Contacts of the helix formed by residues 846 - 864 (chain A) in PDB entry 4QUM
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 846 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A VAL* 3.7 23.1 - - + -
842A SER* 4.0 0.2 + - - -
844A ALA* 4.0 7.0 - - + -
845A GLY* 1.3 84.5 - - - +
847A GLY* 1.3 78.3 + - - +
849A THR* 3.3 6.2 + - - -
850A GLY 3.2 6.6 + - - -
881A ARG* 3.7 13.9 - - + +
882A ALA 3.2 26.2 - - - +
883A MET* 3.7 30.7 - - + +
884A MET* 3.1 8.2 - - - +
885A VAL 2.9 23.4 + - - -
886A GLN* 4.1 11.2 - - + -
185B PTR 3.0 32.7 + - + +
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Residues in contact with GLY 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A ILE* 1.3 75.0 - - - +
848A ARG* 1.3 63.6 + - - +
850A GLY 3.3 4.5 + - - -
851A VAL* 3.3 17.5 + - - +
885A VAL* 3.8 2.8 - - - -
886A GLN* 3.8 25.1 - - - -
890A GLN* 3.6 13.1 - - - +
185B PTR 2.6 23.8 + - - -
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Residues in contact with ARG 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A LEU* 3.3 36.5 + - + +
744A THR* 3.5 23.6 + - - +
745A THR 5.1 0.4 - - - +
748A GLU* 4.0 3.6 + - - -
753A LYS* 5.7 0.4 - - - +
809A TRP* 3.0 76.3 + - + +
810A PRO 3.9 4.7 - - - -
811A ALA* 3.1 29.7 - - - +
813A GLY 4.4 0.2 - - - +
842A SER* 3.8 1.9 - - - -
843A SER* 3.5 14.1 - - - +
847A GLY* 1.3 71.1 - - - +
849A THR* 1.3 64.5 + - - +
851A VAL 3.4 0.3 + - - -
852A LEU 3.1 16.6 + - - -
890A GLN* 4.0 10.1 - - - +
185B PTR 2.6 44.3 + - - +
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Residues in contact with THR 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ALA* 5.0 1.3 - - - +
743A LEU* 3.7 8.1 - - + -
840A VAL* 3.7 27.1 - - + +
841A HIS* 3.6 27.1 - - - +
842A SER* 3.4 20.4 - - - +
845A GLY* 3.0 28.2 + - - -
846A ILE* 3.3 3.5 + - - -
847A GLY 4.2 0.2 - - - +
848A ARG* 1.3 76.2 - - - +
850A GLY* 1.3 65.8 + - - +
852A LEU* 3.1 2.6 + - - +
853A VAL* 2.9 28.5 + - - +
884A MET* 4.2 6.9 - - - -
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Residues in contact with GLY 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A ILE 3.2 17.9 + - - -
848A ARG 3.2 0.8 - - - -
849A THR* 1.3 83.9 + - - +
851A VAL* 1.3 55.6 + - - +
853A VAL 3.4 0.2 + - - -
854A THR* 2.9 33.6 + - - -
877A MET* 3.6 3.6 - - - +
884A MET* 4.0 17.7 - - - -
885A VAL* 3.5 17.6 - - - +
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Residues in contact with VAL 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A TRP* 3.6 28.3 - - + -
821A PHE* 3.9 13.0 - - + -
847A GLY 3.3 15.1 + - - +
848A ARG 3.6 8.1 - - - +
850A GLY* 1.3 74.8 - - - +
852A LEU* 1.3 62.2 + - - +
854A THR* 3.5 5.8 + - - -
855A MET* 3.1 21.8 + - - +
885A VAL* 3.8 10.7 - - + +
890A GLN* 3.7 35.9 - - + +
893A PHE* 4.3 10.8 - - + -
894A VAL* 3.8 17.5 - - + +
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Residues in contact with LEU 852 (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 TYR* 4.6 17.9 - - + -
