Contacts of the helix formed by residues 866 - 884 (chain A) in PDB entry 7CN9
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 866 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863A PRO* 4.1 8.5 - - - -
864A LEU 2.9 9.6 + - - -
865A LEU* 1.3 70.1 - - - +
867A ASP* 1.3 69.4 + - - +
868A GLU* 2.1 47.8 + - + +
869A MET* 2.8 36.6 + - + +
870A ILE* 3.0 10.0 + - - +
668C ALA* 4.5 12.8 - - - +
669C GLY* 4.3 10.5 - - - -
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Residues in contact with ASP 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A PHE* 3.9 29.0 - - + -
863A PRO* 5.5 5.7 - - + +
865A LEU 3.5 2.0 + - - -
866A THR* 1.3 73.1 + - - +
868A GLU* 1.3 92.2 + - - +
870A ILE* 3.1 23.0 + - + +
871A ALA* 2.9 24.9 + - - +
1057A PRO* 5.7 5.4 - - + +
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Residues in contact with GLU 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A ARG* 5.6 10.6 + - - +
866A THR* 2.1 43.5 + - + +
867A ASP* 1.3 80.5 + - - +
869A MET* 1.3 56.5 + - + +
871A ALA* 3.4 18.3 - - - +
872A GLN* 3.7 5.7 + - - +
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Residues in contact with MET 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A LEU* 3.5 29.6 - - + -
866A THR* 2.8 43.0 + - + +
868A GLU* 1.3 80.6 - - + +
870A ILE* 1.3 56.5 + - - +
871A ALA 2.9 2.0 - - - -
872A GLN* 2.5 34.9 + - + +
873A TYR* 2.9 12.9 + - + +
669C GLY* 4.4 3.8 - - - +
697C MET* 3.6 18.8 - - + +
699C LEU* 3.5 35.4 - - + -
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Residues in contact with ILE 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A THR* 6.6 0.2 - - - -
782A PHE* 4.6 27.9 - - + -
865A LEU* 3.2 36.6 - - + +
866A THR 3.0 14.5 + - - +
867A ASP* 3.1 23.5 + - + +
869A MET* 1.3 73.8 - - - +
871A ALA* 1.3 67.1 + - - +
873A TYR* 3.2 13.0 + - - +
874A THR* 2.9 29.6 + - + +
1055A SER* 5.3 11.4 - - - -
1056A ALA 4.7 14.1 - - - +
1057A PRO 5.8 1.8 - - - +
1059A GLY 5.7 1.1 - - - +
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Residues in contact with ALA 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A ARG* 4.7 19.4 + - + +
819A GLU* 5.5 2.0 - - - +
867A ASP 2.9 12.5 + - - +
868A GLU* 3.4 17.7 - - - +
870A ILE* 1.3 79.4 - - - +
872A GLN* 1.3 57.0 + - - +
874A THR* 2.2 25.8 + - - -
875A SER* 2.8 16.9 + - - -
1055A SER* 5.1 9.2 - - - -
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Residues in contact with GLN 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A ILE* 3.2 31.1 - - + +
789A TYR 5.2 3.6 - - - +
868A GLU 3.7 3.7 + - - +
869A MET* 2.5 28.9 + - + +
871A ALA* 1.3 75.5 - - - +
873A TYR* 1.3 58.0 + - - +
875A SER* 2.2 27.4 + - - +
876A ALA* 2.9 10.7 + - - +
699C LEU* 4.1 16.5 - - - +
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Residues in contact with TYR 873 (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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782A PHE* 4.4 26.5 - - + +
783A ALA* 4.6 17.5 - - + +
785A VAL* 3.8 25.5 + - + -
786A LYS 4.2 1.7 + - - -
787A GLN 4.4 5.2 - - - -
788A ILE* 3.4 17.9 - - + +
865A LEU* 4.7 21.8 - - + -
869A MET* 2.9 13.4 + - + +
870A ILE* 3.5 11.4 - - - +
872A GLN* 1.3 77.5 - - + +
874A THR* 1.3 64.7 + - - +
876A ALA* 3.2 6.6 + - + +
877A LEU* 2.8 24.2 + - - +
699C LEU* 3.1 54.0 + - + +
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Residues in contact with THR 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A PHE* 4.3 26.5 - - + -
870A ILE* 2.9 18.7 + - + +
871A ALA* 2.2 34.3 + - - -
873A TYR* 1.3 74.2 - - - +
875A SER* 1.3 62.0 + - - +
877A LEU* 3.1 8.4 + - - +
878A LEU* 2.9 34.0 + - - +
1053A PRO* 5.2 6.0 - - + +
1054A GLN* 3.9 28.9 - - - +
1055A SER* 4.7 8.5 - - - -
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Residues in contact with SER 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A TYR 5.3 1.6 + - - -
806A LEU* 5.4 0.3 - - - +
807A PRO* 4.2 27.8 - - - -
815A ARG 5.3 3.6 - - - -
871A ALA 2.8 11.2 + - - -
872A GLN* 2.2 41.5 + - - +
874A THR* 1.3 76.6 + - - +
876A ALA* 1.3 57.2 + - - +
878A LEU* 3.2 15.6 - - - +
879A ALA* 2.8 32.2 + - - +
