Contacts of the helix formed by residues 840 - 854 (chain D) in PDB entry 2HVI
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 GLU 840 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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819D ARG 4.7 0.7 - - - +
820D LEU* 3.5 24.0 - - + +
821D GLN* 2.7 34.4 + - - +
822D ALA* 2.9 32.2 + - - +
836D ALA* 4.5 1.1 - - + -
837D PRO* 2.9 28.7 + - + +
839D GLU* 1.3 82.8 - - + +
841D MET* 1.3 65.5 + - - +
842D GLU 3.3 2.9 - - - -
843D ARG* 3.1 14.6 + - - +
844D LEU* 2.8 35.6 + - + +
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Residues in contact with MET 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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648D LEU* 3.8 34.1 - - + +
650D PHE* 4.0 19.3 - - + -
836D ALA* 3.5 40.6 - - + +
837D PRO 3.7 7.5 + - - +
838D LYS* 3.2 19.6 + - - +
840D GLU* 1.3 77.9 - - - +
842D GLU* 1.3 67.0 + - + +
844D LEU* 3.0 7.7 + - + +
845D CYS* 2.9 28.1 + - - -
868D TYR* 3.9 44.2 - - + -
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Residues in contact with GLU 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 LYS 4.8 1.7 + - - +
839D GLU 4.9 4.4 + - - +
840D GLU 3.3 0.8 - - - -
841D MET* 1.3 80.1 - - + +
843D ARG* 1.3 64.5 + - + +
845D CYS* 3.4 15.8 + - - +
846D ARG* 3.6 14.7 + - - +
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Residues in contact with ARG 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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818D GLU* 3.3 37.1 + - - +
819D ARG 5.5 1.2 + - - -
820D LEU* 3.4 34.1 - - + +
839D GLU 5.5 3.2 + - - +
840D GLU* 3.1 17.0 + - - +
842D GLU* 1.3 79.3 - - + +
844D LEU* 1.3 61.6 + - + +
846D ARG* 3.2 8.5 + - - +
847D LEU* 2.9 30.7 + - + +
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Residues in contact with LEU 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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650D PHE* 3.8 20.8 - - + -
815D LEU* 3.9 24.9 - - + -
820D LEU* 4.3 9.6 - - + -
822D ALA* 4.1 18.2 - - + -
834D LEU* 4.5 6.1 - - + -
836D ALA* 4.6 6.1 - - + -
840D GLU* 2.8 47.9 + - + +
841D MET* 3.0 11.6 + - + +
843D ARG* 1.3 74.0 - - + +
845D CYS* 1.3 65.6 + - - +
846D ARG 3.0 1.6 - - - -
847D LEU* 4.2 6.7 - - + +
848D VAL* 3.0 47.4 + - + +
849D PRO* 3.5 4.0 - - - +
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Residues in contact with CYS 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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650D PHE* 3.9 17.5 - - - -
841D MET 2.9 19.6 + - - -
842D GLU* 3.7 11.9 - - - +
843D ARG 3.3 0.2 - - - -
844D LEU* 1.3 76.0 - - - +
846D ARG* 1.3 58.8 + - + +
849D PRO* 3.2 21.5 - - - +
866D TYR* 3.7 29.5 + - + +
868D TYR* 3.9 27.1 - - - -
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Residues in contact with ARG 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 GLU 3.8 13.0 - - - +
843D ARG* 3.2 8.0 + - - +
844D LEU 3.0 0.4 - - - -
845D CYS* 1.3 81.7 - - + +
847D LEU* 1.3 63.7 + - - +
849D PRO* 4.0 0.9 - - - +
850D GLU* 3.4 22.7 + - - +
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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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811D LEU* 4.7 3.4 - - + -
814D ARG* 3.1 56.3 - - + +
815D LEU* 3.9 17.5 - - + +
818D GLU* 4.4 12.3 - - + +
820D LEU* 3.8 28.9 - - + -
843D ARG* 2.9 16.7 + - + +
844D LEU* 4.1 5.8 - - + +
