Contacts of the helix formed by residues 765 - 797 (chain C) in PDB entry 2W4T
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 GLY 765 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763C LYS 3.7 0.6 + - - -
764C ALA* 1.3 70.1 - - - +
766C VAL* 1.3 55.0 + - - +
767C LEU* 3.2 3.1 - - - +
768C GLY* 2.7 28.0 + - - -
769C ASN* 3.1 20.0 + - - -
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Residues in contact with VAL 766 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C SER* 5.7 0.2 - - - -
748C MET* 6.1 4.7 - - + -
752C GLU* 2.9 49.8 - - + +
762C PHE* 2.9 33.4 - - + -
763C LYS 2.5 26.9 - - - +
764C ALA 2.8 14.7 + - - +
765C GLY* 1.3 69.8 - - - -
767C LEU* 1.3 72.9 + - + +
769C ASN* 3.0 17.7 + - - +
770C LEU* 2.9 25.3 + - + +
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Residues in contact with LEU 767 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C SER* 4.1 24.9 - - - +
710C ARG 5.1 1.3 - - - +
711C LEU* 4.3 25.4 - - + -
716C PHE* 4.9 0.2 - - + -
720C TYR* 3.4 32.6 + - + +
762C PHE* 4.1 26.2 - - + -
765C GLY 3.1 1.6 + - - +
766C VAL* 1.3 83.3 - - + +
768C GLY* 1.3 63.6 + - - +
770C LEU* 3.3 13.6 + - + -
771C GLU* 3.2 19.9 + - - +
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Residues in contact with GLY 768 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765C GLY* 2.7 15.2 + - - -
767C LEU* 1.3 74.2 - - - +
769C ASN* 1.3 62.4 + - - +
771C GLU* 3.3 10.2 + - - +
772C GLU* 3.3 17.2 + - - +
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Residues in contact with ASN 769 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765C GLY* 3.1 26.4 + - - -
766C VAL* 3.0 14.4 + - - +
768C GLY* 1.3 75.7 - - - +
770C LEU* 1.3 58.5 + - + +
772C GLU* 3.0 27.3 - - + +
773C MET* 3.2 16.2 + - - +
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Residues in contact with LEU 770 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C PHE* 4.3 10.1 - - + -
720C TYR* 3.0 40.7 - - + +
723C LEU* 3.8 23.7 - - + +
742C ILE* 5.4 0.7 - - + -
743C LEU* 4.5 2.5 - - + -
746C LEU* 3.9 18.4 - - + -
748C MET* 4.2 15.9 - - + -
762C PHE* 4.3 22.4 - - + -
766C VAL* 2.9 14.0 + - + +
767C LEU* 3.3 18.6 + - + +
769C ASN* 1.3 76.0 - - - +
771C GLU* 1.3 58.1 + - - +
772C GLU 3.0 4.9 - - - -
773C MET* 3.5 7.1 + - + +
774C ARG 2.8 23.4 + - - -
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Residues in contact with GLU 771 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720C TYR* 3.2 8.0 + - - +
767C LEU 3.2 11.7 + - - +
768C GLY* 3.5 12.6 - - - +
769C ASN 3.3 0.2 - - - -
770C LEU* 1.3 73.8 - - - +
772C GLU* 1.3 61.5 + - - +
774C ARG* 2.3 58.5 + - - +
775C ASP* 2.5 40.2 + - - +
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Residues in contact with GLU 772 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C GLY 3.3 6.5 + - - +
769C ASN* 3.0 23.3 + - - +
770C LEU 3.0 0.2 - - - -
771C GLU* 1.3 74.9 - - - +
773C MET* 1.3 68.4 + - - +
775C ASP* 2.7 28.6 + - - +
776C GLU* 2.8 49.1 + - - +
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Residues in contact with MET 773 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C LEU* 3.8 25.6 - - + -
746C LEU* 4.6 21.8 - - + -
769C ASN 3.2 15.7 + - - +
770C LEU* 3.9 8.5 - - + +
772C GLU* 1.3 86.8 + - + +
774C ARG* 1.3 62.2 + - - +
776C GLU* 3.5 10.0 + - - +
777C ARG* 3.2 31.7 + - - +
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Residues in contact with ARG 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C ARG* 3.5 38.3 - - - +
