Contacts of the helix formed by residues 695 - 718 (chain D) in PDB entry 5ON2
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 THR 695 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D LEU* 1.3 76.7 - - - +
696D GLU* 1.3 57.8 + - + +
697D ASN* 4.1 13.7 - - + +
698D GLN* 3.1 31.9 + - - -
699D LYS* 2.8 33.9 + - - +
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Residues in contact with GLU 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D LEU 4.0 1.1 + - - +
695D THR* 1.3 78.1 - - + +
697D ASN* 1.3 59.0 + - - +
699D LYS* 3.9 14.3 - - + +
700D ALA* 3.6 19.6 + - - +
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Residues in contact with ASN 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695D THR* 3.2 11.3 - - + +
696D GLU* 1.3 77.1 - - - +
698D GLN* 1.3 64.1 + - + +
700D ALA* 3.7 11.9 + - - +
701D LEU* 3.7 10.4 + - - +
740D PRO* 5.6 8.9 - - - +
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Residues in contact with GLN 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D LEU* 3.6 29.1 - - + +
695D THR* 3.1 35.6 + - - +
697D ASN* 1.3 77.9 - - + +
699D LYS* 1.3 63.2 + - - +
701D LEU* 3.2 8.8 + - - +
702D ARG* 3.2 18.6 + - - +
740D PRO* 6.1 0.9 - - + -
745D GLN* 4.8 11.9 + - - +
746D ASP* 2.7 43.5 + - - +
749D LEU* 3.7 20.6 - - + +
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Residues in contact with LYS 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D LEU* 4.9 13.6 - - + +
695D THR 2.8 19.3 + - - +
696D GLU* 4.0 15.5 - - + +
697D ASN 3.4 0.2 - - - -
698D GLN* 1.3 73.0 - - - +
700D ALA* 1.3 57.0 + - - +
702D ARG* 3.4 7.8 + - + +
703D ARG* 3.0 41.2 + - - +
793D LYS 5.5 6.7 - - - -
794D ALA 4.8 7.2 - - - +
796D VAL* 5.0 15.8 + - - +
798D ASP* 5.7 7.1 + - - +
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Residues in contact with ALA 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696D GLU 3.6 12.0 + - - +
697D ASN* 3.9 12.1 - - - +
698D GLN 3.3 0.8 - - - -
699D LYS* 1.3 74.9 - - - +
701D LEU* 1.3 61.1 + - - +
703D ARG* 3.6 30.9 - - - +
704D ASP* 3.1 36.3 + - - +
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Residues in contact with LEU 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697D ASN 3.7 8.7 + - - +
698D GLN* 3.2 11.1 + - - +
700D ALA* 1.3 77.4 - - - +
702D ARG* 1.3 58.7 + - - +
704D ASP* 3.1 6.9 + - + +
705D VAL* 2.8 34.1 + - + +
732D LEU* 5.2 3.6 - - + -
735D LYS* 4.0 40.8 - - + +
736D LEU* 4.3 21.8 - - + -
739D ALA* 3.9 23.6 - - + -
740D PRO* 6.1 0.2 - - + -
749D LEU* 3.9 21.5 - - + -
750D MET* 5.4 2.9 - - + -
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Residues in contact with ARG 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689D LEU* 4.0 9.4 - - - +
691D VAL* 4.4 30.7 - - - +
694D LEU* 4.2 20.9 - - + +
698D GLN 3.2 8.5 + - - +
699D LYS* 3.9 10.3 - - + +
701D LEU* 1.3 76.0 - - - +
703D ARG* 1.3 64.5 + - - +
705D VAL* 4.2 7.2 - - + -
706D HIS* 3.2 48.8 + - + -
749D LEU* 3.8 22.4 - - + +
752D GLU* 2.9 34.4 + - - +
791D ASP* 4.5 7.5 + - - +
794D ALA* 3.2 32.3 - - + +
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Residues in contact with ARG 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696D GLU 5.8 0.2 + - - -
699D LYS* 3.0 30.4 + - - +
700D ALA* 3.6 34.2 + - - +
702D ARG* 1.3 75.7 - - - +
704D ASP* 1.3 61.1 + - - +
706D HIS* 3.3 2.6 + - - +
707D LYS* 3.0 36.7 + - - +
794D ALA 3.4 14.7 + - - +
795D MET* 3.9 18.0 - - + +
