Contacts of the helix formed by residues 723 - 742 (chain A) in PDB entry 5LUQ
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 ASP 723 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A PRO* 4.3 3.1 - - - +
599A GLY* 3.6 20.1 + - - +
600A VAL 4.5 10.4 - - - +
602A MSE 5.6 6.1 - - - +
721A TYR 3.0 15.2 + - - +
722A LYS* 1.3 71.2 - - - +
724A GLU* 1.3 53.4 + - - +
725A LEU 3.1 1.6 - - - +
726A LEU* 2.6 36.5 + - + +
727A ALA 2.3 32.5 + - - +
1022A ASP* 4.5 21.8 - - - +
1023A SER* 5.4 1.2 + - - -
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Residues in contact with GLU 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A LYS 3.7 1.7 + - - +
723A ASP* 1.3 71.2 - - - +
725A LEU* 1.3 66.0 + - + +
727A ALA* 3.5 8.8 - - - +
728A SER* 3.0 25.1 + - - -
754A MSE 6.6 0.2 - - + -
758A LEU* 4.3 15.5 - - + +
762A TYR* 5.8 6.6 - - - -
971A ARG* 4.1 19.2 + - - -
1020A PRO 6.2 0.2 - - - +
1021A VAL* 6.0 1.7 - - - -
1022A ASP* 4.7 13.8 + - - +
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Residues in contact with LEU 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A SER* 5.7 1.3 - - - -
508A HIS* 3.3 54.4 - - + +
723A ASP* 2.8 2.0 + - + -
724A GLU* 1.3 80.7 - - + +
726A LEU* 1.3 70.2 + - + +
728A SER* 2.0 34.2 + - - +
729A CYS* 2.8 10.4 - - - -
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Residues in contact with LEU 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A HIS 3.3 26.7 - - - +
509A ARG* 4.0 1.6 - - - -
512A GLY* 3.4 18.6 - - - -
602A MSE 3.3 34.8 - - + -
654A ILE* 3.4 5.6 - - + +
722A LYS* 3.3 26.9 - - - +
723A ASP* 2.6 33.7 + - + +
725A LEU* 1.3 79.0 - - + +
727A ALA* 1.3 59.1 + - - +
729A CYS* 3.1 14.1 + - - +
730A LEU 2.9 25.5 + - - -
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Residues in contact with ALA 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A MSE 4.9 2.9 - - - +
722A LYS* 3.3 35.5 - - + +
723A ASP 2.3 32.1 + - - +
724A GLU* 3.5 10.1 - - - +
726A LEU* 1.3 67.3 - - - +
728A SER* 1.3 63.1 + - - +
730A LEU* 3.4 1.0 + - - +
731A THR* 2.8 35.3 + - + +
754A MSE 5.1 13.5 - - + -
758A LEU* 5.3 1.3 - - + -
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Residues in contact with SER 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A SER* 4.4 13.3 + - - -
724A GLU 3.0 15.3 + - - -
725A LEU* 2.0 30.8 + - - +
727A ALA* 1.3 74.4 - - - +
729A CYS* 1.3 68.7 + - - +
731A THR* 2.3 25.4 + - - -
732A PHE* 3.1 25.9 + - - -
758A LEU* 3.7 22.1 - - - +
763A THR* 5.0 6.7 - - - -
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Residues in contact with CYS 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A SER 4.6 1.6 - - - -
509A ARG* 3.0 43.3 - - + +
654A ILE* 3.4 18.4 - - + -
725A LEU 2.8 19.3 - - - -
726A LEU* 3.1 18.8 + - - +
728A SER* 1.3 76.8 + - - +
730A LEU* 1.3 65.7 + - - +
731A THR 2.7 2.3 + - - -
732A PHE* 2.9 26.8 + - - -
733A LEU* 3.0 12.6 - - + +
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Residues in contact with LEU 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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649A PHE* 3.8 22.0 - - + -
652A GLU* 4.0 1.3 - - - +
654A ILE* 3.9 7.8 - - + +
657A SER* 3.6 32.5 - - - +
717A LYS* 3.8 23.3 - - + -
