Contacts of the helix formed by residues 719 - 738 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549C VAL* 3.8 27.1 - - + -
715C CYS* 3.7 1.4 - - - -
717C ALA* 4.3 1.3 - - + -
718C GLY* 1.3 80.4 - - - +
720C GLY* 1.3 78.6 + - - +
723C GLY 3.0 12.9 + - - +
757C ARG* 3.5 16.4 - - + +
758C MET* 3.3 22.9 - - + +
759C GLY* 3.4 15.0 - - - +
760C LEU* 3.2 10.0 - - + -
761C ILE 2.9 20.2 + - - -
762C GLN* 3.6 21.8 - - - +
804C BGD 2.9 37.2 + - + +
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Residues in contact with GLY 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719C ILE* 1.3 75.5 - - - +
721C ARG* 1.3 61.4 + - - -
724C THR* 2.9 22.2 + - - -
761C ILE* 3.7 2.3 - - - -
762C GLN* 3.7 13.7 - - - -
766C GLN* 3.7 13.4 - - - +
804C BGD 2.4 40.2 + - - -
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Residues in contact with ARG 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C LEU* 3.4 25.6 - - + +
611C ASN* 3.5 23.3 - - - +
615C GLU* 2.8 34.2 + - - -
679C TRP* 2.8 81.5 + - + +
680C PRO 3.7 3.6 - - - -
681C ASP* 3.4 22.4 - - - +
715C CYS* 3.9 3.4 - - + +
716C SER* 3.9 6.1 - - - +
720C GLY* 1.3 69.6 - - - -
722C SER* 1.3 66.2 + - - +
724C THR* 3.2 3.7 + - - -
725C PHE* 3.0 18.7 + - - +
766C GLN* 4.1 8.0 - - - +
804C BGD 2.8 42.6 + - - +
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Residues in contact with SER 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C LEU* 4.0 21.3 - - - -
610C LEU* 3.5 10.7 - - - +
713C VAL* 4.0 12.3 - - - +
714C HIS* 3.5 19.7 + - - -
715C CYS* 2.9 24.2 - - - -
718C GLY* 3.6 8.8 - - - -
720C GLY 3.3 0.6 - - - -
721C ARG* 1.3 77.4 - - - +
723C GLY* 1.3 63.7 + - - +
725C PHE* 3.2 1.6 + - - +
726C CYS* 3.0 29.3 + - - -
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Residues in contact with GLY 723 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C LEU* 4.4 3.1 - - - +
719C ILE 3.0 23.0 + - - -
720C GLY 3.7 0.2 - - - -
722C SER* 1.3 78.7 - - - +
724C THR* 1.3 57.0 + - - +
726C CYS* 4.0 2.3 - - - +
727C LEU* 2.9 32.2 + - - +
750C LEU* 5.4 0.5 - - - +
753C MET* 4.7 2.8 - - - +
760C LEU* 4.0 23.3 - - - +
761C ILE* 3.8 7.1 - - - +
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Residues in contact with THR 724 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679C TRP* 3.7 23.6 - - + -
691C PHE* 4.9 4.0 - - + -
720C GLY 2.9 14.0 + - - -
721C ARG 3.4 8.7 - - - -
723C GLY* 1.3 77.8 - - - +
725C PHE* 1.3 61.5 + - - +
727C LEU* 3.8 1.7 - - - +
728C ALA* 3.1 23.8 + - + +
761C ILE* 3.6 19.2 - - - +
766C GLN* 3.7 24.5 + - + +
769C PHE* 4.6 13.5 - - + -
770C SER* 3.8 18.7 + - - +
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Residues in contact with PHE 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C TYR* 5.2 5.8 - + - -
608C VAL* 4.2 16.8 - - + -
610C LEU* 3.6 24.9 - - + -
691C PHE* 3.9 28.5 - + + -
694C PHE* 3.8 26.0 - + - -
695C LEU* 3.7 31.7 - - + +
698C VAL* 4.5 9.9 - - + -
704C LEU* 5.5 5.4 - - + -
711C VAL* 5.9 0.2 - - + -
713C VAL* 4.1 27.1 - - + -
721C ARG 3.0 13.7 + - - +
722C SER 3.5 6.3 - - - +
