.6 + - - +
797D ALA 3.2 19.2 + - - -
867D THR* 5.7 0.2 + - - -
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Residues in contact with VAL 794 (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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610D ARG* 5.4 0.4 - - + -
611D LEU* 3.6 38.8 - - + +
790D VAL 4.8 2.9 - - - +
791D TRP* 3.1 22.1 + - - +
792D LEU 4.5 2.7 - - - +
793D GLY* 1.3 74.7 - - - +
795D GLY* 1.3 61.3 + - - +
797D ALA* 3.1 4.3 + - - +
798D PHE* 2.8 63.1 + - + -
829D LEU* 4.2 24.2 - - + -
867D THR* 4.2 8.3 - - + -
871D LEU* 6.2 0.2 - - + -
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Residues in contact with GLY 795 (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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793D GLY 3.4 1.2 - - - +
794D VAL* 1.3 78.8 - - - +
796D ALA* 1.3 62.0 + - - +
798D PHE* 4.7 1.1 - - - -
799D LYS* 2.9 27.2 + - - +
866D GLU* 5.1 5.4 - - - -
867D THR* 3.5 37.6 + - - +
870D LEU* 3.6 12.7 - - - +
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Residues in contact with ALA 796 (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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723D VAL* 3.8 12.0 - - + +
727D GLU* 3.7 43.6 + - + +
793D GLY* 3.6 4.5 + - - +
794D VAL 3.3 0.2 - - - -
795D GLY* 1.3 75.0 - - - +
797D ALA* 1.3 57.2 + - - +
799D LYS* 3.8 7.8 - - - +
800D PHE* 2.9 31.2 + - - +
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Residues in contact with ALA 797 (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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611D LEU* 4.7 7.0 - - + -
720D MET* 3.4 45.6 - - + +
723D VAL* 4.2 10.3 - - - +
724D ALA* 4.0 6.5 - - + +
793D GLY 3.2 12.3 + - - +
794D VAL* 3.1 11.5 + - - +
796D ALA* 1.3 81.2 - - - +
798D PHE* 1.3 61.7 + - - +
800D PHE* 3.4 5.2 + - - +
801D ALA* 3.1 18.2 + - - +
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Residues in contact with PHE 798 (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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611D LEU* 4.2 9.4 - - + -
720D MET* 3.2 26.2 - - + -
794D VAL* 2.8 47.6 + - + +
795D GLY* 3.9 3.4 - - - +
797D ALA* 1.3 71.0 - - + +
799D LYS* 1.3 63.9 + - - +
801D ALA* 3.2 3.3 + - - +
802D ILE* 3.1 31.0 + - + +
812D LEU* 4.8 5.6 - - + +
822D PHE* 4.3 13.5 - + - -
826D LEU* 3.9 30.7 - - + -
867D THR* 5.1 2.9 - - + -
870D LEU* 4.0 23.1 - - + -
871D LEU* 4.1 16.8 - - + -
874D ILE* 3.4 31.4 - - + -
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Residues in contact with LYS 799 (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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795D GLY 2.9 18.6 + - - +
796D ALA* 3.8 7.6 - - - +
798D PHE* 1.3 77.1 - - - +
800D PHE* 1.3 63.7 + - - +
802D ILE* 3.3 10.0 + - + +
803D ASP* 2.9 52.6 + - - +
866D GLU* 4.6 20.0 - - - +
870D LEU* 4.2 12.2 - - + +
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Residues in contact with PHE 800 (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* 4.8 3.4 - - + -
719D GLU* 3.8 48.0 - - + -
720D MET* 4.2 7.2 - - + -
723D VAL* 3.7 33.4 - - + -
796D ALA 2.9 19.3 + - - +
797D ALA 3.6 7.2 - - - +
799D LYS* 1.3 76.9 - - - +
801D ALA* 1.3 68.4 + - + +
803D ASP* 3.4 6.8 + - - +
804D LYS* 2.9 49.1 + - + +
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Residues in contact with ALA 801 (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 20.9 - - + -
720D MET* 3.6 31.9 - - + -
797D ALA 3.1 6.0 + - - +
798D PHE 3.2 3.6 + - - +
800D PHE* 1.3 83.4 - - - +
802D ILE* 1.3 63.8 + - - +
804D LYS* 3.4 5.1 + - - -
805D ASP 3.6 0.5 + - - -
808D ASN* 2.9 31.9 + - + +
812D LEU* 4.2 10.8 - - + -
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Residues in contact with ILE 802 (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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798D PHE* 3.1 22.6 + - + +
799D LYS* 3.8 4.3 - - - +
801D ALA* 1.3 75.7 - - - +
803D ASP* 1.3 68.6 + - - +
805D ASP 3.4 19.0 + - - +
806D VAL* 4.3 3.0 + - - -
808D ASN* 4.7 2.5 - - - -
809D PHE* 3.9 42.0 - - + +
812D LEU* 4.5 10.8 - - + -
870D LEU* 3.7 29.2 - - + -
873D GLN* 6.0 0.2 - - - +
874D ILE* 5.4 3.1 - - + -
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Residues in contact with ASP 803 (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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799D LYS* 2.9 51.3 + - - +
800D PHE* 3.7 7.1 - - - +
802D ILE* 1.3 83.1 - - - +
804D LYS* 1.3 62.4 + - - +
805D ASP* 3.4 0.9 + - - -
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Residues in contact with LYS 804 (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* 5.6 1.9 - - + +
719D GLU* 3.0 40.0 + - - +
800D PHE* 2.9 37.7 + - + +
801D ALA* 3.9 5.4 - - - +
802D ILE 3.3 0.8 - - - -
803D ASP* 1.3 77.8 - - - +
805D ASP* 1.3 64.2 + - + +
808D ASN* 4.1 11.0 - - - +
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Residues in contact with ASP 805 (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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801D ALA 3.6 1.8 + - - -
802D ILE* 3.4 13.4 - - - +
803D ASP 3.3 1.7 - - - -
804D LYS* 1.3 84.4 - - + +
806D VAL* 1.3 75.8 + - - +
807D ARG* 3.0 33.1 + - - +
808D ASN* 2.9 36.8 + - - +
809D PHE 4.4 0.2 + - - -
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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