741A VAL* 4.2 7.4 - - + -
743A LEU* 3.9 21.5 - - + -
809A TRP* 4.8 5.6 - - + -
821A PHE* 4.5 8.7 - - + -
824A PHE* 3.8 32.8 - - + -
825A VAL* 4.6 13.8 - - + +
828A VAL* 4.6 20.0 - - + -
838A VAL* 6.2 0.9 - - + -
840A VAL* 4.6 12.6 - - + -
848A ARG 3.1 13.0 + - - +
849A THR* 3.1 7.3 + - - +
851A VAL* 1.3 78.9 - - - +
853A VAL* 1.3 58.5 + - + +
855A MET* 3.3 1.9 + - - +
856A GLU* 3.0 30.8 + - + +
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Residues in contact with VAL 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A VAL* 4.7 2.7 - - + -
703A MET* 3.6 29.2 - - + -
714A TYR* 3.7 45.0 + - + -
840A VAL* 4.7 9.2 - - + -
849A THR 2.9 19.0 + - - +
852A LEU* 1.3 78.0 - - + +
854A THR* 1.3 56.4 + - - +
856A GLU 3.6 0.2 + - - -
857A THR* 2.7 33.9 + - - +
877A MET* 3.5 27.6 - - + -
884A MET* 4.3 13.5 - - + -
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Residues in contact with THR 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850A GLY 2.9 18.8 + - - -
851A VAL* 3.7 5.4 - - - -
852A LEU 3.3 0.2 - - - -
853A VAL* 1.3 76.2 - - - +
855A MET* 1.3 58.7 + - - +
857A THR* 3.3 3.1 + - - -
858A ALA* 2.9 27.9 + - - +
870A PRO* 4.8 8.5 - - + -
873A ILE* 3.9 24.3 - - + +
874A VAL* 4.1 5.5 - - + +
877A MET* 3.1 18.7 - - - +
885A VAL* 3.8 6.2 - - - +
894A VAL* 3.9 27.4 - - + -
898A ILE* 4.4 11.2 - - + -
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Residues in contact with MET 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A PHE* 3.6 24.9 - - + -
822A LEU* 3.8 6.7 - - + -
825A VAL* 4.0 14.8 - - + -
851A VAL 3.1 17.5 + - - +
852A LEU 3.8 3.4 - - - +
854A THR* 1.3 75.0 - - - +
856A GLU* 1.3 65.9 + - - +
858A ALA* 3.4 4.6 + - + -
859A MET* 3.1 47.8 + - + +
894A VAL* 4.0 12.6 - - + -
897A ALA* 3.9 29.2 - - - +
898A ILE* 4.3 15.3 - - + -
901A VAL* 3.8 24.5 - - + -
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Residues in contact with GLU 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ASN* 4.2 12.3 + - - +
714A TYR* 2.4 35.5 + - - +
825A VAL* 4.0 16.5 - - + +
828A VAL* 4.4 13.0 - - + +
829A ARG* 3.5 35.6 + - + +
832A ARG* 3.0 37.0 + - - -
852A LEU* 3.0 18.1 + - + +
853A VAL 4.1 0.2 - - - +
855A MET* 1.3 77.9 - - - +
857A THR* 1.3 61.6 + - - +
859A MET* 3.4 2.8 + - - +
860A CYS* 3.1 22.7 + - - -
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Residues in contact with THR 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A MET* 3.9 30.1 - - + +
704A GLU 5.9 0.7 - - - +
705A ILE* 4.4 17.7 - - + -
712A ASN* 5.1 3.7 + - - +
714A TYR* 4.8 1.9 + - - -
853A VAL* 2.7 23.9 + - - +
854A THR 3.5 4.9 - - - -
855A MET 3.2 0.2 - - - -
856A GLU* 1.3 77.1 - - - +
858A ALA* 1.3 64.7 - - - +
860A CYS* 3.2 8.3 + - - +
861A LEU* 3.1 28.3 + - + +
873A ILE* 3.9 28.0 - - + -
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Residues in contact with ALA 858 (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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854A THR 2.9 16.8 + - - +
