Contacts of the helix formed by residues 894 - 914 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.1 10.9 - - + +
109A ALA* 5.6 5.6 - - + -
110A ASN* 3.6 13.8 - - - +
113A GLU* 3.5 27.8 + - - +
679A PHE* 4.5 2.8 - - - -
835A LYS* 4.6 5.1 - - - +
890A GLY 3.3 18.4 + - - +
891A LEU* 3.0 24.9 + - - +
893A LEU* 1.3 80.0 - - - +
895A ASN* 1.3 64.6 + - - +
896A PRO* 3.3 1.6 - - - -
897A TYR* 3.1 22.9 + - - -
898A ILE* 3.3 24.2 + - + +
965A GLY* 2.9 29.9 + - - -
966A MET 4.6 0.2 + - - -
967A GLN* 3.7 24.1 - - - +
1004A FLC 2.7 36.9 + - - -
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Residues in contact with ASN 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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72A GLU* 2.9 36.3 + - - +
785A ARG* 3.6 19.9 + - - +
834A ALA 4.8 10.9 + - - +
835A LYS* 5.6 2.8 - - - +
891A LEU* 3.6 12.1 + - - +
892A VAL* 3.2 27.3 + - - +
894A ARG* 1.3 76.1 - - - +
896A PRO* 1.3 58.2 - - + +
897A TYR 3.1 0.3 + - - -
898A ILE* 3.9 15.1 - - - +
899A THR* 2.7 38.0 + - - +
966A MET* 6.0 0.5 - - - +
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Residues in contact with PRO 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 5.0 1.6 - - + -
23A LEU* 3.9 24.9 - - + -
65A TYR* 3.5 37.0 - - + +
68A SER* 3.2 19.0 - - - +
69A ALA* 4.1 15.9 - - + +
72A GLU* 4.6 2.7 - - + -
892A VAL 3.4 14.1 - - - +
893A LEU 3.9 8.1 - - - +
894A ARG 3.4 3.6 - - - -
895A ASN* 1.3 91.6 - - + +
897A TYR* 1.3 59.1 + - + +
900A THR* 2.8 25.1 + - - -
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Residues in contact with TYR 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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16A ILE* 4.1 7.8 - - - +
20A LEU* 4.6 2.9 - - - +
38A ASP* 4.4 9.4 + - - -
42A VAL* 3.9 18.9 - - + +
65A TYR* 3.7 33.9 + + - -
102A ILE* 3.4 26.0 - - + +
105A MET* 3.5 46.2 - - + -
106A LEU* 4.0 28.0 - - + -
109A ALA* 4.0 13.7 - - + +
893A LEU 3.4 20.4 + - - -
894A ARG* 3.1 16.5 + - - +
896A PRO* 1.3 73.7 - - + +
898A ILE* 1.3 64.7 + - - +
900A THR* 3.7 0.4 + - - -
901A LEU* 3.3 20.9 + - - +
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Residues in contact with ILE 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.1 9.0 - - + -
785A ARG* 4.2 7.6 - - - +
894A ARG* 3.3 37.5 - - + +
895A ASN* 3.1 15.1 + - - +
897A TYR* 1.3 73.1 - - - +
899A THR* 1.3 61.4 + - - +
901A LEU* 3.1 8.9 + - - +
902A ASN* 2.8 41.8 + - - +
962A ILE* 4.0 33.7 - - + +
965A GLY* 3.9 29.2 - - - +
966A MET* 4.6 12.1 - - - -
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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
----------------------------------------------------------
68A SER* 4.1 18.4 - - - +
71A TYR* 4.0 18.2 - - + -
72A GLU* 2.6 24.6 + - - -
80A LEU* 5.3 2.9 - - + -
83A LEU* 5.6 1.1 - - + -
785A ARG* 3.3 17.6 + - - +
840A ILE* 3.6 17.5 - - + +
895A ASN 2.7 20.0 + - - -
896A PRO* 4.8 0.2 - - - -
898A ILE* 1.3 72.6 - - - +
900A THR* 1.3 62.2 + - - +
902A ASN* 3.1 12.9 + - - +
903A VAL* 3.1 22.9 + - + +
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Residues in contact with THR 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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64A CYS* 3.6 24.4 + - + -
65A TYR* 4.4 2.1 - - - -
68A SER* 2.4 29.6 + - - +
83A LEU* 4.3 9.2 - - + -
87A LEU* 4.9 10.8 - - + -
98A VAL* 5.8 0.7 - - + -
102A ILE* 3.9 29.8 - - + +
896A PRO 2.8 16.1 + - - -
897A TYR 3.8 5.6 - - - -
898A ILE 3.3 0.6 - - - -
899A THR* 1.3 79.0 - - - +
901A LEU* 1.3 61.7 + - + +
903A VAL* 3.3 5.2 - - - +
904A PHE* 3.1 23.9 + - + +