846D ARG* 1.3 77.1 - - - +
848D VAL* 1.3 67.5 + - + +
850D GLU* 3.4 3.9 + - + +
851D VAL* 3.1 38.3 + - + +
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Residues in contact with VAL 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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650D PHE* 3.7 17.7 - - + -
652D ALA* 3.7 16.8 - - + -
811D LEU* 4.1 24.9 - - + -
832D LEU* 5.6 0.2 - - + -
834D LEU* 4.5 14.4 - - + -
844D LEU* 3.0 40.1 + - + +
847D LEU* 1.3 70.8 - - + +
849D PRO* 1.3 70.5 - - + +
851D VAL* 3.4 1.9 + - - +
852D MET* 3.0 45.1 + - + +
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Residues in contact with PRO 849 (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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650D PHE* 4.6 1.1 - - + -
844D LEU 3.5 2.9 - - - +
845D CYS* 3.2 28.0 - - - +
846D ARG 4.0 1.3 - - - +
847D LEU 3.7 1.1 - - - -
848D VAL* 1.3 95.4 - - + +
850D GLU* 1.3 57.8 + - - +
852D MET* 3.4 0.9 + - - +
853D GLU* 2.9 45.1 + - - +
864D VAL* 4.1 21.8 - - + +
866D TYR* 3.4 37.7 - - + -
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Residues in contact with GLU 850 (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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814D ARG* 5.4 9.4 - - - +
846D ARG 3.4 18.9 + - - +
847D LEU* 3.4 5.1 + - - +
848D VAL 3.3 0.4 - - - -
849D PRO* 1.3 79.9 - - - +
851D VAL* 1.3 57.4 + - + +
853D GLU* 3.3 12.5 + - - +
854D GLN* 3.0 61.5 + - + +
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Residues in contact with VAL 851 (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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807D ALA* 3.9 6.0 - - - +
810D ASP* 3.7 15.8 - - + +
811D LEU* 3.4 39.9 - - + +
814D ARG* 3.8 22.0 - - + +
847D LEU* 3.1 40.5 + - + +
848D VAL 3.8 4.0 - - - +
850D GLU* 1.3 76.2 - - + +
852D MET* 1.3 63.4 + - + +
854D GLN* 3.4 3.8 + - - +
855D ALA* 3.2 22.0 + - - +
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Residues in contact with MET 852 (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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652D ALA* 3.7 43.7 - - - +
653D ASP* 4.5 2.5 - - - -
654D TYR* 2.6 58.0 + - + +
804D ILE* 4.8 0.2 - - + -
807D ALA* 4.3 8.7 - - + +
811D LEU* 5.6 2.5 - - + -
830D ASP 4.6 2.0 - - - +
832D LEU* 3.9 31.2 - - + -
848D VAL* 3.0 28.0 + - + +
851D VAL* 1.3 79.5 - - + +
853D GLU* 1.3 60.8 + - - +
854D GLN 3.4 0.3 + - - -
855D ALA* 3.4 9.2 + - - +
862D LEU* 4.1 1.9 - - - +
864D VAL* 3.7 19.1 - - + -
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Residues in contact with GLU 853 (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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849D PRO* 2.9 28.2 + - - +
850D GLU* 3.9 14.2 - - - +
852D MET* 1.3 76.5 - - - +
854D GLN* 1.3 74.1 + - - +
855D ALA 3.7 0.2 + - - -
856D VAL 3.8 10.0 - - - +
862D LEU* 3.3 43.2 + - - +
863D LYS* 3.9 6.8 - - - +
864D VAL* 3.2 39.8 + - + +
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Residues in contact with GLN 854 (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 LYS* 4.9 1.7 + - - -
810D ASP* 4.9 1.4 - - - +
850D GLU* 3.0 44.6 + - + +
851D VAL* 3.7 4.9 - - - +
853D GLU* 1.3 91.2 + - - +
855D ALA* 1.3 65.3 + - - +
856D VAL* 3.1 9.9 + - - +
857D THR* 5.0 8.7 + - - -
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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