Contacts of the helix formed by residues 89 - 118 (chain M) 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 M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M VAL 2.9 2.2 + - - -
88M ASN* 1.3 72.9 - - - +
90M GLY* 1.3 65.6 + - - +
91M PHE* 3.3 22.2 - - - -
92M MET* 3.1 9.1 + - - +
93M LEU* 3.0 28.0 + - - +
33O PRO* 6.1 4.7 - - - -
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Residues in contact with GLY 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M ILE* 3.1 34.2 - - - +
87M VAL* 2.8 19.0 + - - -
88M ASN 3.1 1.4 - - - -
89M GLY* 1.3 77.1 - - - +
91M PHE* 1.3 65.0 - - - +
93M LEU* 2.8 18.3 + - - +
94M ARG* 2.9 14.6 + - - +
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Residues in contact with PHE 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M ILE 3.5 5.3 + - - -
84M MET* 3.5 35.5 + - + +
87M VAL 5.5 0.7 - - - -
89M GLY* 4.2 17.7 - - - -
90M GLY* 1.3 77.3 - - - +
92M MET* 1.3 110.2 + - + +
94M ARG* 3.9 1.4 - - - +
95M TYR* 3.3 30.5 + + + -
220N GLU* 5.5 2.7 - - - +
222N LYS* 3.1 39.7 - - + -
225N ALA* 3.9 21.8 - - + -
226N ARG* 3.6 25.4 - - + -
229N ALA* 5.3 2.9 - - + -
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Residues in contact with MET 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M GLY* 3.1 10.3 + - - +
91M PHE* 1.3 114.9 - - + +
93M LEU* 1.3 60.6 + - + +
95M TYR* 4.2 2.3 - - + +
96M LEU* 3.2 40.0 + - + +
264M PHE* 5.5 9.9 - - + -
267M VAL* 4.4 23.6 - - + +
268M GLY* 5.3 1.8 - - - -
226N ARG* 3.4 30.3 - - + +
229N ALA* 4.3 14.1 - - + -
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Residues in contact with LEU 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M THR* 4.2 23.5 - - + +
64M VAL* 3.4 31.6 - - + -
65M LEU* 4.1 15.8 - - + +
83M ILE* 6.2 0.2 - - + -
87M VAL* 5.2 2.2 - - + -
88M ASN 4.8 0.4 - - - +
89M GLY 3.0 20.2 + - - +
90M GLY* 2.8 12.4 + - - +
92M MET* 1.3 79.2 - - + +
94M ARG* 1.3 68.8 + - - +
96M LEU* 3.0 12.1 + - + +
97M HIS* 2.9 20.8 + - - +
33O PRO* 4.9 12.6 - - + +
34O LEU* 4.7 14.1 - - + -
37O GLN* 4.2 17.3 - - + -
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Residues in contact with ARG 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M LEU* 4.2 18.7 - - + +
77M PHE* 6.2 1.6 - - - -
80M VAL* 3.8 25.9 - - + +
81M GLU* 5.3 0.6 + - - -
83M ILE* 4.8 2.9 - - + -
84M MET* 3.5 46.7 - - + +
90M GLY 2.9 8.8 + - - +
93M LEU* 1.3 75.0 - - - +
95M TYR* 1.3 72.0 + - - +
97M HIS* 2.8 14.9 + - - +
98M ALA* 3.0 13.5 + - - +
150M PRO* 4.2 9.9 - - - +
279M ASN* 5.6 4.2 + - - +
280M TYR* 4.3 23.1 + - - -
502M HEM 3.0 56.3 + - - +
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Residues in contact with TYR 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M MET* 3.5 20.6 - - + -
91M PHE* 3.3 20.8 + + + +
92M MET* 4.2 3.1 - - - +
93M LEU 3.3 0.4 - - - -
94M ARG* 1.3 85.5 - - - +
96M LEU* 1.3 63.7 + - - +
98M ALA* 4.6 4.3 - - + -
99M ASN* 2.9 33.7 + - - +
267M VAL* 3.9 17.3 - - + -
271M PRO* 3.5 26.5 - - + -
272M ASN* 3.0 29.6 + - - -
280M TYR* 3.6 7.2 - - - -
105N LYS* 2.9 19.2 + - - -
220N GLU* 2.7 23.6 + - - -
226N ARG* 3.5 31.6 - - + -
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Residues in contact with LEU 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M LEU* 4.5 13.3 - - + +
58M GLN* 3.9 0.9 - - - +
61M THR* 4.4 13.7 - - + -
92M MET* 3.2 41.4 + - + +
93M LEU* 3.0 18.4 + - + +