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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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99A ALA* 4.1 26.9 - - + +
102A ILE* 4.0 16.6 - - + -
103A LEU* 4.9 10.1 - - + -
106A LEU* 5.1 3.1 - - + -
897A TYR 3.3 16.1 + - - +
898A ILE* 3.1 9.4 + - - +
900A THR* 1.3 75.5 - - + +
902A ASN* 1.3 60.2 + - - +
904A PHE* 3.7 7.5 - - + +
905A GLN* 2.8 30.7 + - - +
957A LEU 4.4 2.7 - - - +
958A THR* 3.7 27.5 - - + +
961A GLY* 3.7 35.0 - - - -
962A ILE* 3.9 13.5 - - + +
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Residues in contact with ASN 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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783A GLN 2.8 29.3 + - - -
785A ARG* 3.0 36.9 + - - +
840A ILE* 3.6 24.2 - - + -
844A TYR* 3.0 26.7 + - - +
898A ILE* 2.8 17.7 + - - +
899A THR* 3.1 10.5 + - - +
901A LEU* 1.3 74.9 - - - +
903A VAL* 1.3 62.6 + - - +
905A GLN 3.1 1.7 + - - -
906A ALA* 3.0 22.3 + - - +
962A ILE* 3.7 8.1 - - - +
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Residues in contact with VAL 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.2 35.9 - - + +
83A LEU* 3.6 35.7 - - + -
84A GLY 4.5 3.6 - - - +
87A LEU* 3.7 9.2 - - + -
840A ILE* 5.5 1.3 - - + -
843A LEU* 4.3 19.3 - - + -
899A THR* 3.1 17.5 + - + +
900A THR 3.3 10.8 - - - +
902A ASN* 1.3 78.0 - - + +
904A PHE* 1.3 66.6 + - - +
906A ALA 3.4 0.8 + - - +
907A TYR* 3.1 34.0 + - + +
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Residues in contact with PHE 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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87A LEU* 3.6 51.1 - - + -
90A LEU* 4.4 2.9 - - + -
95A ALA* 3.6 42.6 - - + -
98A VAL* 4.5 5.2 - - + -
99A ALA* 4.3 21.1 - - + -
102A ILE* 6.4 0.7 - - + -
900A THR* 3.1 16.6 + - + +
901A LEU* 3.7 9.6 - - + +
903A VAL* 1.3 83.6 - - - +
905A GLN* 1.3 51.8 + - - +
907A TYR* 3.7 3.7 + - + -
908A THR* 2.4 45.8 + - + -
911A ARG* 6.2 2.0 - - - -
954A THR* 3.7 17.5 - - + -
958A THR* 4.1 8.3 - - + -
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Residues in contact with GLN 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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747A PRO* 3.9 17.0 - - - +
783A GLN* 2.9 33.7 + - - +
844A TYR* 2.6 26.4 + - - +
901A LEU 2.8 18.3 + - - +
902A ASN* 3.1 5.6 + - - +
904A PHE* 1.3 75.2 - - - +
906A ALA* 1.3 59.8 + - - +
908A THR* 2.8 17.5 + - - -
909A LEU* 2.9 31.0 + - + +
955A LEU* 3.7 11.7 - - + -
958A THR* 3.0 27.3 + - - +
959A MET* 3.4 13.3 - - - +
962A ILE* 3.6 7.5 - - - +
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Residues in contact with ALA 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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843A LEU* 4.6 10.5 - - + -
844A TYR* 4.0 32.5 - - + -
847A LEU* 3.5 26.5 - - + +
848A LEU* 4.1 7.2 - - + +
902A ASN 3.0 14.7 + - - +
903A VAL 3.4 4.5 + - - +
905A GLN* 1.3 78.0 - - - +
907A TYR* 1.3 62.9 + - + +
909A LEU* 3.4 11.5 + - - +
910A LYS* 3.4 10.9 + - - +
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Residues in contact with TYR 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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80A LEU 4.6 3.1 - - - -
81A GLY* 3.5 24.3 + - - -
84A GLY* 3.8 37.7 - - - +
85A ALA* 5.1 0.7 - - - -
87A LEU* 6.3 2.5 - - + -
88A THR* 4.9 6.7 - - - +
843A LEU* 4.2 18.4 - - + +
846A GLU* 5.6 0.5 + - - -
847A LEU* 3.7 39.9 - - + +
903A VAL* 3.1 26.4 + - + +
904A PHE* 4.3 4.5 - - + +
906A ALA* 1.3 75.5 - - + +
