Contacts of the helix formed by residues 886 - 907 (chain A) in PDB entry 3NC0
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 MET 886 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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838A PHE 4.0 20.9 - - - +
839A GLU* 5.3 3.4 - - - +
842A PRO* 4.3 27.4 - - + +
845A ARG* 4.3 12.6 - - - -
846A THR* 4.4 8.3 - - - +
884A HIS* 3.4 5.1 - - + +
885A THR* 1.3 78.4 - - - +
887A ARG* 1.3 69.5 + - - +
888A ASN* 3.0 15.8 + - - +
889A VAL* 3.1 34.0 + - + +
890A ALA* 3.2 11.3 + - - +
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Residues in contact with ARG 887 (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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884A HIS 5.7 0.4 - - - -
885A THR 3.2 8.2 + - - +
886A MET* 1.3 70.7 - - - +
888A ASN* 1.3 62.3 + - - +
890A ALA* 3.5 28.8 + - - +
891A ASP* 2.9 50.6 + - - +
894A LEU* 4.6 4.4 - - - +
934A SER 4.9 2.4 + - - -
935A HIS* 4.1 18.0 - - - +
937A ALA* 3.1 40.1 - - + +
938A GLY* 3.2 22.7 - - - +
942A HIS* 5.5 1.2 + - - -
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Residues in contact with ASN 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A THR* 3.3 37.8 + - - +
886A MET* 3.6 21.4 - - - +
887A ARG* 1.3 76.4 + - - +
889A VAL* 1.3 67.6 + - - +
891A ASP* 3.3 5.4 + - - +
892A THR* 3.0 35.4 + - - +
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Residues in contact with VAL 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A ARG* 4.3 3.4 - - + -
846A THR* 4.2 21.3 - - - +
849A PHE* 3.7 29.0 - - + -
881A ALA* 3.8 7.6 - - - +
884A HIS* 3.5 32.8 - - + +
886A MET* 3.1 31.3 + - + +
888A ASN* 1.3 90.3 + - - +
890A ALA* 1.3 62.1 + - - +
892A THR* 3.6 6.5 + - - -
893A GLY 3.2 16.1 + - - -
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Residues in contact with ALA 890 (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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881A ALA 3.3 15.7 + - - +
882A PHE* 3.3 23.7 - - - +
884A HIS* 3.4 26.0 - - - +
886A MET 3.2 9.0 + - - +
887A ARG* 3.5 21.5 - - - +
889A VAL* 1.3 78.4 - - - +
891A ASP* 1.3 62.2 + - - +
893A GLY 3.3 0.7 + - - -
894A LEU* 3.3 18.2 + - + +
935A HIS* 5.0 1.6 - - + -
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Residues in contact with ASP 891 (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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887A ARG* 2.9 49.7 + - - +
888A ASN* 3.8 5.2 - - - +
890A ALA* 1.3 73.5 - - - +
892A THR* 1.3 66.3 + - - +
893A GLY 3.0 1.3 - - - -
894A LEU* 2.9 26.3 + - - +
895A GLN* 2.9 31.8 + - - +
937A ALA 4.6 4.9 - - - +
938A GLY* 4.5 4.7 - - - -
941A MET* 4.3 13.3 - - - +
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Residues in contact with THR 892 (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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846A THR 5.6 1.2 + - - +
849A PHE* 3.5 38.1 - - + +
850A LEU* 4.5 9.9 - - + +
853A GLN* 4.1 15.9 - - - +
888A ASN* 3.0 19.1 + - - +
889A VAL* 3.8 7.2 - - - -
891A ASP* 1.3 75.2 - - - +
893A GLY* 1.3 57.1 + - - +
895A GLN* 3.4 15.8 + - - +
896A ILE* 2.9 43.6 + - + +
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Residues in contact with GLY 893 (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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878A ILE* 3.4 13.2 - - - +
881A ALA* 3.7 25.7 - - - +
882A PHE* 4.4 5.8 - - - -
889A VAL 3.2 7.1 + - - -
