Contacts of the helix formed by residues 940 - 971 (chain D) in PDB entry 6MZL
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 VAL 940 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLY 5.7 0.4 - - - +
85C ARG* 3.7 26.9 - - + -
86C THR* 4.9 9.9 - - + +
87C ASP* 5.4 2.0 - - - +
938D SER 3.2 4.7 - - - +
939D ASP* 1.3 80.4 - - - +
941D ARG* 1.3 57.2 + - - +
942D ALA 3.3 0.9 - - - +
943D GLN* 3.3 5.7 + - - +
944D LEU* 2.7 31.4 + - - +
576F THR* 4.8 19.1 - - + +
577F CYS 5.9 1.3 - - - +
578F LEU* 6.0 1.0 - - - +
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Residues in contact with ARG 941 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLY 5.8 1.8 - - - -
85C ARG* 3.5 38.5 - - + +
940D VAL* 1.3 75.8 - - - +
942D ALA* 1.3 60.4 + - - +
944D LEU* 3.2 10.6 + - + +
945D LYS* 2.9 26.2 + - - +
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Residues in contact with ALA 942 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ARG* 5.0 0.8 - - - +
938D SER* 4.8 6.3 - - - +
939D ASP* 3.7 21.9 - - - +
940D VAL 3.3 0.8 - - - +
941D ARG* 1.3 78.8 - - - +
943D GLN* 1.3 57.0 + - - +
945D LYS* 3.2 8.4 + - - +
946D PHE* 2.9 26.3 + - - +
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Residues in contact with GLN 943 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939D ASP* 3.4 32.4 + - - +
940D VAL* 3.3 9.1 + - - +
941D ARG 3.3 0.2 - - - -
942D ALA* 1.3 76.0 - - - +
944D LEU* 1.3 60.1 + - - +
946D PHE* 3.6 8.5 - - - +
947D PHE* 2.9 28.8 + - - +
573F GLN* 4.4 4.4 + - - +
574F THR* 3.7 24.4 + - + +
576F THR* 6.1 0.2 - - + -
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Residues in contact with LEU 944 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940D VAL 2.7 17.9 + - - +
941D ARG* 3.4 14.1 - - + +
942D ALA 3.2 0.2 - - - -
943D GLN* 1.3 75.6 - - - +
945D LYS* 1.3 55.8 + - - +
947D PHE* 3.4 6.8 + - - +
948D GLU* 2.9 27.8 + - - +
578F LEU* 5.6 10.3 - - + -
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Residues in contact with LYS 945 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941D ARG 2.9 14.3 + - - +
942D ALA* 3.2 11.2 + - - +
944D LEU* 1.3 72.0 - - - +
946D PHE* 1.3 60.9 + - - +
948D GLU* 3.3 8.3 + - - +
949D GLN* 2.9 27.2 + - - +
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Residues in contact with PHE 946 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942D ALA 2.9 14.0 + - - +
943D GLN* 3.6 11.7 - - - +
944D LEU 3.3 0.2 - - - -
945D LYS* 1.3 75.6 - - - +
947D PHE* 1.3 59.4 + - - +
949D GLN* 3.2 8.5 + - - +
950D LEU* 2.9 27.9 + - - +
573F GLN* 5.2 2.0 - - - +
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Residues in contact with PHE 947 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943D GLN 2.9 14.4 + - - +
944D LEU* 3.7 8.1 - - - +
946D PHE* 1.3 74.9 - - - +
948D GLU* 1.3 59.0 + - - +
950D LEU* 3.4 7.1 + - - +
951D ASP* 2.9 29.3 + - - +
573F GLN* 3.4 27.2 - - - +
578F LEU* 6.3 2.9 - - + -
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Residues in contact with GLU 948 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944D LEU 2.9 18.2 + - - +
945D LYS* 3.6 9.6 - - - +
946D PHE 3.3 0.2 - - - -
947D PHE* 1.3 74.8 - - - +
949D GLN* 1.3 58.6 + - - +
951D ASP* 3.7 6.2 - - - +
952D GLN* 2.8 28.9 + - - +
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Residues in contact with GLN 949 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945D LYS 2.9 16.7 + - - +
