Contacts of the helix formed by residues 703 - 721 (chain A) in PDB entry 5M9O
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 703 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700A ASP* 3.2 20.5 + - + +
702A GLU* 1.3 81.7 - - + +
704A GLY* 1.3 57.1 + - - +
705A THR 3.5 2.7 - - - -
706A GLN* 3.3 30.1 + - - +
707A LEU 3.0 22.2 + - - -
789A LEU* 5.3 2.9 - - + -
792A GLN* 2.7 36.0 + - - +
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Residues in contact with GLY 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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699A GLN* 6.2 2.0 - - - -
700A ASP 3.4 7.1 + - - -
701A VAL* 3.1 15.0 + - - -
702A GLU 3.4 0.4 - - - -
703A THR* 1.3 74.7 - - - +
705A THR* 1.3 61.4 + - - +
707A LEU* 3.3 10.1 + - - +
708A GLU* 3.0 36.3 + - - +
792A GLN* 5.3 0.4 - - - -
111B 2MR 6.0 5.6 - - - -
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Residues in contact with THR 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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701A VAL 4.7 2.1 + - - +
702A GLU 4.8 6.4 + - - -
704A GLY* 1.3 74.9 - - - +
706A GLN* 1.3 65.1 + - - +
708A GLU* 3.4 18.0 + - - +
709A LYS* 2.8 29.2 + - - +
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Residues in contact with GLN 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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702A GLU 3.7 6.4 - - - +
703A THR* 3.3 37.7 + - - +
704A GLY 3.2 0.6 - - - -
705A THR* 1.3 79.1 + - - +
707A LEU* 1.3 59.9 + - - +
709A LYS* 3.3 7.2 + - - +
710A LEU* 2.9 30.8 + - - +
789A LEU* 4.0 25.5 - - + +
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Residues in contact with LEU 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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699A GLN* 3.6 33.9 - - + +
703A THR 3.0 13.0 + - - +
704A GLY* 3.3 11.0 + - - +
706A GLN* 1.3 75.7 - - - +
708A GLU* 1.3 59.3 + - + +
710A LEU* 3.2 1.0 + - - +
711A MET* 2.9 55.2 + - + +
765A ASP* 3.7 32.5 - - + +
766A TYR* 4.5 10.1 - - + +
789A LEU* 3.8 13.5 - - + +
792A GLN* 4.0 24.2 - - + +
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Residues in contact with GLU 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 GLY 3.0 22.6 + - - +
705A THR* 3.7 17.6 - - - +
707A LEU* 1.3 77.0 - - + +
709A LYS* 1.3 58.5 + - - +
711A MET* 3.4 6.4 + - - +
712A GLU* 2.9 30.5 + - - +
111B 2MR 3.9 23.5 + - - -
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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 THR 2.8 18.1 + - - +
706A GLN* 3.6 8.1 - - - +
708A GLU* 1.3 74.5 - - - +
710A LEU* 1.3 60.0 + - - +
712A GLU* 3.3 35.1 + - - +
713A ASN* 2.9 55.5 + - - +
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Residues in contact with LEU 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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706A GLN 2.9 17.4 + - - +
707A LEU 3.2 3.6 + - - +
709A LYS* 1.3 75.1 - - - +
711A MET* 1.3 64.3 + - + +
713A ASN* 3.3 5.2 + - + +
714A MET* 2.7 37.1 + - - +
747A ARG* 3.6 42.0 - - - +
783A ALA 4.3 0.9 - - - +
784A PHE* 3.8 29.3 - - + +
788A VAL* 4.0 24.9 - - + -
789A LEU* 3.9 20.4 - - + -
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Residues in contact with MET 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 LEU* 2.9 35.1 + - + +
708A GLU* 3.8 6.7 - - - +
710A LEU* 1.3 92.6 - - + +
712A GLU* 1.3 63.4 + - - +
714A MET* 3.9 23.3 - - + -
715A ARG* 3.0 66.2 + - - +
745A TRP 4.3 1.6 - - - +
746A TYR* 4.5 11.4 - - - -
747A ARG* 3.8 27.6 - - + -
765A ASP* 4.2 7.9 - - - +
766A TYR* 5.2 7.2 - - - +
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Residues in contact with GLU 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 GLU 2.9 16.2 + - - +