855A MET* 3.7 8.7 - - + +
856A GLU 3.4 0.2 - - - -
857A THR* 1.3 76.5 - - - +
859A MET* 1.3 54.6 + - - +
861A LEU* 3.1 11.4 + - - +
862A THR* 2.7 35.5 + - - -
868A ILE* 3.5 16.8 - - + +
873A ILE* 4.6 1.5 - - + +
898A ILE* 3.5 36.6 - - + -
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Residues in contact with MET 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A LEU* 5.1 2.9 - - - -
825A VAL* 3.8 19.5 - - + -
826A ASN* 2.9 41.1 - - - +
829A ARG* 3.3 30.5 - - - +
855A MET* 3.1 44.5 + - + +
856A GLU 3.8 3.8 - - - +
857A THR 3.2 0.2 - - - -
858A ALA* 1.3 77.3 - - - +
860A CYS* 1.3 60.5 + - - +
862A THR* 3.4 7.1 + - - -
863A GLU* 3.3 30.8 + - - +
901A VAL* 4.3 19.7 - - + -
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Residues in contact with CYS 860 (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 ILE* 3.5 20.9 - - + -
710A LEU* 4.4 5.4 - - + -
712A ASN* 3.4 27.8 - - - -
829A ARG* 3.5 27.4 - - - +
856A GLU* 3.1 18.6 + - - -
857A THR 3.2 3.8 + - - +
859A MET* 1.3 77.0 - - - +
861A LEU* 1.3 61.4 + - - +
863A GLU 3.8 0.2 + - - -
864A ARG* 2.7 48.2 + - - +
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Residues in contact with LEU 861 (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 ILE* 3.6 32.8 - - + -
857A THR* 3.1 30.9 + - + +
858A ALA 3.4 5.8 - - - +
860A CYS* 1.3 75.2 - - - +
862A THR* 1.3 64.1 + - - +
864A ARG* 3.0 9.2 + - - -
866A LEU* 2.9 48.3 + - + +
867A PRO 3.7 17.5 - - - +
868A ILE* 3.7 21.1 - - + -
869A TYR 5.3 0.2 - - - +
873A ILE* 4.1 13.7 - - + -
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Residues in contact with THR 862 (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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630A LEU* 3.6 28.6 - - + +
858A ALA* 2.7 19.9 + - - +
859A MET* 3.4 8.4 + - - -
861A LEU* 1.3 74.5 - - - +
863A GLU* 1.3 64.1 + - - +
865A ASN* 3.2 9.4 + - - -
868A ILE* 3.3 13.4 - - + +
898A ILE* 5.6 1.6 + - - +
901A VAL* 4.8 14.1 - - + +
902A TYR* 4.3 29.8 - - + -
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Residues in contact with GLU 863 (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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826A ASN* 4.9 2.6 - - - +
829A ARG* 2.7 45.0 + - - -
859A MET* 3.3 14.7 + - - +
860A CYS 4.2 3.4 - - - +
862A THR* 1.3 77.6 - - - +
864A ARG* 1.3 68.9 + - + +
865A ASN* 3.3 1.5 + - - +
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Residues in contact with ARG 864 (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 ILE* 5.2 1.6 - - - -
708A ALA* 3.4 32.9 - - + +
710A LEU* 3.5 27.3 - - - +
829A ARG* 4.3 4.4 - - - +
860A CYS* 2.7 51.6 + - - +
861A LEU 3.0 5.5 + - - +
863A GLU* 1.3 92.5 + - + +
865A ASN* 1.3 71.9 + - - +
866A LEU* 3.2 23.4 + - + +
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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