720C TYR* 4.1 11.8 + - + -
722C ILE* 3.8 21.5 - - + +
723C LEU* 4.3 9.2 - - - +
770C LEU 2.8 19.7 + - - +
771C GLU* 2.3 58.1 + - - +
772C GLU 2.9 0.2 + - - -
773C MET* 1.3 78.7 - - - +
775C ASP* 1.3 62.2 + - - +
777C ARG* 3.8 2.8 - - - +
778C LEU* 3.1 37.0 + - + +
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Residues in contact with ASP 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771C GLU* 2.5 41.7 - - - +
772C GLU* 2.7 12.2 + - - +
774C ARG* 1.3 74.5 + - - +
776C GLU* 1.2 82.7 - - - +
777C ARG 3.0 1.3 - - - -
778C LEU* 3.0 11.4 + - - +
779C SER* 2.7 23.3 + - - -
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Residues in contact with GLU 776 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772C GLU* 2.8 37.3 + - - +
773C MET* 3.7 13.9 - - - +
775C ASP* 1.2 91.0 - - - +
777C ARG* 1.3 58.3 + - + +
779C SER* 2.3 35.1 + - - -
780C LYS* 3.0 7.1 + - - +
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Residues in contact with ARG 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722C ILE* 2.6 31.4 + - + +
723C LEU* 2.4 50.8 + - - +
724C ALA* 5.1 0.8 - - - +
725C PRO* 4.7 8.7 - - - +
746C LEU* 5.0 7.5 - - - +
773C MET* 3.2 13.1 + - - +
774C ARG 3.8 4.3 - - - +
775C ASP 3.0 0.4 - - - -
776C GLU* 1.3 79.3 - - + +
778C LEU* 1.3 58.2 + - + +
779C SER 3.1 0.2 + - - -
780C LYS* 3.2 8.8 + - + +
781C ILE* 2.4 42.3 + - + +
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Residues in contact with LEU 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722C ILE* 5.2 14.8 - - + -
774C ARG* 3.1 30.6 + - + +
775C ASP* 3.0 14.9 + - - +
777C ARG* 1.3 79.4 - - + +
779C SER* 1.3 51.5 + - - +
781C ILE* 3.1 8.1 - - + +
782C ILE* 2.3 40.2 - - + +
88Z GLU* 5.1 0.9 - - + -
89Z ALA* 3.5 39.5 - - + +
92Z THR* 3.9 28.5 - - + +
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Residues in contact with SER 779 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775C ASP 2.7 15.6 + - - -
776C GLU* 2.3 31.9 + - - -
778C LEU* 1.3 73.1 - - - +
780C LYS* 1.3 73.2 + - - +
782C ILE* 3.0 9.9 + - - +
783C SER* 2.9 18.5 + - - -
114Z GLY* 4.5 12.9 - - - +
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Residues in contact with LYS 780 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776C GLU 3.0 6.4 + - - +
777C ARG* 3.5 11.9 - - + +
779C SER* 1.3 80.5 + - - +
781C ILE* 1.3 57.0 + - + +
783C SER* 2.2 43.0 + - - -
784C MET* 2.7 13.3 + - + +
45Z ARG* 2.9 39.1 - - - +
79Z GLU* 2.8 52.6 + - - +
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Residues in contact with ILE 781 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777C ARG* 2.4 39.2 + - + +
778C LEU* 3.1 18.8 - - + +
780C LYS* 1.3 75.4 - - + +
782C ILE* 1.3 75.8 + - + +
784C MET* 3.3 11.2 + - - +
785C PHE* 3.1 22.7 + - + +
85Z ASP* 3.9 33.7 - - + +
86Z TYR* 4.0 9.6 - - + -
89Z ALA* 2.4 39.7 - - + -
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Residues in contact with ILE 782 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778C LEU* 2.3 32.1 - - + +
779C SER* 3.2 9.2 - - - +
780C LYS 2.8 2.2 + - - -
781C ILE* 1.3 100.2 - - + +
783C SER* 1.3 61.7 + - - +
785C PHE* 3.6 6.6 + - + +
786C GLN* 3.2 20.4 + - - +
89Z ALA* 3.7 13.7 - - + +
109Z VAL* 4.2 24.2 - - + +
110Z LEU* 5.5 4.6 - - + +
113Z LEU* 4.4 27.6 - - + +
114Z GLY* 4.8 4.0 - - - -
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Residues in contact with SER 783 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779C SER 2.9 9.6 + - - -