724C THR* 1.3 77.1 - - - +
726C CYS* 1.3 70.0 + - - +
728C ALA* 3.6 2.6 - - - +
729C ASP* 3.1 24.6 + - + +
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Residues in contact with CYS 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C TYR* 3.7 34.3 + - + -
583C LEU* 3.7 30.3 - - + -
713C VAL* 4.2 5.6 - - - -
722C SER 3.0 20.1 + - - +
723C GLY* 4.0 2.7 - - - +
725C PHE* 1.3 85.7 - - - +
727C LEU* 1.3 68.3 + - - +
729C ASP* 3.3 5.0 + - - +
730C THR* 2.8 29.8 + - - -
753C MET* 4.1 12.1 - - - -
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Residues in contact with LEU 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723C GLY 2.9 19.6 + - - +
724C THR 3.8 3.4 - - - +
726C CYS* 1.3 76.3 - - - +
728C ALA* 1.3 65.7 + - - +
730C THR* 3.7 0.5 - - - -
731C CYS* 2.9 38.4 + - - -
746C ILE* 3.8 21.5 - - + +
749C VAL* 3.7 29.2 - - + -
750C LEU* 3.7 31.6 - - + +
753C MET* 4.0 10.7 - - - -
761C ILE* 3.3 27.1 - - + -
767C LEU* 4.7 2.9 - - + -
770C SER* 4.1 12.1 - - - +
774C VAL* 5.9 0.4 - - + -
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Residues in contact with ALA 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691C PHE* 4.0 23.8 - - + -
692C LEU* 6.3 0.4 - - + -
695C LEU* 4.9 3.1 - - + -
724C THR* 3.1 15.6 + - + +
725C PHE 3.6 4.9 - - - +
727C LEU* 1.3 81.3 - - - +
729C ASP* 1.3 65.1 + - - +
731C CYS* 3.2 1.4 + - - +
732C LEU* 2.9 31.8 + - + +
770C SER* 5.2 4.4 - - - +
773C ALA* 4.9 7.4 - - + -
774C VAL* 3.9 21.2 - - + +
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Residues in contact with ASP 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579C ARG* 2.8 36.3 + - - -
581C TYR* 2.6 26.4 + - + +
695C LEU* 3.8 25.9 - - + +
699C ARG* 2.9 31.8 + - - +
704C LEU* 4.3 4.4 - - - +
725C PHE* 3.1 17.2 + - + +
726C CYS* 3.6 6.1 - - - +
728C ALA* 1.3 81.3 - - - +
730C THR* 1.3 63.8 + - - +
732C LEU 3.1 0.5 + - - -
733C LEU* 3.0 16.7 + - - +
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Residues in contact with THR 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C MET* 4.0 12.0 - - + +
577C ALA* 3.9 21.0 - - + +
579C ARG* 5.3 0.9 - - - +
581C TYR* 2.8 25.3 + - - -
726C CYS 2.8 19.0 + - - -
727C LEU 3.7 2.7 - - - -
729C ASP* 1.3 72.3 - - - +
731C CYS* 1.3 63.8 + - - +
733C LEU* 2.9 21.9 + - - +
734C LEU* 2.9 18.2 + - + +
749C VAL* 4.1 20.0 - - + -
753C MET* 3.3 19.8 - - + +
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Residues in contact with CYS 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727C LEU* 2.9 46.4 + - - +
728C ALA 3.7 1.1 - - - +
730C THR* 1.3 72.1 - - - +
732C LEU* 1.3 63.9 + - - +
734C LEU* 3.0 11.4 + - - +
735C MET* 3.0 27.1 + - - +
744C VAL* 4.4 6.0 - - + +
746C ILE* 3.9 25.1 - - + -
749C VAL* 4.0 17.9 - - - -
774C VAL* 3.6 22.7 - - + -
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Residues in contact with LEU 732 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692C LEU* 4.2 19.1 - - + -
695C LEU* 4.2 22.9 - - + -
696C PHE* 4.6 12.3 - - + -
699C ARG* 3.5 15.4 + - - +
728C ALA* 2.9 17.2 + - + +