796D VAL 3.9 17.5 + - - +
797D GLU* 3.6 35.1 + - - +
798D ASP* 4.4 16.8 + - - -
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Residues in contact with ASP 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700D ALA* 3.1 16.8 + - - +
701D LEU* 3.1 11.5 + - + +
703D ARG* 1.3 77.8 + - - +
705D VAL* 1.3 58.5 + - - +
707D LYS* 4.1 19.9 + - - +
708D THR* 2.6 34.5 + - - +
732D LEU* 3.6 7.5 - - + +
735D LYS* 3.5 38.4 - - + +
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Residues in contact with VAL 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701D LEU* 2.8 24.5 + - + +
702D ARG* 3.7 12.1 - - + +
703D ARG 3.2 0.2 - - - -
704D ASP* 1.3 75.9 - - - +
706D HIS* 1.3 70.9 + - + +
708D THR* 3.3 5.7 + - - -
709D ILE* 3.1 37.5 + - + +
732D LEU* 3.7 24.1 - - + +
736D LEU* 4.7 5.4 - - + -
749D LEU* 5.3 4.9 - - + -
752D GLU* 5.0 6.1 - - + +
753D ALA* 3.9 37.5 - - + +
756D ALA* 4.6 4.9 - - + -
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Residues in contact with HIS 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702D ARG* 3.2 37.9 + - + +
703D ARG 4.0 2.0 - - - +
705D VAL* 1.3 89.3 - - + +
707D LYS* 1.3 60.1 + - - +
709D ILE* 3.5 12.7 + - + +
710D ALA* 3.1 21.3 + - - +
752D GLU* 2.7 29.0 + - - -
789D VAL 4.8 5.4 - - - -
790D ALA* 3.5 15.1 - - + +
791D ASP* 3.3 32.3 + - + +
794D ALA* 3.4 21.5 - - + +
795D MET* 3.6 21.4 - - + +
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Residues in contact with LYS 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703D ARG* 3.0 24.7 + - - +
704D ASP* 4.1 21.8 + - - +
706D HIS* 1.3 73.7 - - - +
708D THR* 1.3 60.7 + - - +
710D ALA* 3.3 5.5 + - + +
711D LYS* 2.9 29.9 + - - +
795D MET* 4.0 22.2 - - + +
797D GLU* 3.2 31.0 + - - +
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Residues in contact with THR 708 (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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704D ASP 2.6 25.5 + - - -
705D VAL 3.3 4.7 + - - -
707D LYS* 1.3 72.6 - - - +
709D ILE* 1.3 60.0 + - - +
711D LYS* 4.6 4.3 - - - -
712D VAL* 3.0 40.6 + - + +
728D ALA* 3.4 34.4 + - + +
729D ILE* 4.1 6.7 - - - +
732D LEU* 3.9 27.7 - - + +
760D MET* 4.1 10.1 - - + -
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Residues in contact with ILE 709 (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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705D VAL* 3.1 24.1 + - + +
706D HIS* 3.6 20.6 - - + +
707D LYS 3.3 0.2 - - - -
708D THR* 1.3 76.6 - - - +
710D ALA* 1.3 56.7 - - - +
712D VAL* 4.0 0.5 - - - +
713D THR* 2.6 37.7 + - - +
752D GLU* 5.9 0.9 - - - +
756D ALA* 3.7 27.6 - - + -
760D MET* 3.8 21.2 - - + +
787D TRP* 5.0 1.2 + - + +
788D PRO* 3.1 42.6 - - + +
789D VAL 4.8 5.8 - - - +
790D ALA* 3.9 14.6 - - + +
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Residues in contact with ALA 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D HIS 3.1 14.7 + - - +
707D LYS* 3.3 12.1 + - - +
709D ILE* 1.3 78.1 - - - +
711D LYS* 1.3 59.6 - - - +
713D THR* 3.7 6.0 + - - -
714D ASP* 3.2 22.3 + - - +
790D ALA* 4.2 13.2 - - + -
795D MET* 4.5 11.0 - - + -
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Residues in contact with LYS 711 (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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707D LYS 2.9 17.2 + - - +
708D THR* 4.1 6.5 - - - +
710D ALA* 1.3 74.3 - - - +
712D VAL* 1.3 56.0 + - - +
714D ASP* 3.2 5.1 + - - +
