Contacts of the helix formed by residues 89 - 118 (chain P) in PDB entry 2QJK
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 89 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P VAL 2.9 2.2 + - - -
88P ASN* 1.3 73.8 - - - +
90P GLY* 1.3 64.7 + - - +
91P PHE* 3.3 22.7 - - - -
92P MET* 3.1 9.9 + - - +
93P LEU* 3.0 28.8 + - - +
33R PRO* 6.0 4.9 - - - -
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Residues in contact with GLY 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P ILE* 3.0 35.2 - - - +
87P VAL* 2.8 19.9 + - - -
88P ASN 3.1 1.0 - - - -
89P GLY* 1.3 76.0 - - - +
91P PHE* 1.3 64.4 + - - +
93P LEU* 2.8 17.8 + - - +
94P ARG* 2.9 14.6 + - - +
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Residues in contact with PHE 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P ILE 3.5 5.7 + - - -
84P MET* 3.5 35.7 + - + +
87P VAL 5.5 0.7 - - - -
89P GLY* 4.1 18.2 - - - -
90P GLY* 1.3 76.9 - - - +
92P MET* 1.3 108.1 + - + +
94P ARG* 3.7 1.6 + - - +
95P TYR* 3.3 30.9 + - + -
220Q GLU* 5.5 3.1 - - - +
222Q LYS* 3.2 38.4 - - + -
225Q ALA* 3.9 21.8 - - + -
226Q ARG* 3.6 25.8 - - + -
229Q ALA* 5.4 3.1 - - + -
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Residues in contact with MET 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P GLY* 3.1 10.4 + - - +
90P GLY 3.1 1.2 - - - -
91P PHE* 1.3 112.8 - - + +
93P LEU* 1.3 59.9 + - + +
95P TYR* 4.2 2.1 - - + +
96P LEU* 3.2 40.4 + - + +
264P PHE* 5.5 9.2 - - + -
267P VAL* 4.4 23.6 - - + +
268P GLY* 5.3 1.8 - - - -
226Q ARG* 3.4 30.1 - - + +
229Q ALA* 4.5 13.5 - - + -
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Residues in contact with LEU 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P THR* 4.2 22.9 - - + -
64P VAL* 3.4 30.7 - - + -
65P LEU* 4.1 16.4 - - + +
87P VAL* 5.2 2.2 - - + -
88P ASN 4.7 0.4 - - - +
89P GLY 3.0 19.5 + - - +
90P GLY* 2.8 12.2 + - - +
92P MET* 1.3 77.7 - - + +
94P ARG* 1.3 69.4 + - - +
96P LEU* 3.0 13.6 + - + +
97P HIS* 2.9 20.6 + - - +
33R PRO* 4.8 12.6 - - + +
34R LEU* 4.6 14.6 - - + -
37R GLN* 4.1 18.4 - - + -
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Residues in contact with ARG 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P LEU* 4.2 18.4 - - + +
77P PHE* 6.2 1.8 - - - -
80P VAL* 3.6 29.9 - - + +
81P GLU* 5.1 0.8 + - - -
83P ILE* 4.8 2.9 - - + -
84P MET* 3.5 46.7 - - + +
90P GLY 2.9 9.6 + - - +
93P LEU* 1.3 78.3 - - - +
95P TYR* 1.3 72.8 + - - +
97P HIS* 2.9 11.1 + - - +
98P ALA* 3.0 14.6 + - - +
150P PRO* 4.2 9.3 - - - +
279P ASN* 5.7 2.2 + - - +
280P TYR* 4.5 21.6 + - - -
502P HEM 2.9 52.4 + - - +
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Residues in contact with TYR 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P MET* 3.5 19.7 - - + -
91P PHE* 3.3 21.3 + + + +
92P MET* 4.2 2.9 - - + +
94P ARG* 1.3 85.4 - - - +
96P LEU* 1.3 64.1 + - - +
98P ALA* 4.6 3.8 - - + -
99P ASN* 3.0 33.4 + - - +
267P VAL* 3.9 17.3 - - + -
271P PRO* 3.5 28.5 - - + -
272P ASN* 3.1 24.7 + - - -
280P TYR* 3.6 7.4 - - - -
105Q LYS* 2.7 26.0 + - - -
220Q GLU* 2.7 24.8 + - - -
226Q ARG* 3.6 24.2 - - + -
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Residues in contact with LEU 96 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P LEU* 4.5 13.9 - - + +
58P GLN* 3.9 0.9 - - - +
61P THR* 4.5 13.2 - - + -
92P MET* 3.2 36.8 + - + +
93P LEU* 3.0 19.1 + - + +
