Contacts of the helix formed by residues 894 - 914 (chain D) in PDB entry 6V3O
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 ARG 894 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 3.8 18.3 - - + +
109D ALA* 5.5 3.6 - - + -
110D ASN* 2.6 31.8 + - - +
113D GLU* 3.1 30.0 + - - +
679D PHE* 4.5 3.2 - - - -
890D GLY 3.4 17.6 + - - +
891D LEU* 3.2 20.6 + - - +
893D LEU* 1.3 79.4 - - - +
895D ASN* 1.3 65.4 + - - +
896D PRO 3.3 0.2 - - - -
897D TYR* 3.0 19.6 + - - -
898D ILE* 3.1 24.5 + - + +
964D ALA 4.4 0.8 + - - -
965D GLY* 3.4 24.0 + - - -
967D GLN* 3.0 25.6 - - - +
1001D PG0 3.2 33.0 - - - -
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Residues in contact with ASN 895 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D SER 5.8 0.2 - - - -
72D GLU* 2.9 42.8 + - + +
785D ARG* 3.5 22.2 + - - +
834D ALA 4.9 10.5 + - - +
835D LYS* 5.7 2.8 - - - -
891D LEU* 3.7 14.8 + - - +
892D VAL* 3.5 11.9 + - - +
894D ARG* 1.3 75.5 - - - +
896D PRO* 1.3 70.3 - - + +
898D ILE* 3.0 16.6 + - - +
899D THR* 2.8 32.1 + - + +
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Residues in contact with PRO 896 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 5.0 1.1 - - + -
23D LEU* 3.8 21.8 - - + -
65D TYR* 3.4 35.7 - - + +
68D SER* 3.2 18.0 - - - +
69D ALA* 4.0 20.6 - - + +
72D GLU* 5.6 1.1 - - + -
892D VAL 3.6 11.2 - - - +
893D LEU 3.7 8.3 - - - +
894D ARG 3.5 4.3 - - - -
895D ASN* 1.3 92.3 - - + +
897D TYR* 1.3 55.9 + - + +
900D THR* 2.4 32.2 + - - -
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Residues in contact with TYR 897 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 4.0 7.4 - - - +
20D LEU* 4.7 4.7 - - - +
38D ASP* 4.9 4.1 + - - +
42D VAL* 3.7 20.0 - - + +
65D TYR* 3.6 35.9 + + - -
102D ILE* 3.5 33.4 - - + +
105D MET* 3.8 38.1 - - + -
106D LEU* 3.9 33.4 - - + -
109D ALA* 4.1 17.2 - - + +
893D LEU 3.4 20.5 + - - -
894D ARG 3.0 12.9 + - - +
896D PRO* 1.3 72.7 - - + +
898D ILE* 1.3 67.4 + - - +
900D THR* 3.7 1.0 + - - -
901D LEU* 3.3 19.5 + - - +
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Residues in contact with ILE 898 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 4.1 13.7 - - + -
785D ARG* 3.8 25.6 - - - +
894D ARG* 3.1 36.3 - - + +
895D ASN* 3.0 19.0 + - - +
897D TYR* 1.3 76.8 - - - +
899D THR* 1.4 57.5 + - - +
901D LEU* 3.0 13.2 + - - +
902D ASN* 2.9 28.1 + - - +
962D ILE* 4.3 19.6 - - + +
965D GLY* 3.7 24.5 - - - +
966D MET* 4.5 12.3 - - - -
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Residues in contact with THR 899 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D SER* 3.4 28.0 + - - +
71D TYR* 4.9 7.8 - - + -
72D GLU* 4.5 6.1 - - + +
80D LEU* 4.6 6.4 - - - +
785D ARG* 3.2 27.8 - - - +
837D ASP* 5.6 0.4 - - - +
840D ILE* 3.6 20.0 - - + -
895D ASN* 2.8 24.3 + - + +
898D ILE* 1.4 67.7 - - - +
900D THR* 1.3 69.4 + - - +
902D ASN* 3.3 10.1 - - - +
903D VAL* 3.0 28.6 + - - +
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Residues in contact with THR 900 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D CYS* 3.8 33.4 + - + -
65D TYR* 4.5 1.9 - - - -
68D SER* 2.6 17.3 + - - +
83D LEU* 4.2 7.4 - - + -
87D LEU* 4.2 7.7 - - + +
98D VAL* 6.1 0.9 - - + -
102D ILE* 4.1 21.6 - - + +
896D PRO 2.4 27.1 + - - -
897D TYR* 3.7 6.9 - - - -
898D ILE 3.3 0.2 - - - -
899D THR* 1.3 80.0 + - - +
901D LEU* 1.3 61.4 + - + -