729C ASP 3.5 8.5 - - - +
731C CYS* 1.3 76.4 - - - +
733C LEU* 1.3 63.0 + - - +
735C MET* 3.7 8.1 + - + +
736C ASP* 3.4 18.7 + - - +
774C VAL* 3.4 36.5 - - + +
777C GLY* 4.0 3.1 - - - +
778C ALA* 3.8 20.0 - - + +
781C ILE* 4.3 13.3 - - + +
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Residues in contact with LEU 733 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700B GLU* 5.9 1.8 - - - +
577C ALA* 4.0 23.8 - - + +
578C GLN 5.2 0.4 - - - +
579C ARG* 3.5 55.4 - - + +
699C ARG* 3.1 25.1 - - - +
729C ASP 3.0 16.2 + - - +
730C THR* 2.9 10.8 + - - +
732C LEU* 1.3 75.6 - - - +
734C LEU* 1.3 66.1 + - - +
736C ASP* 3.0 10.1 + - + +
737C LYS* 2.9 25.9 + - - +
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Residues in contact with LEU 734 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C MET* 6.4 0.2 - - + -
576C GLU* 3.3 46.7 - - + +
577C ALA* 4.0 16.8 - - + +
730C THR* 2.9 22.1 + - + +
731C CYS* 3.4 9.0 - - - +
733C LEU* 1.3 76.5 - - - +
735C MET* 1.3 57.0 + - - +
737C LYS* 4.5 6.5 - - + -
738C ARG* 2.8 45.8 + - + +
744C VAL* 4.0 19.1 - - + -
749C VAL* 3.7 29.6 - - + -
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Residues in contact with MET 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503C MET* 4.3 17.0 - - - +
731C CYS 3.0 17.7 + - - +
732C LEU* 3.9 9.2 - - + +
733C LEU 3.1 0.2 + - - -
734C LEU* 1.3 76.3 - - - +
736C ASP* 1.3 67.0 + - - +
737C LYS 3.3 0.7 + - - -
738C ARG* 3.5 13.9 + - - +
741C PRO* 3.1 46.8 - - + +
744C VAL* 3.9 23.6 - - + +
746C ILE* 5.2 4.7 - - + -
774C VAL* 4.0 25.1 - - + -
775C ILE* 5.9 3.1 - - + +
778C ALA* 4.1 22.7 - - + -
781C ILE* 5.7 2.2 - - + -
782C MET* 5.9 7.4 - - + +
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Residues in contact with ASP 736 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B ASP* 4.3 19.3 - - - +
650B LYS* 4.8 6.8 + - - +
697B LYS* 3.9 21.6 + - - -
699C ARG* 5.9 0.2 + - - -
732C LEU 3.4 10.8 + - - +
733C LEU* 3.0 12.2 + - + +
735C MET* 1.3 80.1 - - - +
737C LYS* 1.3 60.6 + - + +
738C ARG 4.4 2.3 - - - +
781C ILE* 3.4 32.3 - - + +
782C MET* 5.8 4.6 - - - +
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Residues in contact with LYS 737 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C GLU* 3.0 40.4 + - + +
577C ALA* 3.7 15.2 + - - +
578C GLN* 3.3 23.2 + - - -
733C LEU* 2.9 17.0 + - - +
734C LEU* 4.0 5.6 - - + +
736C ASP* 1.3 78.8 - - - +
738C ARG* 1.3 66.6 + - + +
739C LYS 4.0 0.2 + - - -
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Residues in contact with ARG 738 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C GLU* 3.3 38.8 + - - +
734C LEU* 2.8 37.3 + - + +
735C MET* 3.5 12.8 + - - +
736C ASP 4.4 2.6 - - - +
737C LYS* 1.3 80.1 - - + +
739C LYS* 1.3 64.3 + - - +
740C ASP* 3.3 13.0 - - - +
741C PRO* 4.8 1.7 - - - +
743C SER* 3.2 27.4 + - - +
744C VAL* 3.2 39.2 - - - +
745C ASP 4.1 3.0 - - - +
748C LYS* 6.0 4.8 - - - +
749C VAL* 5.5 1.6 - - - +
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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