95P TYR* 1.3 79.4 - - - +
97P HIS* 1.3 54.0 + - - +
100P GLY* 2.7 33.3 + - - -
263P PHE* 3.4 37.8 - - + -
264P PHE* 4.1 22.2 - - + -
267P VAL* 3.9 17.0 - - + +
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Residues in contact with HIS 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58P GLN* 2.9 64.8 + - - +
61P THR* 3.3 20.9 + - - +
62P GLY* 3.8 7.1 + - - -
65P LEU* 3.6 20.0 - - + -
93P LEU 2.9 6.8 + - - +
94P ARG 3.4 8.1 - - - +
96P LEU* 1.3 76.0 - - - +
98P ALA* 1.3 64.3 + - - +
100P GLY 3.3 0.5 + - - -
101P ALA* 3.3 2.9 + - - +
502P HEM 2.0 89.0 + + + +
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Residues in contact with ALA 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P ARG* 3.0 18.7 + - - +
95P TYR* 3.9 6.3 - - + +
97P HIS* 1.3 72.6 - - - +
99P ASN* 1.3 67.3 + - - +
100P GLY 2.8 4.0 - - - -
101P ALA* 2.8 23.0 + - - +
102P SER* 3.6 4.7 + - - -
502P HEM 4.0 36.6 + - + +
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Residues in contact with ASN 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P TYR* 3.0 34.0 + - - +
98P ALA* 1.3 78.6 - - - +
100P GLY* 1.3 62.1 + - - +
102P SER* 3.3 11.0 + - - -
103P LEU* 3.0 23.0 + - - +
263P PHE* 3.6 19.2 - - + -
266P ILE* 4.1 15.8 - - - +
267P VAL* 4.3 8.5 - - + +
271P PRO* 3.2 42.8 + - - +
274P LEU* 4.2 16.6 - - - +
504P LOP 4.1 5.4 - - + +
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Residues in contact with GLY 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P CYS* 4.2 3.9 - - - +
57P LEU* 4.5 6.1 - - - -
58P GLN* 3.1 23.1 - - - -
96P LEU 2.7 15.8 + - - -
98P ALA 2.8 0.8 - - - -
99P ASN* 1.3 78.8 - - - +
101P ALA* 1.3 51.7 + - - +
103P LEU* 3.3 4.5 + - - +
104P PHE* 2.7 34.3 + - - +
263P PHE* 4.1 11.6 - - - -
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Residues in contact with ALA 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58P GLN* 3.5 4.4 + - - -
97P HIS 3.3 6.8 + - - +
98P ALA 2.8 12.4 + - - +
100P GLY* 1.3 73.3 - - - +
102P SER* 1.3 66.0 + - - +
104P PHE* 3.0 10.9 + - - +
105P PHE* 2.9 29.7 + - + -
143P ALA* 5.5 0.2 - - + -
297P TYR* 4.3 14.1 - - + +
502P HEM 3.7 40.4 - - + -
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Residues in contact with SER 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P ALA 3.6 7.6 + - - -
99P ASN* 3.3 8.9 + - - -
101P ALA* 1.3 73.6 - - - +
103P LEU* 1.3 68.8 + - - +
105P PHE* 3.0 1.7 + - - -
106P ILE* 2.8 30.1 + - - +
274P LEU* 3.5 38.7 + - - +
296P TRP* 3.7 25.5 + - - +
297P TYR* 4.3 8.5 - - - -
504P LOP 4.3 1.6 - - - -
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Residues in contact with LEU 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P TRP* 5.9 2.2 - - + -
50P VAL* 4.5 12.6 - - + -
53P PHE* 4.9 11.0 - - + -
54P CYS* 3.4 21.8 - - - -
57P LEU* 5.3 2.2 - - + -
99P ASN 3.0 12.7 + - - +
100P GLY 3.4 7.6 - - - +
102P SER* 1.3 76.9 - - - +
104P PHE* 1.3 65.2 + - - +
106P ILE* 3.3 8.1 + - + +
107P ALA* 3.0 24.1 + - + +
259P VAL* 4.1 18.8 - - + -
260P LEU* 4.9 2.2 - - + -
263P PHE* 4.2 29.4 - - + -
504P LOP 3.6 41.1 - - + +
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Residues in contact with PHE 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P LEU* 3.4 37.5 - - + +
54P CYS* 3.5 18.8 - - + -
55P LEU* 4.2 28.7 - - + -
58P GLN* 4.3 9.0 - - + -
100P GLY 2.7 17.7 + - - +
101P ALA* 3.0 14.8 + - - +
