Contacts of the helix formed by residues 781 - 798 (chain A) in PDB entry 5FBQ
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 781 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A ARG* 5.3 0.2 - - - +
779A SER 3.7 1.4 + - - -
780A MET* 1.3 74.3 - - - +
782A GLU* 1.3 61.7 + - - +
783A GLU* 3.1 28.9 + - + +
784A GLN* 2.5 63.4 + - + +
785A LEU* 2.9 13.1 + - - +
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Residues in contact with GLU 782 (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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734A LEU* 4.7 4.3 - - + +
738A ILE* 4.2 33.6 - - + +
741A ARG* 5.0 10.0 - - - +
780A MET 4.2 0.2 + - - -
781A THR* 1.3 76.4 + - - +
783A GLU* 1.3 66.3 + - - +
785A LEU* 3.0 10.5 + - + +
786A GLN* 2.9 33.2 + - - +
44B ILE* 5.7 4.2 - - - +
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Residues in contact with GLU 783 (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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781A THR* 3.1 26.7 + - + +
782A GLU* 1.3 86.5 - - - +
784A GLN* 1.3 63.4 + - + +
786A GLN* 3.5 16.2 + - - +
787A LEU* 3.4 18.2 + - - +
75B ALA* 6.0 4.3 - - + -
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Residues in contact with GLN 784 (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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779A SER 4.3 1.6 - - - +
780A MET* 3.0 29.0 - - + +
781A THR* 2.5 50.4 + - + +
783A GLU* 1.3 78.1 - - + +
785A LEU* 1.3 57.8 + - - +
787A LEU* 3.3 9.5 + - - +
788A LEU* 3.0 25.3 + - - +
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Residues in contact with LEU 785 (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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734A LEU* 3.6 15.0 - - + -
737A LEU* 4.5 13.0 - - + -
738A ILE* 4.4 19.1 - - + -
741A ARG* 3.8 34.8 - - - +
776A PHE 5.2 1.1 - - - +
777A HIS* 4.3 7.9 - - + +
780A MET* 3.7 24.9 - - + -
781A THR 2.9 14.6 + - - +
782A GLU* 3.0 12.5 + - + +
784A GLN* 1.3 74.5 - - - +
786A GLN* 1.3 62.0 + - - +
788A LEU* 3.1 27.5 + - + +
789A VAL* 2.8 33.8 + - - +
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Residues in contact with GLN 786 (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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734A LEU* 3.7 28.2 - - + +
782A GLU 2.9 10.4 + - - +
783A GLU* 3.5 20.2 - - - +
785A LEU* 1.3 77.8 - - - +
787A LEU* 1.3 60.7 + - - +
789A VAL* 3.4 5.2 + - - +
790A GLU* 3.2 26.6 + - - +
75B ALA* 3.5 30.0 - - - +
77B THR* 5.1 13.3 - - - +
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Residues in contact with LEU 787 (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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783A GLU 3.4 9.0 + - - +
784A GLN* 3.3 12.7 + - - +
785A LEU 3.2 0.4 - - - -
786A GLN* 1.3 79.8 - - - +
788A LEU* 1.3 56.6 + - - +
790A GLU* 3.2 12.9 + - + +
791A GLN* 2.9 50.1 + - + +
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Residues in contact with LEU 788 (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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665A TYR* 4.5 7.0 - - + +
737A LEU* 3.8 21.8 - - + -
777A HIS* 4.0 36.8 - - + +
780A MET* 4.4 9.9 - - + -
784A GLN 3.0 14.6 + - - +
785A LEU* 3.4 31.2 - - + +
787A LEU* 1.3 73.8 - - - +
789A VAL* 1.3 58.7 + - - +
791A GLN* 3.3 18.1 + - + +
792A MET* 2.9 43.1 + - + +
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Residues in contact with VAL 789 (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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662A LEU* 6.5 0.2 - - + -
730A LYS* 3.8 32.5 - - + +
733A MET* 4.4 19.3 - - + -
734A LEU* 3.9 35.0 - - + +
737A LEU* 4.7 12.3 - - + -
785A LEU 2.8 19.9 + - - +
786A GLN* 3.6 7.0 - - - +
788A LEU* 1.3 77.1 - - - +
790A GLU* 1.3 65.1 + - + +
