Contacts of the helix formed by residues 719 - 738 (chain A) in PDB entry 1LQF
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 ILE 719 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A VAL* 4.3 21.1 - - + -
715A CYS* 3.7 1.2 - - - -
717A ALA* 4.0 7.6 - - + +
718A GLY* 1.3 85.2 - - - +
720A GLY* 1.3 70.1 + - - +
723A GLY 3.1 12.7 + - - +
757A ARG* 3.4 15.7 - - + +
758A MET* 3.2 26.9 - - + +
759A GLY* 3.5 13.9 - - - +
760A LEU* 3.2 8.6 - - - -
761A ILE 2.8 20.2 + - - -
762A GLN* 3.5 25.6 - - - +
802A BGD 3.2 25.2 + - + +
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Residues in contact with GLY 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A ILE* 1.3 78.5 - - - +
721A ARG* 1.3 64.5 + - - -
724A THR* 3.0 21.7 + - - -
761A ILE* 3.7 2.9 - - - -
762A GLN* 3.6 20.6 - - - -
766A GLN* 3.9 7.4 - - - -
802A BGD 2.6 32.1 + - - -
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Residues in contact with ARG 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A LEU* 3.3 27.9 - - + +
611A ASN* 3.6 24.9 - - - +
615A GLU* 2.8 20.8 + - - -
679A TRP* 2.7 80.0 + - + +
680A PRO 3.8 3.4 - - - -
681A ASP* 3.2 28.7 - - - +
715A CYS* 3.9 2.8 - - + +
716A SER* 3.8 7.9 - - - +
720A GLY* 1.3 73.5 - - - +
722A SER* 1.3 58.9 + - - +
724A THR* 3.3 4.2 + - - -
725A PHE 3.0 23.0 + - - -
766A GLN* 4.0 9.1 - - - +
802A BGD 2.6 40.2 + - - +
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Residues in contact with SER 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A LEU* 4.0 20.9 - - - -
610A LEU* 3.5 11.3 - - - +
713A VAL* 3.9 15.3 - - - -
714A HIS* 3.6 15.7 - - - -
715A CYS* 2.8 24.3 - - - +
718A GLY* 3.6 10.1 - - - -
720A GLY 3.3 0.6 - - - -
721A ARG* 1.3 73.3 - - - +
723A GLY* 1.3 67.2 + - - +
725A PHE* 3.1 1.4 + - - +
726A CYS* 2.9 28.4 + - - -
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Residues in contact with GLY 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A LEU* 4.3 3.5 - - - +
719A ILE 3.1 21.7 + - - -
720A GLY 3.8 0.2 - - - -
722A SER* 1.3 79.2 - - - +
724A THR* 1.3 57.6 + - - +
726A CYS* 3.9 2.5 - - - +
727A LEU* 2.8 33.1 + - - +
750A LEU* 5.3 0.5 - - - +
753A MET* 4.6 2.1 - - - +
760A LEU* 4.1 24.0 - - - +
761A ILE* 3.8 7.0 - - - -
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Residues in contact with THR 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A TRP* 3.8 22.2 - - + -
691A PHE* 5.2 2.2 - - + -
720A GLY 3.0 14.3 + - - -
721A ARG 3.4 8.7 - - - -
723A GLY* 1.3 76.7 - - - +
725A PHE* 1.3 64.1 + - - +
727A LEU* 3.8 1.4 - - - +
728A ALA* 3.1 24.9 + - + +
761A ILE* 3.4 20.2 - - - +
766A GLN* 3.6 22.4 - - + +
769A PHE* 4.4 14.6 - - + -
770A SER* 3.3 21.5 + - - +
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Residues in contact with PHE 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A TYR* 5.2 5.6 - + - -
608A VAL* 4.3 17.9 - - + -
610A LEU* 3.6 23.1 - - + -
679A TRP* 4.4 0.2 - - - -
691A PHE* 4.0 28.1 - + + -
694A PHE* 3.8 25.8 - + - -
695A LEU* 3.7 32.8 - - + +
698A VAL* 4.5 9.4 - - + -
704A LEU* 5.6 4.7 - - + -
711A VAL* 5.9 0.2 - - + -
713A VAL* 4.1 20.4 - - + -