103P LEU* 1.3 73.3 - - - +
105P PHE* 1.3 59.1 + + + +
107P ALA* 4.6 0.2 - - - -
108P VAL* 3.3 17.5 + - - +
139P MET* 3.5 33.4 - - + -
205P ILE* 5.3 1.1 - - + -
501P HEM 4.2 11.9 - - + -
502P HEM 3.8 42.0 - - + -
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Residues in contact with PHE 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P ALA* 2.9 22.5 + - + -
102P SER 3.8 4.0 - - - +
104P PHE* 1.3 72.5 - - + +
106P ILE* 1.3 68.2 + - - +
107P ALA 2.8 1.8 - - - -
108P VAL* 2.7 35.3 + - + +
109P TYR* 2.9 24.6 + + + -
136P TYR* 4.3 7.9 - + - -
139P MET* 4.0 20.6 - - + -
140P MET* 4.0 33.4 - - + -
143P ALA* 3.7 23.3 - - + -
296P TRP* 4.1 2.5 - - + -
297P TYR* 3.2 62.1 - + + -
298P PHE* 5.1 0.4 - + - -
502P HEM 5.5 2.7 - - + -
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Residues in contact with ILE 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P TRP* 5.6 2.7 - - + -
102P SER* 2.8 27.1 + - - +
103P LEU* 3.7 7.6 - - + +
105P PHE* 1.3 72.5 - - - +
107P ALA* 1.3 64.3 + - - +
109P TYR* 3.8 5.3 + - - +
110P LEU* 3.3 34.1 + - + +
274P LEU* 5.0 5.6 - - + -
296P TRP* 3.4 26.9 - - + -
504P LOP 4.1 51.1 - - + -
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Residues in contact with ALA 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P TRP* 4.2 24.8 - - + +
50P VAL* 4.5 14.1 - - + -
51P LEU* 3.5 19.7 - - + +
54P CYS* 5.2 0.4 - - - -
103P LEU* 3.0 17.8 + - + +
104P PHE* 3.5 7.6 - - - +
105P PHE 2.7 0.8 + - - -
106P ILE* 1.3 76.0 - - - +
108P VAL* 1.3 55.0 + - - +
110P LEU* 2.9 6.1 + - - +
111P HIS* 2.7 36.1 + - - +
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Residues in contact with VAL 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P LEU* 3.7 17.0 - - + +
104P PHE 3.3 2.7 + - - +
105P PHE* 2.7 60.3 + - + +
107P ALA* 1.3 75.3 - - - +
109P TYR* 1.3 58.7 + - + +
111P HIS* 3.8 6.5 - - - -
112P ILE* 2.5 47.6 + - + +
136P TYR* 4.5 4.3 - - + -
139P MET* 3.7 27.1 - - + -
501P HEM 4.0 22.2 - - + -
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Residues in contact with TYR 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P PHE* 2.9 34.7 + + + +
106P ILE* 4.2 4.5 - - - +
108P VAL* 1.3 80.0 - - + +
110P LEU* 1.3 54.8 + - + +
112P ILE* 3.5 11.8 - - + +
113P PHE* 2.7 46.2 + + + -
136P TYR* 2.7 42.2 + + - -
140P MET* 5.0 0.5 - - - -
296P TRP* 4.3 23.1 - + - -
297P TYR* 2.9 27.7 + - - -
300P PRO* 5.1 1.2 - - + +
301P PHE* 4.0 4.7 - + - -
343P MET* 6.5 0.2 - - + -
374P PHE* 3.7 44.2 - + + -
504P LOP 4.5 12.6 - - + -
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Residues in contact with LEU 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P MET* 5.0 7.1 - - - +
47P TRP* 3.4 55.9 - - + +
106P ILE* 3.3 25.2 + - + +
107P ALA 2.9 7.0 + - - +
109P TYR* 1.3 77.1 - - + +
111P HIS* 1.3 58.6 + - - +
113P PHE* 4.3 2.6 - - - +
114P ARG* 2.9 32.4 + - - +
504P LOP 4.4 61.1 - - + +
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Residues in contact with HIS 111 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P MET 5.7 0.2 + - - -
47P TRP* 4.1 9.7 - - + +
48P GLY* 3.8 10.9 + - - -
51P LEU* 3.4 11.7 - - + -
107P ALA 2.7 16.4 + - - +
108P VAL* 3.3 11.9 - - - +
110P LEU* 1.3 72.3 - - - +
112P ILE* 1.3 62.0 + - - +
114P ARG* 3.4 15.0 + - - +
115P GLY* 3.1 17.2 + - - -
129P TRP* 5.8 0.2 - - - -
501P HEM 1.9 123.9 + + + +
