Contacts of the helix formed by residues 807 - 824 (chain D) in PDB entry 2QMR
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 ASN 807 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804D ILE* 3.9 13.3 - - - +
805D ARG* 3.0 24.9 + - + +
806D ASP* 1.3 75.2 - - - +
808D GLU* 1.3 59.0 + - - +
809D GLU* 3.0 19.4 - - + +
810D LYS* 2.8 38.2 - - - +
811D ASP* 3.0 28.6 + - - +
842D TRP* 4.1 2.1 - - - -
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Residues in contact with GLU 808 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737D ILE* 5.1 6.1 - - - +
777D ARG* 4.8 8.8 + - - +
807D ASN* 1.3 75.1 - - - +
809D GLU* 1.3 66.1 + - + +
811D ASP* 3.6 9.1 - - - +
812D SER* 3.2 27.7 + - - -
846D LYS* 4.0 19.6 + - - +
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Residues in contact with GLU 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696D LYS* 5.9 0.7 + - - -
730D TRP* 4.2 18.2 + - - -
734D GLU* 4.4 2.1 - - - +
770D ASN* 4.6 5.4 - - - +
773D ILE* 3.7 35.5 - - + +
777D ARG* 4.0 19.5 + - - +
804D ILE* 6.2 0.9 - - + -
807D ASN* 3.0 15.7 - - + +
808D GLU* 1.3 78.9 - - + +
810D LYS* 1.3 64.5 + - - +
812D SER* 2.9 21.5 + - - -
813D ALA* 3.0 13.7 + - - +
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Residues in contact with LYS 810 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773D ILE* 5.3 2.9 - - - +
801D LEU* 3.4 24.0 + - + +
802D ARG 4.6 0.4 + - - -
804D ILE* 3.0 27.5 + - + +
805D ARG 3.3 20.6 - - - +
806D ASP* 3.4 17.7 + - - -
807D ASN* 2.8 23.9 - - - +
809D GLU* 1.3 73.1 - - - +
811D ASP* 1.3 56.1 + - - +
813D ALA* 3.5 4.4 + - - +
814D PHE* 3.0 48.2 + - + +
841D SER* 3.1 33.0 + - - -
842D TRP* 3.4 31.8 - - + +
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Residues in contact with ASP 811 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807D ASN 3.0 17.9 + - - +
808D GLU* 3.6 14.5 - - - +
809D GLU 3.2 0.2 - - - -
810D LYS* 1.3 76.8 - - - +
812D SER* 1.3 59.3 + - - +
814D PHE* 3.8 1.2 - - - +
815D ARG* 2.8 73.2 + - - +
842D TRP* 3.5 14.0 - - + -
846D LYS* 4.2 22.9 + - - +
849D LEU* 3.5 18.8 - - - +
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Residues in contact with SER 812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737D ILE* 4.2 15.3 - - - -
776D GLY 4.4 3.6 - - - +
777D ARG* 3.1 34.9 + - - +
780D TYR* 4.4 8.5 - - - +
808D GLU* 3.2 19.1 + - - -
809D GLU 2.9 15.2 + - - -
811D ASP* 1.3 80.8 + - - +
813D ALA* 1.3 61.1 + - - +
815D ARG* 3.4 11.0 - - - +
816D GLY* 3.0 18.4 + - - -
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Residues in contact with ALA 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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772D ALA 4.5 0.4 - - - +
773D ILE* 3.8 23.8 - - + +
776D GLY* 3.7 12.7 - - - -
797D TRP* 3.5 11.1 - - + -
801D LEU* 3.7 27.8 - - + -
809D GLU 3.0 17.5 + - - +
810D LYS* 3.7 3.6 - - - +
812D SER* 1.3 78.1 + - - +
814D PHE* 1.3 56.6 - - - +
816D GLY* 3.0 16.6 + - - -
817D ILE 3.1 9.4 + - - -
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Residues in contact with PHE 814 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797D TRP* 3.7 28.9 - + - -
801D LEU* 3.9 17.3 - - + -
810D LYS* 3.0 45.3 + - + +
811D ASP 3.9 2.2 - - - +
813D ALA* 1.3 72.3 - - - +
815D ARG* 1.3 64.4 + - - +
817D ILE* 3.3 6.6 - - + +
818D CYS* 3.0 31.6 + - - -
835D PHE* 4.9 2.2 - + - -
838D ALA* 3.3 50.5 - - + -
839D VAL* 4.2 6.1 - - + -
842D TRP* 3.5 20.4 - + + +
849D LEU* 4.3 2.0 - - + -
853D PHE* 3.5 31.4 - + + -
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Residues in contact with ARG 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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780D TYR* 3.5 36.2 + - + -
811D ASP* 2.8 56.3 + - - +
812D SER* 3.4 10.5 - - - +
814D PHE* 1.3 75.7 - - - +
816D GLY* 1.3 60.3 + - - +
818D CYS* 3.4 5.1 + - - +
819D THR* 3.1 28.6 + - - -
846D LYS* 3.9 11.3 - - - +
848D ASP* 2.7 40.1 + - - -
849D LEU* 4.1 17.4 - - + +
852D MET* 4.0 19.2 - - + +
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Residues in contact with GLY 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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776D GLY* 3.3 26.5 - - - -