715D ASP* 2.8 63.2 + - - +
719D ARG* 3.8 6.7 - - - +
724D THR* 3.9 20.7 - - - +
728D ALA* 4.0 17.3 - - + -
15E A 4.8 1.6 + - - -
16E U 3.1 34.1 + - - +
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Residues in contact with VAL 712 (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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708D THR* 3.0 23.4 + - + +
709D ILE 4.2 0.2 - - - +
711D LYS* 1.3 72.2 - - - +
713D THR* 1.3 60.3 + - - +
716D ILE* 3.1 52.0 + - + +
725D ALA* 3.4 35.7 - - + +
728D ALA* 4.4 3.8 - - + -
729D ILE* 3.8 19.3 - - + -
760D MET* 3.7 30.5 - - + +
764D PHE* 5.3 0.2 - - + -
787D TRP* 4.1 4.5 - - + -
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Residues in contact with THR 713 (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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65D TYR* 3.4 20.9 + - - +
69D LEU* 5.5 2.2 - - + -
709D ILE* 2.6 28.2 + - - +
710D ALA* 3.8 6.9 - - - -
712D VAL* 1.3 77.0 - - - +
714D ASP* 1.3 57.6 + - - +
717D GLY* 2.9 28.1 + - - -
787D TRP* 3.0 34.4 + - + +
788D PRO 4.4 0.5 + - - -
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Residues in contact with ASP 714 (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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710D ALA 3.2 16.1 + - - +
711D LYS* 3.2 6.5 + - - +
713D THR* 1.3 77.8 - - - +
715D ASP* 1.3 63.7 + - - +
718D ARG* 2.7 73.5 + - - +
719D ARG* 3.1 19.2 + - - -
16E U 3.8 8.5 + - - +
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Residues in contact with ASP 715 (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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711D LYS* 2.8 47.7 + - - +
712D VAL 4.2 0.2 - - - +
714D ASP* 1.3 75.8 - - - +
716D ILE* 1.3 57.3 + - - +
719D ARG* 3.1 25.8 + - - -
720D GLN* 2.8 24.9 + - - -
721D THR* 3.0 29.6 + - - +
724D THR* 2.7 26.7 + - - -
725D ALA* 3.4 18.4 + - + -
16E U 4.7 0.7 + - - -
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Residues in contact with ILE 716 (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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61D VAL* 4.6 5.4 - - + +
62D ILE* 5.2 7.0 - - + +
65D TYR* 3.6 35.4 - - + -
712D VAL* 3.1 38.7 + - + +
713D THR 4.3 0.7 - - - +
715D ASP* 1.3 80.2 - - - +
717D GLY* 1.3 64.8 + - - +
720D GLN* 3.5 19.1 + - - +
722D PHE* 4.1 32.2 - - + -
725D ALA* 4.3 4.9 - - + -
760D MET 4.7 0.2 - - - +
763D PRO* 5.1 5.2 - - + -
764D PHE* 4.0 21.8 - - + -
787D TRP* 3.9 17.0 - - + -
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Residues in contact with GLY 717 (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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65D TYR* 3.9 24.0 - - - -
66D GLN* 5.5 2.5 + - - -
713D THR 2.9 21.3 + - - -
716D ILE* 1.3 74.3 - - - +
718D ARG* 1.3 55.9 + - - +
720D GLN* 2.9 17.2 + - - -
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Residues in contact with ARG 718 (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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562D GLN* 5.3 0.5 + - - -
713D THR 4.2 0.4 + - - -
714D ASP* 2.7 48.5 + - - +
717D GLY* 1.3 72.2 - - - -
719D ARG* 1.3 77.6 + - - +
720D GLN* 3.3 16.7 + - - +
16E U 3.1 29.7 + - - -
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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
------------------------------------------------------------
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