908A THR* 1.3 66.4 + - + +
910A LYS* 3.5 7.2 + - + +
911A ARG* 3.2 31.4 + - - +
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Residues in contact with THR 908 (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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904A PHE* 2.4 43.2 + - + +
905A GLN* 2.8 15.6 + - - -
907A TYR* 1.3 76.9 - - + +
909A LEU* 1.3 56.2 + - - +
911A ARG* 3.5 13.0 + - - +
912A ILE* 2.9 35.1 + - - +
951A LEU* 4.8 16.2 - - + +
954A THR* 3.6 32.4 - - + +
955A LEU* 3.8 16.4 - - - +
958A THR* 4.9 0.2 - - - +
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Residues in contact with LEU 909 (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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746A THR 5.0 0.2 - - - -
747A PRO* 3.9 22.2 - - + -
750A GLU* 3.5 35.4 - - + +
844A TYR* 4.1 12.3 - - + -
848A LEU* 3.9 25.4 - - + -
905A GLN* 2.9 34.1 + - + +
906A ALA 3.6 5.4 - - - +
907A TYR 3.2 0.2 - - - -
908A THR* 1.3 74.9 - - - +
910A LYS* 1.3 61.6 + - - +
912A ILE* 3.3 4.0 + - + +
913A ARG* 3.0 39.2 + - - +
955A LEU* 3.8 24.2 - - + -
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Residues in contact with LYS 910 (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 GLU 5.4 0.6 + - - -
847A LEU* 3.1 48.4 + - + +
848A LEU* 3.4 19.0 - - + +
906A ALA 3.4 7.3 + - - +
907A TYR* 4.0 9.2 - - + +
908A THR 3.4 0.2 - - - -
909A LEU* 1.3 74.7 - - - +
911A ARG* 1.3 67.3 + - + +
913A ARG* 3.4 4.5 + - + +
914A ASP* 3.1 25.9 + - + +
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Residues in contact with ARG 911 (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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87A LEU 5.1 2.5 + - - -
88A THR* 2.6 53.1 + - - +
90A LEU 5.1 5.3 + - - -
904A PHE* 6.2 2.0 - - - -
907A TYR* 3.2 19.9 + - - +
908A THR* 3.7 16.0 - - - +
909A LEU 3.3 0.2 - - - -
910A LYS* 1.3 81.7 - - + +
912A ILE* 1.3 62.7 + - - +
914A ASP* 3.3 9.2 + - - +
917A PHE* 3.5 64.4 - - + +
919A VAL* 6.1 1.6 - - - +
948A PRO* 5.7 0.3 - - - +
951A LEU* 4.1 20.3 - - + +
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Residues in contact with ILE 912 (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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750A GLU* 4.3 21.1 - - + +
754A MET* 3.9 12.1 - - + -
908A THR* 2.9 21.4 + - - +
909A LEU* 3.7 4.9 - - - +
911A ARG* 1.3 77.6 - - - +
913A ARG* 1.3 65.7 + - - +
914A ASP 3.4 4.3 + - - +
947A TYR* 4.2 26.6 - - + -
948A PRO* 5.8 2.4 - - - +
951A LEU* 3.6 45.5 - - + +
955A LEU* 3.9 28.5 - - + -
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Residues in contact with ARG 913 (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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743A ARG 3.5 11.8 + - - -
744A SER* 2.9 29.7 + - - +
746A THR 2.9 28.3 + - - -
747A PRO* 4.1 1.2 - - - +
749A THR* 4.6 1.6 + - - -
750A GLU* 3.0 39.6 + - - +
848A LEU* 3.6 25.5 + - - +
909A LEU* 3.0 30.6 + - - +
910A LYS* 4.0 4.9 - - - +
911A ARG 3.3 0.2 - - - -
912A ILE* 1.3 77.6 - - + +
914A ASP* 1.3 60.0 + - - +
915A PRO* 3.3 11.8 - - - +
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Residues in contact with ASP 914 (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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910A LYS* 3.1 20.9 + - + +
911A ARG* 3.6 8.1 - - - +
912A ILE 3.3 4.2 - - - +
913A ARG* 1.3 75.4 - - - +
915A PRO* 1.3 70.2 - - - +
916A ASN* 2.9 26.7 + - - +
917A PHE* 3.3 30.0 + - + +
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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