780C LYS* 2.2 32.2 + - - -
782C ILE* 1.3 72.8 - - - +
784C MET* 1.3 53.5 + - - -
786C GLN* 2.7 11.3 + - - +
787C ALA* 2.6 36.6 + - - +
45Z ARG* 2.6 47.9 + - - +
114Z GLY* 5.0 0.6 - - - -
115Z GLU* 4.3 20.3 - - - +
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Residues in contact with MET 784 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C LYS* 2.7 27.3 + - + +
781C ILE* 3.5 15.0 - - - +
783C SER* 1.3 82.5 + - - +
785C PHE* 1.3 53.8 + - - +
787C ALA* 3.5 6.1 - - - +
788C HIS* 3.0 19.4 + - - +
43Z ASN* 4.5 14.7 - - - +
44Z PRO* 5.9 0.4 - - - -
45Z ARG* 4.2 14.4 - - + +
79Z GLU* 3.2 46.7 - - + +
80Z GLN* 4.2 2.9 - - + -
81Z GLY* 3.1 31.4 - - - +
86Z TYR* 2.7 19.8 + - + +
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Residues in contact with PHE 785 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781C ILE* 3.1 12.0 + - + +
782C ILE* 3.9 7.9 - - + +
783C SER 3.1 0.4 - - - -
784C MET* 1.3 74.5 - - - +
786C GLN* 1.3 53.3 - - - +
787C ALA 3.3 0.2 - - - -
788C HIS* 3.6 7.7 - - - +
789C ILE* 2.2 47.5 + - + +
86Z TYR* 2.6 46.7 - + + -
110Z LEU* 4.5 16.6 - - + -
141Z TYR* 3.6 22.0 - + - +
144Z PHE* 3.0 41.3 - + - -
145Z VAL* 4.0 8.1 - - + -
148Z VAL* 3.2 31.4 - - + -
149Z MET* 5.1 1.1 - - + -
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Residues in contact with GLN 786 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C ILE 3.2 13.3 + - - +
783C SER* 2.7 12.5 + - - +
785C PHE* 1.3 79.1 - - - +
787C ALA* 1.3 58.3 + - - +
788C HIS 3.2 0.2 - - - -
789C ILE* 2.6 33.7 - - + +
790C ARG* 2.3 56.7 + - - +
110Z LEU* 4.2 14.1 - - + +
113Z LEU 5.9 1.1 - - - +
115Z GLU* 3.4 23.7 - - + +
116Z ARG 4.5 0.2 - - - -
117Z LEU* 2.6 39.6 - - + +
121Z ASP* 5.8 1.0 + - - +
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Residues in contact with ALA 787 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783C SER 2.6 14.6 + - - +
784C MET* 3.5 14.1 - - - +
786C GLN* 1.3 80.7 + - - +
788C HIS* 1.3 52.2 + - - +
790C ARG* 2.9 2.1 + - - +
791C GLY 2.7 31.9 + - - -
38Z ARG* 2.8 14.7 + - - +
43Z ASN* 3.5 16.3 - - - +
44Z PRO 3.3 25.6 - - - +
45Z ARG* 4.2 7.6 - - + +
----------------------------------------------------------
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Residues in contact with HIS 788 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784C MET 3.0 18.4 + - - +
785C PHE* 3.6 13.3 - - - +
787C ALA* 1.3 77.4 - - - +
789C ILE* 1.3 55.8 + - - +
791C GLY 4.0 0.2 - - - -
792C TYR* 3.1 26.9 + - - +
795C ARG* 5.1 4.0 + - - -
43Z ASN* 4.0 25.7 + - + +
80Z GLN* 4.1 14.1 - - - +
86Z TYR* 4.0 2.5 - - - +
148Z VAL* 2.5 46.3 + - - +
149Z MET* 2.6 53.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 789 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785C PHE* 2.2 54.5 - - + +
786C GLN* 2.6 38.1 - - + +
787C ALA 3.1 0.4 - - - -
788C HIS* 1.3 74.7 - - + +
790C ARG* 1.3 73.7 + - + +
792C TYR* 3.1 29.6 - - + -
793C LEU* 3.3 4.7 + - + +
110Z LEU* 4.8 10.3 - - + -
117Z LEU* 4.8 4.0 - - + -
121Z ASP* 4.4 18.2 - - + +
125Z ILE* 4.2 27.1 - - + -
144Z PHE* 5.6 1.1 - - + -
148Z VAL* 5.3 8.3 - - + -
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Residues in contact with ARG 790 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786C GLN* 2.3 45.9 + - - +
787C ALA* 2.9 4.0 + - - +
789C ILE* 1.3 84.9 - - + +
791C GLY* 1.3 50.4 - - - +
793C LEU* 3.6 4.3 + - - +
794C ILE* 2.3 38.0 + - + +
38Z ARG* 2.7 38.4 - - - +