718A MSE 4.6 2.5 - - + +
722A LYS* 3.5 47.6 - - + +
726A LEU 2.9 6.0 + - - +
727A ALA 4.0 1.8 - - - +
729A CYS* 1.3 77.1 - - - +
731A THR* 1.3 56.7 + - - +
733A LEU* 3.1 8.9 + - + +
734A LEU* 2.9 48.5 + - + +
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Residues in contact with THR 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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718A MSE 3.4 40.8 - - + -
727A ALA* 2.8 27.3 + - + +
728A SER* 2.3 32.2 + - - -
729A CYS 2.7 5.1 + - - -
730A LEU* 1.3 70.7 - - - +
732A PHE* 1.3 64.9 + - - -
733A LEU 2.9 1.6 - - - -
734A LEU* 4.2 5.6 - - - +
735A SER* 2.9 26.0 + - - -
754A MSE 5.1 6.5 - - + +
755A ALA* 5.2 12.6 - - - +
758A LEU* 5.0 7.8 - - + +
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Residues in contact with PHE 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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505A SER* 4.1 18.2 - - - -
506A GLU* 6.0 0.4 - - + -
509A ARG* 3.8 24.7 - - - +
662A LEU* 6.2 0.7 - - + -
728A SER* 3.1 27.3 + - - -
729A CYS* 2.9 34.5 + - + -
731A THR* 1.3 75.1 + - - +
733A LEU* 1.3 69.7 + - + +
735A SER* 2.3 26.5 + - - -
736A LEU* 3.1 23.1 + - + +
763A THR* 5.2 1.6 - - + -
768A VAL* 3.3 37.5 - - + -
769A GLY* 3.4 27.1 - - - -
772A ALA* 5.3 8.3 - - + -
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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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654A ILE 3.5 10.8 - - - +
657A SER* 3.2 18.6 + - - +
658A THR* 3.0 63.0 - - + +
661A PRO* 3.1 23.3 - - + +
662A LEU* 4.9 4.9 - - + -
729A CYS 3.0 19.7 - - - +
730A LEU* 3.3 15.9 - - - +
731A THR 2.9 0.6 - - - -
732A PHE* 1.3 91.4 - - + +
734A LEU* 1.3 63.5 + - - +
736A LEU* 5.4 0.2 - - + -
737A PRO* 3.0 21.4 - - - +
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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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649A PHE* 6.0 1.1 - - + -
657A SER* 4.5 10.3 - - - +
714A VAL* 3.4 63.0 - - + +
718A MSE 3.9 25.4 - - + -
730A LEU* 2.9 35.5 + - + +
731A THR* 4.3 4.7 - - - +
733A LEU* 1.3 80.9 - - - +
735A SER* 1.3 63.1 + - - +
737A PRO* 3.2 10.0 - - + +
738A HIS* 2.9 30.8 + - + -
751A ALA* 5.6 2.9 - - - +
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Residues in contact with SER 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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731A THR 2.9 15.0 + - - -
732A PHE* 2.3 29.9 + - - -
734A LEU* 1.3 80.9 - - - +
736A LEU* 1.3 73.0 + - - +
737A PRO* 3.4 0.3 - - - +
738A HIS* 3.5 4.4 + - - +
739A ASN* 3.1 20.6 + - - +
755A ALA* 4.9 10.5 - - - +
772A ALA* 4.1 12.5 - - - +
773A LEU* 4.8 18.2 - - - -
776A TRP* 4.0 13.2 - - - +
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Residues in contact with LEU 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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661A PRO* 3.3 32.5 - - + +
662A LEU* 4.5 18.4 - - + -
665A GLY* 6.1 2.0 - - - -
732A PHE* 3.1 23.6 + - + +
733A LEU* 5.1 0.2 - - - -
735A SER* 1.3 84.7 + - - +
737A PRO* 1.3 67.5 - - - +
739A ASN* 2.9 40.2 + - + +
740A ILE* 3.0 14.6 - - + +
772A ALA* 4.7 13.2 - - + -
775A GLU* 4.9 8.5 - - - +
