Contacts of the helix formed by residues 701 - 720 (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 TYR 701 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676A ASN* 4.4 13.2 - - + -
679A LYS* 3.7 28.6 + - + +
680A ILE* 3.2 51.4 - - + +
700A LYS* 1.3 81.3 - - + +
702A SER* 1.3 59.0 + - - +
704A PHE* 2.8 28.1 + + - +
705A ALA* 2.9 11.8 + - - +
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Residues in contact with SER 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A GLU* 4.2 8.2 + - - -
700A LYS* 4.3 6.7 + - - +
701A TYR* 1.3 78.1 - - - +
703A CYS* 1.3 67.4 + - - +
705A ALA* 3.1 14.2 + - - +
706A LEU* 3.0 25.8 + - - +
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Residues in contact with CYS 703 (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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639A ALA* 3.1 48.2 - - + +
642A PHE* 4.4 0.8 - - + -
643A GLU* 3.2 20.9 - - + +
700A LYS* 3.9 16.6 - - - +
702A SER* 1.3 85.9 + - - +
704A PHE* 1.3 55.0 + - + +
706A LEU* 2.9 24.1 + - - +
707A PHE* 2.7 35.8 + - + -
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Residues in contact with PHE 704 (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* 6.1 1.6 - - + -
639A ALA* 6.4 1.8 - - + -
672A ILE* 6.2 0.2 - - + -
673A THR* 4.0 32.8 - - + -
676A ASN* 3.9 28.9 - - + -
677A ALA* 4.9 6.7 - - + -
680A ILE* 3.4 27.6 - - + -
700A LYS* 3.1 32.5 - - + -
701A TYR* 2.8 18.0 + + - +
703A CYS* 1.3 70.8 - - + +
705A ALA* 1.3 65.9 + - - +
706A LEU 3.1 1.6 - - - -
707A PHE* 3.0 45.5 + + + +
708A VAL* 2.9 27.1 + - - +
741A ILE* 5.7 0.2 - - + -
744A ASP* 6.1 0.2 - - - +
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Residues in contact with ALA 705 (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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680A ILE* 5.4 0.8 - - - +
701A TYR 2.9 11.0 + - - +
702A SER* 3.2 17.9 - - - +
704A PHE* 1.3 74.5 - - - +
706A LEU* 1.3 57.3 + - + +
708A VAL* 3.6 6.9 + - - +
709A LYS* 3.0 41.1 + - + +
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Residues in contact with LEU 706 (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* 4.6 2.5 - - + -
643A GLU* 3.6 43.7 - - + +
702A SER* 3.0 12.9 + - - +
703A CYS 2.9 12.1 + - - +
705A ALA* 1.3 77.1 - - + +
707A PHE* 1.3 55.6 + - - +
709A LYS* 2.7 30.3 + - + +
710A PHE* 3.0 47.9 + - + -
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Residues in contact with PHE 707 (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* 4.8 17.9 - - + -
639A ALA 5.6 0.4 - - - -
642A PHE* 3.4 47.8 - + + -
673A THR* 5.0 7.6 - - + -
703A CYS* 2.7 49.1 + - + -
704A PHE* 3.0 46.2 - + + +
706A LEU* 1.3 73.7 - - - +
708A VAL* 1.3 61.0 + - - +
710A PHE* 3.7 8.2 + - - +
711A GLY* 4.3 3.6 + - - -
741A ILE* 3.7 40.7 - - + +
744A ASP* 4.4 9.9 - - - +
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Residues in contact with VAL 708 (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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704A PHE 2.9 14.0 + - - +
705A ALA* 3.8 9.4 - - - +
707A PHE* 1.3 73.9 - - - +
709A LYS* 1.3 74.5 + - + +
710A PHE 2.9 1.9 + - - -
711A GLY* 3.1 14.9 + - - -
712A LYS 4.6 1.0 + - - -
741A ILE* 6.1 0.2 - - - -
744A ASP* 4.9 14.8 - - + +
1325A GLN* 4.6 18.8 - - + +
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Residues in contact with LYS 709 (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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705A ALA* 3.0 27.8 + - - +
706A LEU* 2.7 27.1 + - + +
708A VAL* 1.3 81.2 - - + +
710A PHE* 1.3 69.4 + - + +
711A GLY 3.4 0.3 + - - -
712A LYS* 3.8 14.0 + - - +
713A GLU* 4.5 8.7 + - - +
1328A GLU* 2.2 41.2 + - - +
1332A TYR* 3.0 30.7 - - + +
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Residues in contact with PHE 710 (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* 3.2 38.4 - + - -
643A GLU* 5.1 4.0 - - - -
646A VAL* 3.4 44.2 - - + -
647A TYR* 5.1 2.9 - - - -
706A LEU* 3.0 46.6 + - + -
707A PHE* 4.3 5.6 - - - +
708A VAL 2.9 1.4 + - - -
709A LYS* 1.3 81.9 - - + +
711A GLY* 1.3 66.8 + - - +
712A LYS 3.1 0.5 + - - -
713A GLU* 3.3 11.6 + - + +
714A VAL* 2.9 37.2 + - + +
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Residues in contact with GLY 711 (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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707A PHE 4.3 2.4 + - - -