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Residues in contact with ALA 876 (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 GLN 4.9 0.9 - - - +
788A ILE* 4.2 5.8 - - + -
789A TYR* 3.3 60.0 - - + +
790A LYS* 5.7 0.4 - - - +
872A GLN 2.9 11.5 + - - +
873A TYR* 3.7 6.7 - - + +
875A SER* 1.3 81.1 + - - +
877A LEU* 1.3 57.6 + - - +
879A ALA* 3.2 5.8 + - - +
880A GLY* 2.8 26.3 + - - -
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Residues in contact with LEU 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A PHE* 4.8 14.1 - - + +
784A GLN* 5.4 2.9 - - + -
785A VAL* 3.7 20.6 - - + -
873A TYR 2.8 14.3 + - - +
874A THR* 3.1 11.9 + - - +
876A ALA* 1.3 76.0 - - - +
878A LEU* 1.3 65.2 + - - +
880A GLY* 2.9 12.4 + - - -
881A THR* 3.0 11.5 + - - +
888A PHE* 3.5 27.8 - - + -
1029A MET* 4.1 31.2 - - + -
1033A VAL* 4.6 15.0 - - + -
1034A LEU* 5.0 10.1 - - + -
1053A PRO* 5.1 6.3 - - + -
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Residues in contact with LEU 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A ILE* 5.3 10.3 - - + +
806A LEU* 4.0 21.1 - - + +
807A PRO* 5.2 1.3 - - + -
819A GLU* 5.5 0.7 - - - +
874A THR* 2.9 27.5 + - - +
875A SER* 3.2 16.2 - - - +
877A LEU* 1.3 77.0 - - - +
879A ALA* 1.3 76.9 + - - +
881A THR* 3.0 13.1 - - + +
882A ILE* 2.9 45.5 + - + +
1052A PHE* 5.6 4.9 - - + -
1053A PRO* 3.6 42.2 - - + +
1054A GLN* 4.2 11.9 - - - +
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Residues in contact with ALA 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A TYR* 5.2 2.7 - - + -
790A LYS 4.8 4.0 - - - +
791A THR* 4.6 25.8 - - - +
806A LEU* 5.0 2.2 - - + -
875A SER 2.8 19.9 + - - +
876A ALA* 3.3 10.5 - - - +
878A LEU* 1.3 79.9 - - + +
880A GLY* 1.3 50.3 + - - +
882A ILE* 3.1 15.0 - - + +
883A THR* 2.3 42.7 + - + +
705C VAL* 5.0 3.1 - - + -
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Residues in contact with GLY 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A TYR* 6.0 1.6 - - - -
876A ALA 2.8 13.6 + - - -
877A LEU 2.9 3.5 + - - -
879A ALA* 1.3 76.7 - - - +
881A THR* 1.3 54.0 + - - +
883A THR* 3.0 6.6 + - - -
884A SER* 2.2 40.6 + - - -
885A GLY 2.5 11.1 + - - -
888A PHE* 4.3 11.2 - - - -
893A ALA* 5.9 0.4 - - - -
705C VAL* 4.7 9.3 - - - +
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Residues in contact with THR 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A LEU* 3.0 7.0 + - - +
878A LEU* 3.0 29.4 - - + +
880A GLY* 1.3 75.2 - - - +
882A ILE* 1.3 66.3 + - + +
885A GLY* 3.4 23.8 - - - +
888A PHE* 4.1 8.1 - - - -
901A GLN* 3.6 10.9 + - - +
905A ARG* 3.5 20.8 + - - -
1033A VAL* 3.7 30.4 + - + +
1050A MET* 3.8 12.4 - - + +
1051A SER 5.8 0.4 - - - +
1052A PHE* 5.7 1.6 - - + -
1053A PRO* 5.1 3.8 - - + -
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Residues in contact with ILE 882 (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 THR* 6.0 0.9 - - - +
797A PHE* 5.6 7.2 - - + -
802A PHE* 4.8 21.8 - - + -
805A ILE* 6.2 1.1 - - + -
806A LEU* 4.3 13.5 - - + -
878A LEU* 2.9 41.1 + - + +
879A ALA* 3.1 23.1 - - - +
881A THR* 1.3 83.6 - - + +
883A THR* 1.3 65.7 + - + +
896A ILE 5.4 0.3 - - - +
898A PHE* 3.0 39.6 - - + -
901A GLN* 3.1 5.2 - - - +
1050A MET* 4.9 0.9 - - + -
1052A PHE* 3.6 36.6 - - + -
707C TYR* 5.7 0.7 - - - -
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Residues in contact with THR 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A THR* 5.6 0.7 - - - +
792A PRO* 4.2 22.2 - - + -
797A PHE* 5.3 8.5 - - + -
879A ALA* 2.3 33.1 + - + +
880A GLY* 3.0 6.5 + - - -
882A ILE* 1.3 85.9 - - + +
884A SER* 1.3 66.1 + - - -
895A GLN* 5.1 2.5 - - - -
896A ILE* 3.0 32.7 + - - +
901A GLN* 4.1 0.7 - - - +
705C VAL* 3.4 28.5 - - + +
707C TYR* 4.5 22.2 - - + -
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Residues in contact with SER 884 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A GLY* 2.2 22.6 + - - -
883A THR* 1.3 79.1 + - - +
885A GLY* 1.3 53.5 + - - -
887A THR* 2.7 25.5 + - - -
888A PHE* 4.1 4.5 - - - -
893A ALA* 2.9 22.6 - - - -
894A LEU 2.5 47.0 + - - +
895A GLN* 4.4 3.1 - - - +
896A ILE* 2.9 15.1 - - - +
705C VAL* 4.7 4.0 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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