903D VAL* 3.3 9.6 - - - +
904D PHE* 3.1 24.1 + - + +
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Residues in contact with LEU 901 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ALA* 4.3 18.6 - - + +
102D ILE* 3.9 25.4 - - + -
103D LEU* 4.9 8.7 - - + +
106D LEU* 5.5 3.1 - - + -
897D TYR 3.3 14.5 + - - +
898D ILE* 3.0 10.0 + - - +
900D THR* 1.3 77.3 - - + +
902D ASN* 1.3 60.3 + - - +
904D PHE* 3.6 8.7 - - + +
905D GLN* 2.8 31.5 + - - +
957D LEU 4.4 3.6 - - - +
958D THR* 3.8 24.6 - - + +
961D GLY* 3.6 35.7 - - - +
962D ILE* 4.0 12.3 - - + +
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Residues in contact with ASN 902 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783D GLN 2.8 28.7 + - - -
785D ARG* 2.9 36.3 + - - +
840D ILE* 3.8 23.6 - - + -
843D LEU* 5.7 0.2 - - - -
844D TYR* 3.1 23.1 + - - +
898D ILE* 2.9 16.6 + - - +
899D THR* 3.0 11.0 + - - +
901D LEU* 1.3 76.3 - - - +
903D VAL* 1.3 58.5 + - + +
905D GLN 3.1 1.6 + - - -
906D ALA* 2.9 27.6 + - - +
962D ILE* 3.5 10.1 - - - +
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Residues in contact with VAL 903 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 3.7 41.3 - - + +
83D LEU* 3.7 26.7 - - + -
84D GLY* 4.4 6.5 - - - +
87D LEU* 3.7 9.4 - - + -
840D ILE* 5.5 2.9 - - + -
843D LEU* 3.9 18.8 - - + -
899D THR 3.0 13.6 + - - +
900D THR* 3.3 11.2 - - - +
902D ASN* 1.3 75.5 - - + +
904D PHE* 1.3 69.2 + - - +
906D ALA* 3.9 5.8 - - - +
907D TYR* 3.1 32.9 + - + +
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Residues in contact with PHE 904 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU* 3.5 55.6 - - + -
88D THR* 5.8 0.7 - - - -
90D LEU* 4.6 1.1 - - + -
95D ALA* 3.9 34.8 - - + -
98D VAL* 4.4 6.5 - - + -
99D ALA* 4.2 20.4 - - + -
102D ILE* 6.3 0.9 - - + -
900D THR* 3.1 19.9 + - + +
901D LEU* 3.6 10.8 - - + +
903D VAL* 1.3 78.8 - - - +
905D GLN* 1.3 51.0 + - - +
907D TYR* 4.0 3.0 - - + -
908D THR* 2.5 44.9 + - + -
911D ARG* 5.9 2.7 - - - -
954D THR* 3.6 23.8 - - + -
958D THR* 4.1 9.6 - - + -
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Residues in contact with GLN 905 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D PRO* 4.0 11.4 - - - +
783D GLN* 2.9 39.3 + - - +
844D TYR* 2.6 27.4 + - - +
901D LEU 2.8 21.4 + - - +
902D ASN 3.1 4.7 + - - +
904D PHE* 1.3 72.3 - - - +
906D ALA* 1.3 64.2 + - - +
908D THR* 2.7 17.9 + - - -
909D LEU* 3.0 21.0 + - + +
955D LEU* 3.6 11.6 - - + +
958D THR* 3.2 28.1 + - - +
959D MET* 3.4 13.9 - - - +
962D ILE* 3.6 8.2 - - + +
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Residues in contact with ALA 906 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843D LEU* 4.7 6.1 - - + -
844D TYR* 4.1 34.5 + - + -
847D LEU* 3.8 19.8 - - + +
848D LEU* 3.8 10.2 - - + +
902D ASN 2.9 16.3 + - - +
903D VAL* 3.9 7.4 - - - +
904D PHE 3.4 0.2 - - - -
905D GLN* 1.3 78.4 - - - +
907D TYR* 1.3 61.4 + - + +
909D LEU* 3.4 5.4 + - - +
910D LYS* 3.2 18.4 + - - +
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Residues in contact with TYR 907 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU 4.6 2.0 - - - -
81D GLY* 3.3 30.3 + - - -
84D GLY* 3.7 26.2 - - - +
85D ALA* 4.7 2.7 - - - -
87D LEU* 6.2 0.9 - - + -
88D THR* 3.6 31.2 - - + +
843D LEU* 4.5 12.8 - - + +
847D LEU* 3.6 38.7 - - + +
903D VAL* 3.1 24.5 + - + +
904D PHE* 4.3 3.8 - - + +