890A ALA 3.7 5.2 - - - -
891A ASP 3.0 1.6 - - - -
892A THR* 1.3 80.0 - - - +
894A LEU* 1.3 56.5 + - - +
896A ILE* 3.5 5.6 + - - +
897A LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 894 (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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882A PHE* 3.7 28.0 - - + -
887A ARG* 4.6 3.8 - - - +
890A ALA 3.3 15.7 + - - +
891A ASP* 2.9 16.8 + - - +
893A GLY* 1.3 72.2 - - - +
895A GLN* 1.3 59.8 + - - +
897A LEU* 3.1 1.6 + - - -
898A PHE* 2.6 36.8 + - - +
926A ILE* 4.2 6.1 - - + -
938A GLY* 4.4 7.6 - - - -
941A MET* 3.6 35.2 - - + -
942A HIS* 3.7 31.9 - - + +
945A ILE* 3.8 21.6 - - + +
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Residues in contact with GLN 895 (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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853A GLN* 3.2 23.0 + - - +
891A ASP* 2.9 42.9 + - - +
892A THR* 3.5 14.2 + - - +
894A LEU* 1.3 74.6 - - - +
896A ILE* 1.3 56.7 + - - +
898A PHE* 3.8 1.4 - - - +
899A THR* 2.9 35.2 + - - +
941A MET* 3.6 26.6 - - + +
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Residues in contact with ILE 896 (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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849A PHE* 3.6 28.9 - - + +
852A LEU* 4.2 16.4 - - + +
853A GLN* 3.7 29.4 - - + +
856A ASN* 3.6 25.2 - - + +
878A ILE* 3.5 28.3 - - + -
892A THR* 2.9 33.7 + - + +
893A GLY* 3.6 9.2 - - - +
895A GLN* 1.3 75.7 - - - +
897A LEU* 1.3 52.2 + - - +
899A THR* 3.1 4.3 + - - -
900A LEU* 2.6 37.7 + - + +
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Residues in contact with LEU 897 (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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875A LEU* 4.4 21.8 - - + -
878A ILE* 3.9 9.8 - - + +
879A ILE* 5.4 2.0 - - + -
882A PHE* 3.7 27.8 - - + -
893A GLY 2.9 19.8 + - - +
894A LEU* 3.7 5.4 - - - +
896A ILE* 1.3 72.7 - - - +
898A PHE* 1.3 64.1 + - - +
900A LEU* 3.6 7.4 - - + +
901A LEU* 2.9 42.3 + - + +
922A ILE* 3.9 31.0 - - + -
926A ILE* 3.9 15.0 - - + -
945A ILE* 4.4 8.1 - - + -
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Residues in contact with PHE 898 (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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894A LEU 2.6 22.1 + - - +
895A GLN 3.8 2.7 - - - +
897A LEU* 1.3 74.1 - - - +
899A THR* 1.3 66.8 + - - +
901A LEU* 3.6 9.6 + - + +
902A GLN* 2.8 65.3 + - - +
941A MET* 4.3 16.8 - - + -
944A SER* 4.4 25.1 - - - -
945A ILE* 3.8 32.5 - - + +
948A TYR* 4.7 16.6 - + + -
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Residues in contact with THR 899 (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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856A ASN* 3.6 8.7 - - - +
857A SER* 4.8 15.0 - - - +
895A GLN* 2.9 24.2 + - - +
896A ILE* 3.5 4.0 - - - -
898A PHE* 1.3 77.8 - - - +
900A LEU* 1.3 59.0 - - - +
902A GLN* 2.9 17.2 + - + +
903A ASN* 2.9 49.0 + - - +
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Residues in contact with LEU 900 (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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856A ASN* 3.7 11.9 + - - +
860A PHE* 3.1 31.6 - - + -
863A PHE* 4.9 5.2 - - + -
871A PHE* 4.8 12.3 - - + -
874A VAL* 6.5 0.4 - - + -
875A LEU* 3.5 32.5 - - + -
878A ILE* 4.1 11.0 - - + -
896A ILE* 2.6 21.2 + - + +
897A LEU* 3.6 9.2 - - + +
899A THR* 1.3 72.7 - - - +