45Z ARG* 6.5 0.2 - - - +
46Z ASN* 5.8 1.1 - - - +
115Z GLU* 3.0 23.5 + - - -
116Z ARG 2.6 30.1 + - - -
117Z LEU* 3.9 4.0 - - - +
118Z SER 4.8 2.0 - - - +
121Z ASP* 5.0 10.4 + - - -
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Residues in contact with GLY 791 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787C ALA 2.7 11.1 + - - -
790C ARG* 1.3 76.1 - - - +
792C TYR* 1.3 58.9 + - - +
794C ILE* 2.9 29.1 - - - +
795C ARG* 3.2 17.6 + - - +
38Z ARG* 2.9 9.7 - - - +
43Z ASN* 2.4 27.1 - - - -
----------------------------------------------------------
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Residues in contact with TYR 792 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C HIS 3.1 17.9 + - - +
789C ILE* 3.1 13.2 - - + -
790C ARG 3.3 0.4 - - - -
791C GLY* 1.3 78.5 - - - +
793C LEU* 1.3 115.7 + - + +
795C ARG* 4.1 9.6 - - - +
796C LYS* 2.9 31.5 + - + +
124Z GLU* 3.9 2.3 - - - +
125Z ILE* 2.8 45.1 + - + +
128Z LEU* 2.6 38.0 - - + +
129Z THR* 4.3 10.5 - - + -
148Z VAL* 4.4 28.3 - - + +
151Z GLY* 5.6 2.7 - - - -
152Z PRO* 3.7 22.1 - - + +
----------------------------------------------------------
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Residues in contact with LEU 793 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789C ILE* 3.3 8.9 + - + +
790C ARG* 3.9 4.7 - - - +
792C TYR* 1.3 108.6 - - + +
794C ILE* 1.3 74.9 + - + +
796C LYS* 3.4 5.6 + - - +
797C ALA* 3.3 20.2 + - + +
121Z ASP* 3.0 36.3 - - + +
124Z GLU* 4.9 15.5 - - + +
125Z ILE* 5.1 0.9 - - + -
128Z LEU* 5.6 2.0 - - + -
----------------------------------------------------------
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Residues in contact with ILE 794 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790C ARG* 2.3 37.2 - - + +
791C GLY 2.9 13.5 - - - +
793C LEU* 1.3 80.1 - - + +
795C ARG* 1.3 81.8 + - + +
797C ALA* 2.8 38.7 + - - +
798C TYR* 4.6 0.2 - - - +
35Z ASP* 3.3 22.4 - - - +
38Z ARG* 3.3 42.0 - - + -
39Z CYS* 3.2 35.4 - - - -
----------------------------------------------------------
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Residues in contact with ARG 795 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C HIS* 5.0 5.5 + - - -
791C GLY 3.2 15.8 + - - +
792C TYR* 3.9 9.8 - - - +
794C ILE* 1.3 92.2 - - + +
796C LYS* 1.3 61.3 + - - +
797C ALA 3.2 0.2 - - - -
798C TYR* 3.3 22.4 - - - +
38Z ARG 2.5 44.1 + - - +
39Z CYS* 3.8 18.2 - - - +
41Z GLY* 2.2 37.2 + - - +
42Z ILE 3.1 5.9 + - - -
43Z ASN* 3.1 28.5 + - - +
152Z PRO* 4.3 17.1 - - + +
----------------------------------------------------------
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Residues in contact with LYS 796 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792C TYR* 2.9 20.3 + - + +
793C LEU* 3.5 9.6 - - - +
794C ILE 2.9 0.4 + - - -
795C ARG* 1.3 78.2 - - - +
797C ALA* 1.3 58.0 + - + +
798C TYR 3.2 4.9 + - - -
799C LYS* 4.5 5.5 + - - +
800C LYS* 5.4 0.5 + - - +
128Z LEU* 2.3 61.1 - - + +
152Z PRO* 3.6 37.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 797 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793C LEU* 3.3 13.0 + - + +
794C ILE* 2.8 15.8 + - - +
796C LYS* 1.3 78.5 - - + +
798C TYR* 1.3 56.3 + - - +
799C LYS 4.6 0.4 - - - +
800C LYS* 4.7 18.8 - - + -
801C LEU* 4.1 13.1 + - - +
----------------------------------------------------------
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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