779D GLY 4.1 1.2 - - - -
780D TYR* 3.5 15.9 - - - +
812D SER 3.0 6.7 + - - -
813D ALA 3.0 6.1 + - - -
815D ARG* 1.3 77.5 - - - +
817D ILE* 1.3 58.4 + - - +
819D THR* 3.6 2.8 + - - -
820D MET* 3.2 34.9 + - - +
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Residues in contact with ILE 817 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776D GLY* 4.9 1.7 - - - -
790D LEU* 4.0 19.5 - - + -
793D PHE* 4.6 3.6 - - + -
794D ILE* 3.7 28.3 - - + -
797D TRP* 3.5 58.8 - - + +
798D CYS* 4.9 1.1 - - - -
813D ALA 3.1 6.3 + - - -
814D PHE* 3.3 14.8 - - + +
816D GLY* 1.3 73.8 - - - +
818D CYS* 1.3 62.5 + - - +
820D MET* 3.8 6.5 - - + -
821D ILE* 2.9 38.3 + - + +
835D PHE* 4.0 22.7 - - + -
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Residues in contact with CYS 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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814D PHE 3.0 24.5 + - - +
815D ARG 3.8 0.7 - - - +
816D GLY 3.3 0.2 - - - -
817D ILE* 1.3 81.3 - - - +
819D THR* 1.3 63.1 - - - +
821D ILE* 3.5 1.7 + - - +
822D SER* 3.1 25.1 + - - -
835D PHE* 4.6 1.6 - - - -
849D LEU* 4.5 2.2 - - - -
852D MET* 3.7 33.7 - - + -
853D PHE* 3.5 34.1 - - - -
856D ILE* 3.8 26.7 - - + +
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Residues in contact with THR 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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779D GLY 4.7 0.4 - - - -
780D TYR* 3.8 23.9 - - + +
783D PRO* 3.6 28.0 - - + -
815D ARG 3.1 16.6 + - - -
816D GLY 4.0 3.8 - - - -
818D CYS* 1.3 77.9 - - - +
820D MET* 1.3 60.8 + - - +
822D SER* 3.3 9.5 + - - +
823D VAL* 3.3 24.9 + - + +
852D MET* 4.0 11.0 - - - +
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Residues in contact with MET 820 (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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775D ILE* 4.5 4.9 - - + +
776D GLY* 5.4 0.7 - - - -
779D GLY* 3.4 36.6 - - - +
783D PRO* 4.3 3.8 - - + -
786D VAL* 3.7 18.4 - - + +
787D ALA* 3.9 22.9 - - + +
790D LEU* 3.5 27.0 - - + +
793D PHE* 2.9 40.6 - - + -
816D GLY 3.2 21.4 + - - +
817D ILE* 3.8 7.0 - - + +
818D CYS 3.2 0.4 - - - -
819D THR* 1.3 76.1 - - - +
821D ILE* 1.3 58.8 + - - +
823D VAL* 3.3 2.7 + - - +
824D ASN* 2.9 25.6 + - - -
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Residues in contact with ILE 821 (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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790D LEU* 3.9 5.2 - - + -
794D ILE* 4.9 0.4 - - + -
817D ILE* 2.9 34.1 + - + +
818D CYS 3.9 4.0 - - - +
820D MET* 1.3 74.2 - - - +
822D SER* 1.3 60.2 + - - +
824D ASN 3.9 6.3 - - - -
825D PRO* 3.0 41.3 - - + +
828D VAL* 3.2 36.8 - - + -
832D PHE* 5.7 0.9 - - + -
835D PHE* 3.6 42.2 - - + -
856D ILE* 4.1 28.0 - - + -
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Residues in contact with SER 822 (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 CYS 3.1 15.7 + - - -
819D THR* 3.3 13.7 + - - +
821D ILE* 1.3 79.3 - - - +
823D VAL* 1.3 66.3 + - - +
825D PRO* 4.2 9.0 - - - +
856D ILE* 5.9 3.8 - - - -
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Residues in contact with VAL 823 (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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783D PRO* 3.9 14.8 - - + +
784D GLN* 3.7 37.2 - - - +
787D ALA* 3.8 20.2 - - + -
788D PRO* 5.8 0.7 - - + -
819D THR* 3.3 20.4 + - + +
820D MET 3.3 3.6 + - - +
822D SER* 1.3 83.9 + - - +
824D ASN* 1.3 60.4 + - + +
825D PRO* 3.6 6.0 - - - +
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Residues in contact with ASN 824 (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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787D ALA* 3.3 33.9 - - + +
788D PRO* 4.0 10.8 - - + +
790D LEU* 3.6 13.9 - - + +
820D MET 2.9 13.9 + - - +
821D ILE* 3.1 5.1 - - - +
823D VAL* 1.3 79.6 - - + +
825D PRO* 1.3 62.3 - - - +
826D SER* 3.0 24.7 + - - +
827D GLY* 3.6 14.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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