946D PHE* 3.2 8.7 + - - +
948D GLU* 1.3 75.7 - - - +
950D LEU* 1.3 60.7 + - - +
952D GLN* 3.3 7.4 + - - +
953D ILE* 2.9 27.7 + - - +
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Residues in contact with LEU 950 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946D PHE 2.9 16.9 + - - +
947D PHE* 3.7 7.0 - - - +
949D GLN* 1.3 75.3 - - - +
951D ASP* 1.3 58.2 + - - +
953D ILE* 3.3 8.6 + - - +
954D GLU* 2.9 27.6 + - - +
573F GLN* 6.0 1.8 - - - +
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Residues in contact with ASP 951 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947D PHE 2.9 17.9 + - - +
948D GLU* 3.8 7.2 - - - +
950D LEU* 1.3 73.0 - - - +
952D GLN* 1.3 61.3 + - - +
954D GLU* 3.7 7.6 - - - +
955D LYS* 2.8 29.1 + - - +
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Residues in contact with GLN 952 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948D GLU 2.8 19.0 + - - +
949D GLN* 3.3 8.5 + - - +
951D ASP* 1.3 73.8 - - - +
953D ILE* 1.3 60.3 + - - +
955D LYS* 3.8 6.4 - - - +
956D GLN* 2.9 30.4 + - - +
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Residues in contact with ILE 953 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949D GLN 2.9 13.4 + - - +
950D LEU* 3.5 11.4 - - - +
952D GLN* 1.3 77.8 - - - +
954D GLU* 1.3 58.1 + - - +
956D GLN* 3.4 6.5 + - - +
957D ARG* 2.9 28.1 + - - +
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Residues in contact with GLU 954 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950D LEU 2.9 17.1 + - - +
951D ASP* 3.7 8.5 - - - +
952D GLN 3.3 0.2 - - - -
953D ILE* 1.3 77.8 - - - +
955D LYS* 1.3 56.6 - - - +
957D ARG* 3.3 7.7 + - - +
958D LYS* 2.9 27.0 + - - +
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Residues in contact with LYS 955 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951D ASP 2.8 17.4 + - - +
952D GLN* 3.8 7.6 - - - +
954D GLU* 1.3 73.2 - - - +
956D GLN* 1.3 60.6 + - - +
958D LYS* 3.3 7.8 + - - +
959D ASP* 2.9 29.3 + - - +
109L PRO* 5.7 8.7 - - + -
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Residues in contact with GLN 956 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952D GLN 2.9 18.3 + - - +
953D ILE* 3.7 7.4 - - - +
955D LYS* 1.3 75.4 - - - +
957D ARG* 1.3 59.0 + - - +
959D ASP* 3.5 6.1 + - - +
960D GLU* 2.9 29.6 + - - +
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Residues in contact with ARG 957 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953D ILE 2.9 16.9 + - - +
954D GLU* 3.6 8.5 - - - +
955D LYS 3.3 0.2 - - - -
956D GLN* 1.3 77.7 - - - +
958D LYS* 1.3 56.5 + - - +
960D GLU* 3.4 7.1 + - - +
961D GLN* 2.9 28.2 + - - +
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Residues in contact with LYS 958 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954D GLU 2.9 17.0 + - - +
955D LYS* 3.7 8.7 - - - +
957D ARG* 1.3 74.8 - - - +
959D ASP* 1.3 60.1 + - - +
961D GLN* 3.3 7.7 + - - +
962D GLU* 2.9 27.4 + - - +
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Residues in contact with ASP 959 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955D LYS 2.9 17.3 + - - +
956D GLN* 3.8 7.0 - - - +
958D LYS* 1.3 74.6 - - - +
960D GLU* 1.3 59.8 + - - +
962D GLU* 3.3 7.2 + - - +
963D ARG* 2.9 28.8 + - - +
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Residues in contact with GLU 960 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956D GLN 2.9 19.0 + - - +