95M TYR* 1.3 76.5 - - - +
97M HIS* 1.3 54.3 + - - +
99M ASN 3.8 0.2 - - - -
100M GLY* 2.8 33.1 + - - -
263M PHE* 3.4 37.4 - - + -
264M PHE* 4.2 22.4 - - + -
267M VAL* 4.0 15.5 - - + -
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Residues in contact with HIS 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M GLN* 2.9 59.7 + - - +
61M THR* 3.3 21.0 + - - +
62M GLY* 3.8 6.3 + - - -
65M LEU* 3.6 21.8 - - + -
93M LEU 2.9 5.1 + - - +
94M ARG 2.8 8.4 + - - +
96M LEU* 1.3 75.1 - - - +
98M ALA* 1.3 63.4 + - - +
101M ALA* 3.3 2.4 + - - +
502M HEM 2.0 95.1 + + + +
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Residues in contact with ALA 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94M ARG* 3.0 16.9 + - - +
95M TYR* 3.9 7.4 - - + +
97M HIS* 1.3 72.8 - - - +
99M ASN* 1.3 61.6 + - - +
100M GLY 2.8 3.4 - - - -
101M ALA* 2.8 29.1 + - - +
102M SER* 3.5 4.2 + - - -
502M HEM 3.4 41.9 - - + +
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Residues in contact with ASN 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M TYR* 2.9 32.9 + - - +
98M ALA* 1.3 77.7 - - - +
100M GLY* 1.3 62.9 + - - +
102M SER* 3.3 11.0 + - - -
103M LEU* 3.0 23.0 + - - +
263M PHE* 3.6 20.6 - - + -
266M ILE* 4.1 17.7 - - + +
267M VAL* 4.3 8.7 - - + +
270M MET 4.7 0.2 - - - +
271M PRO* 3.2 42.8 + - - +
274M LEU* 4.1 17.0 - - + +
504M LOP 4.6 2.4 - - + +
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Residues in contact with GLY 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M CYS* 4.1 3.5 - - - +
57M LEU* 4.5 7.0 - - - -
58M GLN* 3.1 22.3 - - - -
96M LEU 2.8 17.2 + - - -
98M ALA 2.8 0.8 + - - -
99M ASN* 1.3 80.2 - - - +
101M ALA* 1.3 50.9 + - - +
103M LEU* 3.3 4.5 + - - +
104M PHE* 2.7 34.8 + - - +
263M PHE* 4.1 10.8 - - - -
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Residues in contact with ALA 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M GLN* 3.5 1.0 + - - -
97M HIS 3.3 6.7 + - - +
98M ALA 2.8 11.9 + - - +
100M GLY* 1.3 73.1 - - - +
102M SER* 1.3 65.6 + - - +
104M PHE* 2.9 11.8 + - - +
105M PHE* 2.8 29.9 + - + -
143M ALA* 5.5 0.2 - - + -
297M TYR* 4.3 14.1 - - + +
502M HEM 3.9 43.1 - - + -
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Residues in contact with SER 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M ALA 3.5 5.6 + - - -
99M ASN* 3.3 10.6 + - - -
101M ALA* 1.3 76.0 - - - +
103M LEU* 1.3 65.8 + - - +
105M PHE* 2.7 13.9 + - - +
106M ILE* 2.8 20.0 + - - +
274M LEU* 3.4 35.6 + - - +
296M TRP* 3.4 29.1 + - - +
297M TYR* 4.3 8.1 - - - -
504M LOP 4.9 0.4 - - - -
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Residues in contact with LEU 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M TRP* 6.0 2.2 - - + -
50M VAL* 4.6 12.1 - - + -
53M PHE* 4.9 11.2 - - + -
54M CYS* 3.4 21.8 - - - -
57M LEU* 5.3 2.0 - - + -
99M ASN 3.0 10.6 + - - +
100M GLY 3.4 7.2 - - - +
102M SER* 1.3 77.1 - - - +
104M PHE* 1.3 63.8 + - - +
106M ILE* 3.4 8.1 + - + +
107M ALA* 3.0 24.5 + - + +
259M VAL* 4.1 22.7 - - + -
260M LEU* 4.9 1.8 - - + -
263M PHE* 4.1 29.2 - - + -
504M LOP 3.6 38.4 - - + +
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Residues in contact with PHE 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU* 3.4 35.1 - - + +
54M CYS* 3.5 19.3 - - + -
55M LEU* 4.2 25.8 - - + -
58M GLN* 4.3 8.7 - - + -
100M GLY 2.7 19.4 + - - +
101M ALA* 3.0 14.4 - - - +