901A LEU* 1.3 64.1 + - - +
903A ASN* 3.0 9.4 + - - +
904A VAL* 2.9 37.8 + - + +
914A PHE* 4.5 12.8 - - + -
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Residues in contact with LEU 901 (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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897A LEU* 2.9 35.4 + - + +
898A PHE* 3.7 8.1 - - + +
899A THR 3.3 0.2 - - - -
900A LEU* 1.3 75.7 - - - +
902A GLN* 1.3 61.5 + - - +
904A VAL* 3.4 10.4 + - + +
905A ALA* 3.2 18.0 + - - +
914A PHE* 3.9 26.0 - - + -
915A TYR* 5.1 10.1 + - + -
919A PHE* 6.1 0.7 - - + -
922A ILE* 4.6 2.7 - - + -
945A ILE* 3.5 32.5 - - + -
948A TYR* 4.1 23.2 + - + -
949A MET* 4.1 31.0 - - + -
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Residues in contact with GLN 902 (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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898A PHE* 2.8 59.0 + - + +
899A THR* 2.9 14.6 + - + +
901A LEU* 1.3 74.8 - - - +
903A ASN* 1.3 62.5 + - - +
904A VAL 3.0 1.3 - - - -
905A ALA* 2.9 11.7 + - + +
906A GLN* 2.7 28.8 - - - +
948A TYR* 4.1 23.7 - - + +
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Residues in contact with ASN 903 (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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856A ASN* 3.0 33.7 + - - +
857A SER 5.1 3.8 - - - +
860A PHE* 3.5 42.2 - - + +
899A THR* 2.9 43.1 + - - +
900A LEU* 3.3 4.9 - - - +
902A GLN* 1.3 75.9 - - - +
904A VAL* 1.3 59.8 - - - +
906A GLN* 3.4 22.1 + - - +
907A GLU* 4.4 2.6 + - - +
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Residues in contact with VAL 904 (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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860A PHE* 4.1 9.6 - - + -
871A PHE* 6.0 0.4 - - + -
900A LEU* 2.9 36.5 + - + +
901A LEU* 3.4 11.2 - - - +
902A GLN 3.0 0.2 - - - -
903A ASN* 1.3 73.1 - - - +
905A ALA* 1.3 58.8 + - - +
906A GLN 3.0 11.0 + - - -
907A GLU* 3.7 6.5 + - - +
910A ALA 4.3 3.1 - - - +
911A ALA* 3.5 31.8 - - + +
914A PHE* 3.8 44.9 - - + -
915A TYR* 4.7 9.0 - - + +
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Residues in contact with ALA 905 (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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901A LEU 3.2 6.4 + - - +
902A GLN* 2.9 14.6 + - - +
904A VAL* 1.3 76.3 - - - +
906A GLN* 1.3 69.3 + - - +
907A GLU 5.1 0.6 - - - -
908A GLU* 5.6 1.0 - - - +
911A ALA* 5.3 2.9 - - - +
915A TYR* 4.5 11.9 + - - +
948A TYR* 3.7 22.9 - - - +
952A LEU* 6.2 0.2 - - + -
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Residues in contact with GLN 906 (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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902A GLN* 2.7 22.0 - - - +
903A ASN* 3.4 20.0 - - - +
904A VAL 3.0 1.8 - - - -
905A ALA* 1.3 90.3 + - - +
907A GLU* 1.3 63.3 + - + +
908A GLU* 3.0 17.2 + - - +
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Residues in contact with GLU 907 (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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860A PHE* 6.2 2.0 - - + -
864A LEU* 5.0 13.9 - - + -
903A ASN 4.4 2.9 + - - +
904A VAL* 3.7 4.3 + - - +
906A GLN* 1.3 78.8 - - + +
908A GLU* 1.3 77.5 + - - +
909A ALA* 3.1 14.5 + - + +
910A ALA* 3.7 22.4 - - + +
911A ALA* 3.0 25.2 + - - +
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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