957D ARG* 3.7 8.3 - - - +
958D LYS 3.3 0.2 - - - -
959D ASP* 1.3 77.0 - - - +
961D GLN* 1.3 57.4 + - - +
963D ARG* 3.4 7.5 + - - +
964D GLU* 2.8 28.8 + - - +
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Residues in contact with GLN 961 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957D ARG 2.9 17.3 + - - +
958D LYS* 3.3 9.4 + - - +
960D GLU* 1.3 74.8 - - - +
962D GLU* 1.3 59.2 + - - +
964D GLU* 3.3 7.3 + - - +
965D ILE* 2.9 27.7 + - - +
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Residues in contact with GLU 962 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958D LYS 2.9 15.8 + - - +
959D ASP* 3.3 8.5 + - - +
961D GLN* 1.3 76.9 - - - +
963D ARG* 1.3 56.0 + - - +
965D ILE* 3.3 7.7 + - - +
966D LEU* 2.9 27.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 963 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959D ASP 2.9 17.8 + - - +
960D GLU* 3.8 7.6 - - - +
961D GLN 3.3 0.2 - - - -
962D GLU* 1.3 76.2 - - - +
964D GLU* 1.3 57.8 + - - +
966D LEU* 3.4 8.3 + - - +
967D MET* 2.9 28.3 + - - +
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Residues in contact with GLU 964 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960D GLU 2.8 17.9 + - - +
961D GLN* 3.6 9.2 - - - +
962D GLU 3.2 0.2 - - - -
963D ARG* 1.3 76.1 - - - +
965D ILE* 1.3 59.0 + - - +
967D MET* 3.3 6.5 + - - +
968D ARG* 2.9 29.3 + - - +
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Residues in contact with ILE 965 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961D GLN 2.9 16.1 + - - +
962D GLU* 3.3 8.3 + - - +
964D GLU* 1.3 76.8 - - - +
966D LEU* 1.3 56.5 + - - +
968D ARG* 3.4 6.8 + - - +
969D ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962D GLU 2.9 17.2 + - - +
963D ARG* 3.6 9.0 - - - +
964D GLU 3.3 0.2 - - - -
965D ILE* 1.3 77.3 - - - +
967D MET* 1.3 56.4 + - - +
969D ALA* 3.4 9.1 + - - +
970D ALA* 2.9 25.1 + - - +
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Residues in contact with MET 967 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963D ARG 2.9 17.8 + - - +
964D GLU* 3.8 7.6 - - - +
965D ILE 3.3 0.2 - - - -
966D LEU* 1.3 74.1 - - - +
968D ARG* 1.3 54.7 + - - +
970D ALA* 3.1 10.1 + - + +
971D LYS* 2.6 34.2 + - - +
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Residues in contact with ARG 968 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964D GLU 2.9 17.9 + - - +
965D ILE* 3.4 8.0 + - - +
967D MET* 1.3 72.1 - - - +
969D ALA* 1.3 64.6 + - - +
971D LYS* 3.3 24.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA 969 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965D ILE 2.9 14.9 + - - +
966D LEU* 3.5 11.9 - - - +
967D MET 3.3 0.2 - - - -
968D ARG* 1.3 77.4 - - - +
970D ALA* 1.3 59.6 + - - +
971D LYS 3.6 5.2 + - - +
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Residues in contact with ALA 970 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966D LEU 2.9 15.0 + - - +
967D MET* 3.1 12.5 + - - +
969D ALA* 1.3 75.4 - - - +
971D LYS* 1.3 63.8 + - - +
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Residues in contact with LYS 971 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967D MET 2.6 18.9 + - - +
968D ARG* 3.5 21.6 - - - +
969D ALA 3.3 6.7 - - - +
970D ALA* 1.3 78.1 - - - +
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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