103M LEU* 1.3 74.3 - - - +
105M PHE* 1.3 57.5 + + + +
108M VAL* 3.1 20.6 + - - +
139M MET* 3.5 31.0 - - + -
205M ILE* 5.3 1.1 - - + -
501M HEM 4.2 12.8 - - + -
502M HEM 3.8 42.8 - - + -
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Residues in contact with PHE 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101M ALA* 2.8 20.3 + - + -
102M SER 2.7 12.0 + - - +
104M PHE* 1.3 68.6 - - + +
106M ILE* 1.3 68.3 + - - +
107M ALA 2.8 1.6 - - - -
108M VAL* 2.7 35.3 + - + +
109M TYR* 2.9 27.9 + + + -
136M TYR* 4.3 9.0 - + - -
139M MET* 4.1 20.9 - - + -
140M MET* 3.9 33.2 - - + -
143M ALA* 3.7 22.9 - - + -
296M TRP* 4.1 2.9 - - + -
297M TYR* 3.2 61.7 - + + -
298M PHE* 5.1 0.2 - + - -
502M HEM 5.6 3.1 - - + -
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Residues in contact with ILE 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M TRP* 5.5 3.4 - - + -
102M SER* 2.8 32.1 + - - +
103M LEU* 3.6 7.0 - - + +
105M PHE* 1.3 71.0 - - - +
107M ALA* 1.3 64.2 + - - +
109M TYR* 3.8 6.5 + - - +
110M LEU* 3.3 33.5 + - + +
274M LEU* 4.9 5.8 - - + -
296M TRP* 3.4 26.4 - - + -
504M LOP 3.7 55.0 - - + -
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Residues in contact with ALA 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M TRP* 4.3 24.3 - - + +
50M VAL* 4.5 12.8 - - + -
51M LEU* 3.5 21.3 - - + +
54M CYS* 5.2 0.4 - - - -
103M LEU* 3.0 18.5 + - + +
104M PHE* 3.5 7.2 - - - +
105M PHE 2.7 4.0 + - - -
106M ILE* 1.3 73.4 - - - +
108M VAL* 1.3 54.2 + - - +
110M LEU* 3.0 5.5 + - - +
111M HIS* 2.7 36.7 + - - +
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Residues in contact with VAL 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU* 3.7 16.1 - - + +
104M PHE 3.1 13.0 + - - +
105M PHE* 2.7 47.6 + - + +
107M ALA* 1.3 74.5 - - - +
109M TYR* 1.3 53.3 + - + +
111M HIS* 3.3 5.6 - - + +
112M ILE* 2.5 47.6 + - + +
136M TYR* 4.5 6.5 - - + -
139M MET* 3.8 25.1 - - + -
501M HEM 4.0 24.2 - - + -
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Residues in contact with TYR 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M PHE* 2.9 36.1 + + + +
106M ILE* 4.1 5.2 - - - +
108M VAL* 1.3 74.5 - - + +
110M LEU* 1.3 54.9 + - + +
112M ILE* 3.6 15.0 - - + +
113M PHE* 2.7 48.1 + + + -
136M TYR* 2.6 42.8 + + - -
140M MET* 5.0 0.7 - - - -
296M TRP* 4.2 23.1 - + - -
297M TYR* 2.9 26.8 + - - -
300M PRO* 5.1 1.3 - - + +
301M PHE* 4.0 5.3 - + - -
374M PHE* 3.7 44.2 - + + -
504M LOP 4.8 10.3 - - + -
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Residues in contact with LEU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M MET* 4.9 9.9 - - + +
47M TRP* 3.4 53.7 - - + +
106M ILE* 3.3 23.0 + - + +
107M ALA 3.0 7.7 + - - +
109M TYR* 1.3 76.3 - - + +
111M HIS* 1.3 64.4 + - - +
113M PHE* 4.2 2.6 - - - +
114M ARG* 2.9 27.5 + - - +
504M LOP 4.1 54.8 - - + +
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Residues in contact with HIS 111 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M MET 5.8 0.2 - - - -
47M TRP* 4.1 10.2 - - + +
48M GLY* 3.7 19.2 + - - -
51M LEU* 3.4 13.5 - - + -
107M ALA 2.7 16.8 + - - +
108M VAL* 3.3 11.9 - - - +
110M LEU* 1.3 74.1 - - - +
112M ILE* 1.3 61.9 + - - +
114M ARG* 3.3 25.4 + - - +
115M GLY* 3.1 17.5 + - - -
129M TRP* 5.8 0.2 - - - -
501M HEM 2.0 106.0 + + + +
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Residues in contact with ILE 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108M VAL* 2.5 40.0 + - + +