721A ARG 3.0 13.7 + - - +
722A SER 3.5 6.5 - - - +
724A THR* 1.3 78.5 - - - +
726A CYS* 1.3 77.1 + - - +
728A ALA* 3.5 3.1 + - - +
729A ASP* 3.1 24.6 + - + +
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Residues in contact with CYS 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A TYR* 3.6 35.5 + - + -
583A LEU* 3.6 29.6 - - + -
713A VAL* 4.2 6.1 - - - -
722A SER 2.9 19.6 + - - +
723A GLY* 4.1 3.1 - - - +
725A PHE* 1.3 85.6 - - - +
727A LEU* 1.3 61.9 + - - +
729A ASP* 4.3 4.5 - - - -
730A THR* 2.8 34.3 + - - -
753A MET* 4.2 12.3 - - - -
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Residues in contact with LEU 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A GLY 2.8 22.8 + - - +
724A THR 3.8 3.6 - - - +
726A CYS* 1.3 73.2 - - - +
728A ALA* 1.3 65.1 + - - +
730A THR* 3.8 0.5 - - - -
731A CYS* 2.8 38.9 + - - -
746A ILE* 3.8 22.2 - - + +
749A VAL* 3.8 16.8 - - + -
750A LEU* 3.7 43.3 - - + +
753A MET* 4.0 12.0 - - - -
761A ILE* 3.3 27.6 - - + -
767A LEU* 4.6 2.2 - - + -
770A SER* 4.1 11.9 - - - +
774A VAL* 6.0 0.7 - - + -
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Residues in contact with ALA 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A PHE* 3.9 24.9 - - + -
692A LEU* 6.4 0.2 - - + -
695A LEU* 5.0 2.5 - - + -
724A THR* 3.1 15.3 + - + +
725A PHE 3.6 4.3 - - - +
727A LEU* 1.3 80.5 - - - +
729A ASP* 1.3 65.2 + - - +
731A CYS* 3.2 1.4 + - - +
732A LEU* 2.9 32.2 + - + +
770A SER* 5.0 6.0 - - - +
773A ALA* 5.0 6.5 - - + -
774A VAL* 3.9 20.9 - - + +
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Residues in contact with ASP 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A ARG* 2.7 37.4 + - - -
581A TYR* 2.8 26.0 + - + +
695A LEU* 3.7 26.8 - - + +
699A ARG* 3.0 32.9 + - - +
704A LEU* 4.3 4.6 - - - +
725A PHE* 3.1 15.0 + - + +
726A CYS* 3.6 8.5 - - - +
728A ALA* 1.3 82.4 - - - +
730A THR* 1.3 62.5 + - - +
733A LEU* 3.1 17.0 + - - +
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Residues in contact with THR 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A MET* 3.8 16.7 - - + +
577A ALA* 3.9 20.8 - - + +
579A ARG* 5.3 1.0 - - - +
581A TYR* 2.8 24.9 + - - -
726A CYS 2.8 18.8 + - - -
727A LEU 3.8 1.8 - - - -
729A ASP* 1.3 73.1 - - - +
731A CYS* 1.3 65.4 + - - +
733A LEU* 2.9 20.5 + - - +
734A LEU* 2.9 19.0 + - + +
749A VAL* 3.9 20.4 - - + -
753A MET* 3.3 16.5 - - - +
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Residues in contact with CYS 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A LEU* 2.8 45.4 + - - +
728A ALA 3.7 1.1 - - - +
730A THR* 1.3 72.3 - - - +
732A LEU* 1.3 63.8 + - - +
734A LEU* 3.0 10.7 + - - +
735A MET* 3.0 27.2 + - - +
744A VAL* 4.4 10.0 - - + +
746A ILE* 3.9 23.3 - - + -
749A VAL* 4.0 17.3 - - - -
774A VAL* 3.6 23.3 - - + -
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Residues in contact with LEU 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A LEU* 4.2 19.7 - - + -
695A LEU* 4.1 25.4 - - + -
696A PHE* 5.0 2.9 - - + -
699A ARG* 3.4 25.5 + - - +
728A ALA* 2.9 16.8 + - + +
729A ASP 3.6 3.1 - - - +
731A CYS* 1.3 75.8 - - - +
733A LEU* 1.3 63.4 + - - +