792A MET* 3.4 10.1 + - - +
793A VAL* 3.1 25.3 + - + +
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Residues in contact with GLU 790 (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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730A LYS* 2.8 40.7 + - - -
786A GLN 3.2 14.6 + - - +
787A LEU* 3.2 19.4 + - + +
789A VAL* 1.3 79.8 - - + +
791A GLN* 1.3 62.2 + - - +
793A VAL* 3.2 9.1 + - - +
794A ASP* 3.1 33.8 + - - +
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Residues in contact with GLN 791 (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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787A LEU* 2.9 42.3 + - + +
788A LEU* 3.6 21.5 - - + +
790A GLU* 1.3 77.1 - - - +
792A MET* 1.3 63.4 + - - +
794A ASP* 3.5 7.4 + - - +
795A GLY* 3.3 18.2 + - - -
798A ARG* 5.8 0.2 + - - -
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Residues in contact with MET 792 (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 CYS* 4.3 9.4 - - - -
662A LEU* 4.3 7.6 - - + -
665A TYR* 3.5 55.2 - - + -
733A MET* 3.8 28.7 - - + -
737A LEU* 5.1 6.7 - - - -
788A LEU* 2.9 36.1 + - + +
789A VAL* 3.4 13.7 - - - +
791A GLN* 1.3 77.9 - - - +
793A VAL* 1.3 61.1 + - - +
795A GLY* 3.4 2.3 + - - -
796A SER* 3.2 21.1 + - - -
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Residues in contact with VAL 793 (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* 4.2 4.0 - - + -
726A PHE* 4.2 10.8 - - + -
729A TYR* 4.5 7.0 - - + -
730A LYS* 4.0 26.9 - - + +
733A MET* 4.5 19.5 - - + -
789A VAL* 3.1 15.7 + - + +
790A GLU* 3.2 10.5 + - - +
792A MET* 1.3 72.4 - - - +
794A ASP* 1.3 68.1 + - - +
796A SER* 2.3 30.9 + - - +
797A MET* 3.3 36.3 + - + +
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Residues in contact with ASP 794 (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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790A GLU* 3.1 21.5 + - - +
791A GLN* 3.8 10.7 - - - +
793A VAL* 1.3 79.9 - - - +
795A GLY* 1.3 62.0 + - - +
796A SER 3.4 0.3 + - - -
797A MET* 3.4 25.0 + - - +
798A ARG* 3.8 18.8 + - - +
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Residues in contact with GLY 795 (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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791A GLN 3.3 10.4 + - - -
792A MET 3.8 4.3 - - - -
793A VAL 3.2 0.8 - - - -
794A ASP* 1.3 79.0 - - - +
796A SER* 1.3 60.7 + - - +
797A MET 3.3 1.0 + - - -
798A ARG* 3.6 39.6 + - - +
799A SER 4.5 5.2 + - - +
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Residues in contact with SER 796 (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 CYS* 5.8 4.5 - - - -
708A PHE* 4.2 22.4 - - - -
709A LYS* 3.4 4.2 - - - -
710A LEU* 2.3 57.6 + - - +
729A TYR* 5.8 0.9 - - - -
792A MET 3.2 11.2 + - - -
793A VAL* 2.3 34.7 + - - +
795A GLY* 1.3 75.9 - - - +
797A MET* 1.3 58.4 + - - +
798A ARG 3.6 0.2 - - - -
799A SER 4.2 4.5 + - - -
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Residues in contact with MET 797 (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* 3.3 25.4 - - + +
711A THR* 5.1 1.6 - - - -
712A THR* 5.5 7.2 - - + +
715A VAL* 4.9 4.5 - - + -
721A LEU* 3.6 26.0 - - + -
726A PHE* 3.3 27.8 - - + -
793A VAL* 3.3 36.8 + - + +
794A ASP* 3.8 17.5 - - - +
795A GLY 3.2 1.0 - - - -
796A SER* 1.3 78.0 - - - +
798A ARG* 1.3 66.4 + - - +
799A SER* 3.0 10.3 + - - -
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Residues in contact with ARG 798 (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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794A ASP* 4.0 15.7 + - - +
795A GLY* 3.6 29.4 + - - +
796A SER 3.6 0.2 - - - -
797A MET* 1.3 77.9 - - - +
799A SER* 1.3 72.3 + - - +
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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