906D ALA* 1.3 77.3 - - + +
908D THR* 1.3 64.1 + - + +
910D LYS* 3.5 6.6 + - + +
911D ARG* 3.2 27.9 + - - +
917D PHE* 4.2 19.0 - + - -
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Residues in contact with THR 908 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904D PHE* 2.5 48.6 + - + +
905D GLN* 2.7 18.0 + - - -
907D TYR* 1.3 74.1 - - + +
909D LEU* 1.3 58.1 + - - +
911D ARG* 3.4 11.6 + - - +
912D ILE* 2.8 37.9 + - - +
951D LEU* 4.0 24.1 - - + +
954D THR* 4.1 15.0 - - + -
955D LEU* 3.7 13.8 - - - +
958D THR* 5.0 0.5 - - - +
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Residues in contact with LEU 909 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D PRO* 4.0 20.6 - - + -
750D GLU* 3.7 34.5 - - + +
844D TYR* 4.5 7.6 - - + -
848D LEU* 4.1 26.5 - - + -
905D GLN* 3.0 38.0 + - + +
906D ALA 3.7 4.0 - - - +
907D TYR 3.3 0.2 - - - -
908D THR* 1.3 74.5 - - - +
910D LYS* 1.3 59.2 + - - +
912D ILE* 3.2 5.2 + - + +
913D ARG* 2.9 44.6 + - - +
955D LEU* 3.8 24.2 - - + -
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Residues in contact with LYS 910 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847D LEU* 3.2 38.4 + - + +
848D LEU* 3.6 11.0 - - + +
906D ALA 3.2 10.3 + - - +
907D TYR* 3.7 12.3 - - + +
908D THR 3.4 0.2 - - - -
909D LEU* 1.3 78.3 - - - +
911D ARG* 1.3 55.9 + - - +
913D ARG* 4.9 1.8 - - - -
914D ASP* 2.9 66.2 + - + +
917D PHE* 3.6 34.3 - - + -
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Residues in contact with ARG 911 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU 4.5 3.0 + - - -
88D THR* 2.7 42.6 + - + +
90D LEU 4.5 7.5 + - - -
95D ALA* 5.9 3.8 - - - +
904D PHE* 5.9 2.4 - - - -
907D TYR 3.2 14.1 + - - +
908D THR* 3.7 12.8 - - - +
909D LEU 3.3 0.2 - - - -
910D LYS* 1.3 77.6 - - - +
912D ILE* 1.3 64.7 + - - +
913D ARG 3.3 0.5 + - - -
914D ASP 3.5 15.9 + - - +
915D PRO* 5.1 1.2 - - - +
917D PHE* 3.6 27.6 - - + +
918D LYS* 5.3 15.6 + - - +
919D VAL 6.2 0.7 - - - +
948D PRO* 5.6 2.8 - - - +
949D PRO 5.8 1.2 + - - -
951D LEU* 3.9 42.7 - - + +
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Residues in contact with ILE 912 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750D GLU* 4.7 8.7 - - + +
754D MET* 4.4 1.8 - - + -
908D THR* 2.8 23.8 + - - +
909D LEU* 3.2 7.8 + - + +
911D ARG* 1.3 77.2 - - - +
913D ARG* 1.3 69.1 + - + +
914D ASP 5.2 0.2 - - - -
947D TYR* 3.5 41.2 - - + -
948D PRO* 5.4 7.7 - - + +
951D LEU* 3.7 37.9 - - + +
955D LEU* 3.7 31.6 - - + -
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Residues in contact with ARG 913 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743D ARG 3.4 11.9 + - - -
744D SER* 2.8 29.9 + - - +
746D THR 3.0 26.3 + - - -
749D THR* 4.3 1.0 + - - -
750D GLU* 2.8 37.6 + - - +
848D LEU* 3.8 23.6 + - - +
909D LEU* 2.9 34.0 + - - +
910D LYS* 4.2 2.5 - - - +
912D ILE* 1.3 83.6 - - + +
914D ASP* 1.3 60.8 + - + +
915D PRO* 3.6 9.5 - - - +
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Residues in contact with ASP 914 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910D LYS* 2.9 45.7 + - + +
911D ARG* 3.5 12.8 - - - +
912D ILE 3.6 0.6 - - - -
913D ARG* 1.3 77.9 - - + +
915D PRO* 1.3 64.7 - - - +
916D ASN* 2.8 64.7 + - - +
917D PHE 4.3 2.1 - - - +
918D LYS* 4.3 3.8 + - - -
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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