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Residues in contact with ILE 112 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P VAL* 2.5 26.0 + - + +
109P TYR* 3.5 21.5 - - + +
111P HIS* 1.3 69.0 - - - +
113P PHE* 1.3 72.6 - - + +
115P GLY* 2.9 12.6 + - - -
116P LEU* 3.0 24.8 + - + +
129P TRP* 4.0 22.8 - - + -
133P MET* 5.7 1.3 - - - -
136P TYR* 4.4 21.8 - - + -
343P MET* 4.3 24.9 - - + -
501P HEM 3.9 30.5 - - + -
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Residues in contact with PHE 113 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P TYR* 2.7 30.4 + + + +
110P LEU 4.3 0.4 - - - +
112P ILE* 1.3 73.6 - - + +
114P ARG* 1.3 66.8 + - - +
116P LEU* 3.2 17.0 + - + +
117P TYR* 3.0 25.3 + - - +
367P PHE* 3.8 16.2 - + + -
370P LEU* 4.1 27.6 - - + -
371P ALA* 4.2 12.3 - - + -
374P PHE* 3.7 54.5 - + + -
400P TRP* 4.7 7.4 - + - -
504P LOP 3.4 45.8 - - + -
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Residues in contact with ARG 114 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P MET* 3.2 57.1 + - + +
45P TRP* 3.5 33.7 - - - +
110P LEU 2.9 20.6 + - - +
111P HIS* 3.4 15.7 + - - +
113P PHE* 1.3 78.3 - - - +
115P GLY* 1.3 76.1 + - - +
117P TYR* 3.3 0.5 + - - +
118P TYR* 3.1 35.5 + - + +
120P SER* 3.9 8.7 + - - -
501P HEM 2.9 66.3 + - - +
504P LOP 4.0 12.7 - - - +
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Residues in contact with GLY 115 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P HIS 3.1 5.6 + - - -
112P ILE 2.9 9.4 + - - -
114P ARG* 1.3 93.4 - - - +
116P LEU* 1.3 60.7 + - - -
118P TYR 3.2 1.2 + - - -
119P GLY 3.1 19.8 + - - -
120P SER* 3.1 22.8 + - - -
121P TYR* 3.6 7.8 - - - -
129P TRP* 4.5 8.3 - - - -
501P HEM 5.5 1.3 - - - -
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Residues in contact with LEU 116 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P ILE* 3.0 26.1 + - + +
113P PHE* 3.2 33.0 + - + +
115P GLY* 1.3 74.1 - - - +
117P TYR* 1.3 62.3 + - - +
119P GLY 3.8 1.6 + - - -
121P TYR* 3.4 35.8 + - + +
129P TRP* 3.8 24.4 - - + -
343P MET* 4.9 6.7 - - + -
346P VAL* 4.1 15.5 - - + -
363P PHE* 3.6 11.3 - - - -
367P PHE* 4.0 11.9 - - + -
370P LEU* 4.3 13.5 - - + -
400P TRP* 6.0 0.7 - - + -
403P TYR* 4.9 6.2 + - + +
404P PHE* 4.4 14.6 - - + -
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Residues in contact with TYR 117 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P PHE 3.0 10.2 + - - +
114P ARG 3.7 2.9 - - - +
116P LEU* 1.3 79.4 - - - +
118P TYR* 1.3 87.0 + + - +
119P GLY 3.5 0.4 - - - -
357P GLY* 3.1 29.4 + - - -
358P ARG* 3.5 22.2 - - - -
363P PHE* 4.4 7.5 - + - -
364P LYS* 3.6 17.7 + - + +
367P PHE* 3.3 46.0 - + + -
368P TRP* 4.2 18.1 + + - -
504P LOP 3.0 51.3 + - - -
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Residues in contact with TYR 118 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P ASN* 3.5 12.1 + - - -
44P MET* 4.9 1.9 - - + +
45P TRP* 3.8 20.6 - + + -
114P ARG* 3.1 36.6 + - + +
115P GLY 3.2 0.4 + - - -
117P TYR* 1.3 96.8 - + - +
119P GLY* 1.3 64.5 + - - +
120P SER* 3.1 12.6 + - - +
222P ASN* 3.1 17.3 + - - +
223P ASN 4.4 0.4 - - - +
224P PRO* 3.4 44.0 - - + -
355P ARG* 3.8 14.0 - - - +
356P SER* 3.9 9.2 - - - +
357P GLY 4.1 2.9 - - - +
358P ARG* 4.5 4.3 - - - -
504P LOP 3.0 54.6 + - - -
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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