708A VAL 3.1 12.1 + - - -
710A PHE* 1.3 76.7 - - - +
712A LYS* 1.3 64.8 + - - +
714A VAL* 3.2 9.2 - - - +
715A ALA* 2.9 24.9 + - - +
738A HIS* 4.9 14.7 - - - -
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Residues in contact with LYS 712 (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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708A VAL 4.6 1.4 + - - -
709A LYS 3.8 9.7 + - - +
710A PHE 3.3 0.8 - - - -
711A GLY* 1.3 77.1 - - - +
713A GLU* 1.3 77.3 + - + +
714A VAL 2.7 2.4 + - - -
715A ALA* 3.9 1.7 - - - +
716A VAL* 3.1 35.9 + - + +
1119A LYS 5.7 3.0 + - - -
1120A SER* 6.2 1.8 - - - +
1121A LEU* 5.7 10.3 - - - +
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Residues in contact with GLU 713 (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* 6.4 0.2 - - - -
650A SER* 5.3 8.8 - - - -
709A LYS 4.7 7.6 - - - +
710A PHE* 3.3 12.9 + - - +
712A LYS* 1.3 93.8 - - + +
714A VAL* 1.3 54.7 + - + +
716A VAL* 3.7 6.8 + - - +
717A LYS* 2.9 41.8 + - + +
1121A LEU* 5.6 5.8 - - + -
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Residues in contact with VAL 714 (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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646A VAL* 6.1 2.0 - - + -
649A PHE* 5.3 12.3 - - + -
710A PHE* 2.9 37.8 + - + +
711A GLY* 3.2 10.3 - - - +
712A LYS 2.7 1.0 + - - -
713A GLU* 1.3 73.4 - - + +
715A ALA* 1.3 72.8 + - + +
717A LYS* 2.8 19.1 + - - +
718A MSE 3.0 9.6 + - - -
734A LEU* 3.4 50.2 - - + +
737A PRO* 6.3 0.4 - - + -
738A HIS* 4.6 12.1 - - + -
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Residues in contact with ALA 715 (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 2.9 13.6 + - - +
712A LYS* 4.1 2.0 - - - +
714A VAL* 1.3 80.0 - - + +
716A VAL* 1.3 65.9 + - + +
718A MSE 3.0 26.9 + - - +
719A LYS* 3.1 21.4 + - + +
738A HIS* 6.5 0.4 - - + -
750A PRO* 5.5 13.5 - - + -
751A ALA* 5.8 8.5 - - + -
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Residues in contact with VAL 716 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712A LYS* 3.1 33.7 + - + +
713A GLU* 3.7 5.6 - - - +
715A ALA* 1.3 77.7 - - + +
717A LYS* 1.3 62.5 + - - +
719A LYS* 4.9 3.6 - - - -
720A GLN* 2.9 33.4 + - + +
1120A SER* 4.6 4.5 - - - +
1121A LEU* 3.4 51.1 - - + -
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Residues in contact with LYS 717 (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* 5.0 2.5 - - + -
652A GLU* 3.5 42.7 - - + +
713A GLU* 2.9 28.7 + - + +
714A VAL* 2.8 11.2 + - - +
716A VAL* 1.3 77.9 - - - +
718A MSE 1.3 65.9 + - - +
721A TYR* 3.3 53.7 + - + +
722A LYS* 3.1 15.6 - - - +
730A LEU* 3.8 18.2 - - + -
1121A LEU* 4.0 22.3 - - + +
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Residues in contact with MSE 718 (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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714A VAL* 3.0 5.6 + - - -
715A ALA* 3.0 22.9 + - - +
717A LYS* 1.3 80.5 - - - +
719A LYS* 1.3 71.5 + - + +
722A LYS* 3.1 26.2 + - + +
727A ALA* 4.9 2.9 - - + +
730A LEU* 4.6 3.8 - - + +
731A THR* 3.4 39.0 - - + -
734A LEU* 3.9 29.4 - - + -
750A PRO 5.1 1.1 - - - +
751A ALA* 4.0 17.9 - - - +
754A MSE 3.5 43.3 - - + +
755A ALA* 4.1 6.5 - - + +
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Residues in contact with LYS 719 (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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715A ALA* 3.1 17.8 + - + +
716A VAL* 4.0 4.0 - - - +
718A MSE 1.3 86.5 - - + +
720A GLN* 1.3 74.3 + - + +
722A LYS 4.4 2.9 + - - +
750A PRO* 3.9 37.1 - - - +
754A MSE 5.4 16.9 - - + +
1019A ASP 5.6 0.3 - - - +
1020A PRO* 5.0 14.9 - - - +
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Residues in contact with GLN 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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598A PRO 3.6 9.4 - - - +
716A VAL* 2.9 29.4 + - + +
719A LYS* 1.3 82.8 - - + +
721A TYR* 1.3 65.8 + - + +
722A LYS 3.6 0.5 + - - +
1020A PRO 5.6 1.0 - - - +
1120A SER* 4.9 8.6 + - - -
1121A LEU* 3.5 23.1 - - + -
1122A GLY 4.6 0.2 - - - -
1123A THR* 2.6 43.6 + - + +
1124A ILE* 5.4 1.1 - - - +
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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