735A MET* 3.5 8.7 + - + +
736A ASP* 3.3 19.8 + - - +
773A ALA 4.5 2.7 - - - +
774A VAL* 3.4 33.2 - - + +
777A GLY* 4.0 4.3 - - - +
778A ALA* 3.8 20.2 - - + +
781A ILE* 4.3 15.2 - - + +
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Residues in contact with LEU 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A ALA* 4.1 23.8 - - + +
578A GLN 5.3 0.4 - - - +
579A ARG* 3.5 56.1 - - + +
699A ARG* 3.0 28.0 - - - +
729A ASP 3.1 15.8 + - - +
730A THR* 2.9 11.7 + - - +
732A LEU* 1.3 76.1 - - - +
734A LEU* 1.3 65.0 + - - +
736A ASP* 3.0 10.3 + - + +
737A LYS* 2.9 25.1 + - - +
700D GLU* 5.3 2.5 - - - +
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Residues in contact with LEU 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A MET* 6.3 0.2 - - + -
576A GLU* 3.2 47.1 - - + +
577A ALA* 4.1 16.6 - - + +
730A THR* 2.9 22.0 + - + +
731A CYS* 3.4 8.7 - - - +
733A LEU* 1.3 77.2 - - - +
735A MET* 1.3 57.3 + - - +
737A LYS* 4.4 6.7 - - + -
738A ARG* 3.0 42.8 + - - +
744A VAL* 4.0 19.1 - - + -
749A VAL* 3.6 31.6 - - + -
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Residues in contact with MET 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A MET* 3.7 26.5 - - + +
731A CYS 3.0 17.7 + - - +
732A LEU* 3.7 9.2 - - + +
734A LEU* 1.3 74.3 - - - +
736A ASP* 1.3 66.1 + - - +
738A ARG 3.2 17.3 - - - +
741A PRO* 3.2 52.4 - - + +
742A SER* 4.9 0.4 - - - -
744A VAL* 3.9 19.1 - - + +
746A ILE* 5.2 4.5 - - + -
774A VAL* 4.0 25.4 - - + -
775A ILE* 5.9 1.8 - - + +
778A ALA* 4.1 23.3 - - + -
781A ILE* 5.7 2.5 - - + -
782A MET* 6.1 4.5 - - + -
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Residues in contact with ASP 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A ARG* 5.9 0.2 + - - -
732A LEU 3.3 9.9 + - - +
733A LEU* 3.0 12.2 + - + +
735A MET* 1.3 79.9 - - - +
737A LYS* 1.3 61.0 + - - +
738A ARG 4.2 2.3 - - - +
781A ILE* 3.2 20.6 - - + +
782A MET* 5.7 3.9 - - - +
648D ASP* 5.0 12.3 - - - +
650D LYS* 5.1 15.0 + - - +
697D LYS* 2.4 35.6 + - - -
700D GLU* 5.1 1.9 - - - +
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Residues in contact with LYS 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A GLU* 3.1 39.4 + - + +
577A ALA* 3.7 14.9 + - - +
578A GLN* 3.2 24.0 + - - -
733A LEU* 2.9 15.7 + - - +
734A LEU* 3.9 7.0 - - + +
736A ASP* 1.3 78.8 - - - +
738A ARG* 1.3 70.7 + - + +
739A LYS 3.7 1.0 + - - -
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Residues in contact with ARG 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A GLU* 2.9 41.3 + - - +
734A LEU* 3.0 34.7 + - - +
735A MET 3.2 14.2 + - - +
736A ASP 4.2 2.6 - - - +
737A LYS* 1.3 79.7 - - + +
739A LYS* 1.3 68.9 + - - +
740A ASP 3.2 14.3 + - - +
741A PRO* 4.0 1.4 - - + +
743A SER* 3.2 40.9 + - - +
744A VAL* 3.5 21.1 - - - +
745A ASP 4.6 1.4 - - - +
748A LYS* 6.2 0.2 - - - +
749A VAL* 6.1 0.4 - - - +
650D LYS* 5.9 1.0 + - - -
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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
------------------------------------------------------------
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