109M TYR* 3.6 31.0 - - + +
111M HIS* 1.3 69.9 - - - +
113M PHE* 1.3 70.2 + - + +
115M GLY* 3.0 12.5 + - - -
116M LEU* 3.0 20.0 + - + +
129M TRP* 3.8 25.3 - - + -
133M MET* 6.0 1.8 - - - -
136M TYR* 4.3 17.0 - - + -
343M MET* 4.2 26.0 - - + -
501M HEM 4.3 21.3 - - + -
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Residues in contact with PHE 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M TYR* 2.7 31.5 + + + +
110M LEU 4.2 0.4 - - - +
112M ILE* 1.3 73.1 - - + +
114M ARG* 1.3 67.6 + - - +
116M LEU* 3.2 18.3 + - + +
117M TYR* 3.0 24.9 + - - +
367M PHE* 3.7 15.3 - + - -
370M LEU* 4.1 26.5 - - + -
371M ALA* 4.2 11.0 - - - -
374M PHE* 3.7 46.9 - + + -
400M TRP* 4.7 7.0 - + - -
504M LOP 3.4 54.3 - - + -
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Residues in contact with ARG 114 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M MET* 3.2 57.5 + - + +
45M TRP* 3.5 26.6 - - - -
110M LEU 2.9 20.6 + - - +
111M HIS* 3.3 22.2 + - - +
112M ILE 3.1 0.2 - - - -
113M PHE* 1.3 77.5 - - - +
115M GLY* 1.3 75.4 + - - +
117M TYR* 3.4 0.3 + - - +
118M TYR* 3.1 36.3 + - + -
120M SER* 3.9 9.8 + - - -
501M HEM 2.5 63.9 + - - +
504M LOP 3.5 14.2 + - - +
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Residues in contact with GLY 115 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M HIS 3.1 5.8 + - - -
112M ILE 3.0 8.2 + - - -
114M ARG* 1.3 92.8 - - - +
116M LEU* 1.3 59.9 + - - +
118M TYR 3.2 0.7 + - - -
119M GLY 3.0 20.4 + - - -
120M SER* 3.1 22.1 + - - -
121M TYR* 3.6 8.0 - - - -
129M TRP* 4.6 8.1 - - - -
501M HEM 4.8 2.0 - - - -
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Residues in contact with LEU 116 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M ILE* 3.0 25.7 + - + +
113M PHE* 3.2 34.5 + - + +
115M GLY* 1.3 72.7 - - - +
117M TYR* 1.3 61.6 + - - +
118M TYR 3.6 0.2 + - - -
119M GLY 3.8 1.9 + - - -
121M TYR* 3.4 34.8 + - + +
129M TRP* 3.8 24.6 - - + -
343M MET* 4.8 7.2 - - + -
346M VAL* 4.1 15.9 - - + -
363M PHE* 3.6 11.3 - - - -
367M PHE* 4.0 11.7 - - + -
370M LEU* 4.3 13.5 - - + -
400M TRP* 6.0 0.4 - - + -
403M TYR* 4.9 6.0 + - + +
404M PHE* 4.4 13.9 - - + -
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Residues in contact with TYR 117 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M PHE 3.0 10.6 + - - +
114M ARG 3.7 1.1 - - - +
116M LEU* 1.3 79.1 - - - +
118M TYR* 1.3 81.9 + + - +
119M GLY 3.5 0.4 + - - -
357M GLY* 3.1 30.8 + - - -
358M ARG* 3.4 25.9 - - - -
363M PHE* 4.4 6.2 - + - -
364M LYS* 4.1 16.2 - - + +
367M PHE* 3.3 46.4 - + + -
368M TRP* 4.2 16.6 + - - -
504M LOP 2.9 62.4 + - - +
----------------------------------------------------------
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Residues in contact with TYR 118 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M ASN* 3.5 15.9 + - - -
44M MET* 4.9 3.2 - - + +
45M TRP* 3.8 20.0 - + + -
114M ARG* 3.1 37.3 + - + +
117M TYR* 1.3 94.8 - + - +
119M GLY* 1.3 63.9 + - - +
120M SER* 3.1 12.8 + - - +
222M ASN* 3.1 18.1 + - - +
223M ASN 4.4 0.2 - - - -
224M PRO* 3.4 43.5 - - + -
355M ARG* 3.9 14.0 - - - +
356M SER* 3.9 9.1 - - - -
357M GLY 4.1 2.9 - - - +
358M ARG* 4.3 0.2 + - - -
504M LOP 2.8 53.5 + - - -
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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