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Residues in contact with PRO 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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642A PHE* 5.7 10.8 - - + -
661A PRO* 4.2 6.7 - - + -
664A SER* 5.7 2.9 - - - +
733A LEU 3.0 26.0 - - - +
734A LEU* 3.2 24.5 - - + +
736A LEU* 1.3 89.4 - - + +
738A HIS* 1.3 66.7 + - + +
740A ILE* 2.9 27.4 + - + +
741A ILE* 2.9 24.6 + - + +
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Residues in contact with HIS 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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711A GLY* 4.9 12.7 - - - -
714A VAL* 4.6 17.9 - - + -
715A ALA* 6.5 0.7 - - + -
734A LEU* 2.9 24.5 + - + +
735A SER* 3.6 7.2 - - - +
737A PRO* 1.3 81.8 - - + +
739A ASN* 1.3 53.5 + - - +
740A ILE 2.7 2.3 + - - -
741A ILE* 2.7 37.3 + - + +
742A GLU 2.9 11.1 + - - -
744A ASP 4.9 3.6 - - - -
745A VAL* 3.0 42.1 - - + +
748A TYR* 6.3 2.8 - - + +
751A ALA* 5.0 18.4 - - + +
776A TRP* 4.3 6.1 - - - +
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Residues in contact with ASN 739 (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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670A LEU* 4.2 3.5 - - - +
735A SER 3.1 7.9 + - - +
736A LEU* 2.9 37.4 + - + +
738A HIS* 1.3 74.8 - - - +
740A ILE* 1.3 57.3 + - + +
742A GLU* 3.3 25.9 - - - +
772A ALA 3.4 23.4 + - - -
775A GLU* 3.7 12.9 + - - +
776A TRP* 3.1 45.0 - - - +
779A TYR* 4.4 9.7 - - - +
780A ILE* 4.5 4.8 - - - +
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Residues in contact with ILE 740 (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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638A GLN* 5.9 0.7 - - - +
661A PRO* 4.3 3.1 - - + +
664A SER* 3.4 28.0 - - - +
665A GLY* 3.1 39.3 - - - +
667A TYR 5.4 1.3 - - - +
669A LEU 4.6 15.0 - - - +
670A LEU* 3.0 32.8 - - + +
673A THR* 4.4 7.8 + - + +
674A VAL* 3.6 5.9 - - - +
736A LEU* 3.0 20.9 - - + +
737A PRO* 3.2 17.5 - - + +
738A HIS 2.7 4.4 + - - -
739A ASN* 1.3 75.4 - - + +
741A ILE* 1.3 59.5 + - + +
742A GLU 3.1 6.3 + - - -
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Residues in contact with ILE 741 (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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673A THR* 5.4 9.9 - - - +
674A VAL* 4.3 7.6 - - - +
677A ALA* 5.4 4.4 - - + +
704A PHE* 5.7 0.2 - - + -
707A PHE* 3.7 44.6 - - + +
737A PRO* 2.9 25.9 + - + +
738A HIS* 2.7 25.8 + - + +
740A ILE* 1.3 74.7 - - + +
742A GLU* 1.3 48.5 - - - +
743A LEU* 2.4 6.5 + - - +
744A ASP* 2.1 74.5 + - + +
745A VAL* 4.0 0.7 - - + -
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Residues in contact with GLU 742 (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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670A LEU* 3.0 39.8 - - + +
674A VAL* 4.0 2.9 - - + +
738A HIS 2.9 5.8 + - - -
739A ASN 3.3 15.2 - - - +
740A ILE 3.1 0.2 - - - -
741A ILE* 1.3 71.7 - - - +
743A LEU* 1.3 59.0 + - - +
744A ASP 3.1 0.2 - - - -
745A VAL* 3.1 33.1 + - - +
746A ARG* 4.0 0.5 + - - -
779A TYR* 3.4 26.9 - - + +
780A ILE* 4.3 19.1 - - + +
783A HIS* 2.6 60.4 + - + +
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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