709A LYS* 3.3 43.0 + - - +
711A MET* 1.3 76.1 - - - +
713A ASN* 1.3 62.6 + - - +
715A ARG* 3.8 4.8 - - - +
716A ASN* 2.9 29.3 + - + +
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Residues in contact with ASN 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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709A LYS* 2.9 47.7 + - - +
710A LEU* 3.9 4.6 - - + +
712A GLU* 1.3 81.1 - - - +
714A MET* 1.3 65.5 + - - +
716A ASN* 3.4 11.0 + - - +
717A ASP* 3.1 22.3 + - - +
784A PHE* 3.7 17.4 - - + -
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Residues in contact with MET 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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710A LEU 2.7 22.1 + - - +
711A MET* 3.9 20.9 - - + +
713A ASN* 1.3 73.2 - - - +
715A ARG* 1.3 59.2 + - + +
717A ASP* 3.2 5.5 + - - +
718A ILE* 3.0 43.9 + - + +
737A ILE* 3.9 15.7 - - + -
745A TRP 3.6 30.3 - - - +
746A TYR* 4.1 5.2 - - - -
747A ARG* 3.9 20.9 - - - -
780A LEU* 3.9 16.2 - - + -
784A PHE* 3.6 33.9 - - + -
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Residues in contact with ARG 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 MET* 3.0 45.7 + - - +
712A GLU* 3.9 4.0 - - - +
714A MET* 1.3 74.2 - - + +
716A ASN* 1.3 56.4 + - - +
718A ILE* 3.6 9.3 - - + +
719A ALA* 2.8 36.6 + - - +
744A GLU* 3.6 28.8 + - - +
745A TRP* 3.0 38.6 + - + +
746A TYR* 3.1 40.6 + - - -
766A TYR* 5.1 0.6 + - - -
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Residues in contact with ASN 716 (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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712A GLU* 2.9 16.1 + - + +
713A ASN* 3.4 16.1 + - - +
715A ARG* 1.3 75.2 - - - +
717A ASP* 1.3 61.8 + - - +
719A ALA* 3.4 6.2 + - - +
720A SER* 3.0 33.1 + - - -
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Residues in contact with ASP 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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713A ASN 3.1 10.1 + - - +
714A MET 3.4 9.0 - - - +
716A ASN* 1.3 80.7 - - - +
718A ILE* 1.3 57.4 + - - +
720A SER* 3.4 2.8 + - - -
721A HIS* 2.9 58.7 + - - +
781A SER* 4.0 16.3 + - - -
784A PHE* 4.0 18.8 - - + -
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Residues in contact with ILE 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 MET* 3.0 38.7 + - + +
715A ARG* 3.2 10.1 + - + +
717A ASP* 1.3 75.9 - - + +
719A ALA* 1.3 64.4 + - - +
721A HIS 4.5 4.5 - - - -
722A PRO* 3.1 26.6 - - + +
723A PRO* 3.7 20.9 - - + -
737A ILE* 3.6 29.4 - - + -
745A TRP* 3.6 41.3 - - + +
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Residues in contact with ALA 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 ARG 2.8 20.5 + - - +
716A ASN* 3.7 7.4 - - - +
718A ILE* 1.3 75.6 - - - +
720A SER* 1.3 61.1 + - - +
721A HIS 3.7 0.2 + - - -
722A PRO* 3.9 10.4 - - - +
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Residues in contact with SER 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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716A ASN* 3.0 22.8 + - - -
717A ASP* 3.7 1.5 - - - -
718A ILE 3.2 0.2 - - - -
719A ALA* 1.3 78.9 - - - +
721A HIS* 1.3 85.1 + - - +
722A PRO* 3.6 5.7 - - - +
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Residues in contact with HIS 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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717A ASP* 2.9 46.2 + - - +
718A ILE* 3.2 7.0 - - - +
720A SER* 1.3 97.8 + - - +
722A PRO* 1.4 66.3 - - - +
723A PRO* 3.4 6.4 - - - +
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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
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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