Contacts of the helix formed by residues 89 - 112 (chain D) in PDB entry 6S7T
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 SER 89 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLN 5.4 1.7 - - - +
87D GLY 4.3 0.2 - - - -
88D ILE* 1.3 77.9 - - - +
90D PRO* 1.3 74.7 - - - +
91D GLU* 3.6 7.4 + - - +
92D ARG* 3.3 23.0 + - - +
93D ALA* 3.2 19.8 + - - +
463E ILE* 5.3 3.6 - - - +
464E THR* 4.5 21.3 - - - +
625F ALA* 6.5 0.4 - - - -
628F ARG* 4.3 11.2 - - - -
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Residues in contact with PRO 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ARG* 5.9 1.1 - - - +
76D GLN 5.3 1.8 - - - +
77D ILE* 3.6 39.5 - - + +
88D ILE 4.7 0.9 - - - +
89D SER* 1.3 89.6 - - - +
91D GLU* 1.3 65.0 + - - +
93D ALA* 3.3 9.2 + - + +
94D PHE* 3.0 26.0 + - - +
628F ARG* 3.7 36.1 - - - +
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Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ARG* 4.5 13.0 + - - -
77D ILE* 5.8 0.3 - - - +
89D SER* 3.2 6.8 + - - +
90D PRO* 1.3 82.0 - - + +
92D ARG* 1.3 65.6 + - - +
94D PHE* 3.2 6.8 + - - +
95D ALA* 3.0 23.4 + - - +
463E ILE* 4.4 11.2 - - + -
621F LEU* 3.5 47.4 - - + +
624F GLN* 4.4 13.5 - - - +
625F ALA* 4.5 14.1 - - + -
628F ARG* 4.2 22.9 + - - +
447G LEU* 4.2 13.9 - - - +
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Residues in contact with ARG 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 3.0 27.5 + - - -
247A PHE* 4.4 22.3 - - - +
248A TRP* 4.6 10.7 - - - +
87D GLY 5.0 2.2 - - - -
88D ILE* 3.7 29.9 - - + +
89D SER* 3.3 19.9 + - - +
91D GLU* 1.3 77.4 - - - +
93D ALA* 1.3 57.5 + - - +
95D ALA* 3.3 4.7 + - + +
96D ASP* 2.9 37.2 + - + +
463E ILE* 4.2 17.2 - - + +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 6.0 0.7 - - - +
73D LEU* 4.8 10.4 - - + +
76D GLN* 3.3 41.4 - - + +
77D ILE* 5.3 2.5 - - + +
88D ILE* 5.1 4.9 - - + +
89D SER 3.2 12.8 + - - +
90D PRO* 3.3 13.7 - - + +
91D GLU 3.2 0.4 - - - -
92D ARG* 1.3 79.1 - - - +
94D PHE* 1.3 56.8 + - - +
96D ASP* 3.4 4.9 + - - +
97D PHE* 2.9 27.8 + - - +
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 4.1 12.9 - - + +
77D ILE* 6.0 0.4 - - + -
90D PRO 3.0 13.3 + - - +
91D GLU* 3.2 13.2 + - - +
93D ALA* 1.3 74.8 - - - +
95D ALA* 1.3 66.9 + - - +
97D PHE* 3.2 19.2 + + - +
98D LEU* 3.0 50.5 + - + +
579F PHE* 4.8 1.3 - + - -
621F LEU* 4.6 10.3 - - + -
442G PHE* 4.5 9.4 - + - -
443G SER* 3.7 24.7 - - - -
446G PHE* 3.6 38.6 - + + -
447G LEU* 3.7 36.6 - - + -
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLU 3.0 16.2 + - - +
92D ARG* 3.3 7.8 + - + +
94D PHE* 1.3 78.8 - - - +
96D ASP* 1.3 57.6 + - - +
98D LEU* 3.2 14.2 + - + +
99D PHE* 3.0 26.7 + - - +
463E ILE* 5.2 2.7 - - + -
621F LEU* 3.8 19.3 - - + +
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Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 2.8 15.6 + - - -
246A VAL* 3.0 20.0 + - + +
247A PHE* 2.4 50.2 + - - +
250A MET* 4.8 0.2 - - - +
76D GLN* 5.4 1.2 - - - +
92D ARG* 2.9 21.8 + - + +
93D ALA* 3.6 7.4 - - - +
95D ALA* 1.3 73.5 - - - +
97D PHE* 1.3 66.6 + - - +
99D PHE* 3.3 11.2 + - - +
100D ALA* 3.0 22.3 + - - +
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Residues in contact with PHE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 5.5 4.8 - - - +
30D TYR* 5.2 5.8 - + - -
66D SER* 5.1 2.7 - - - -
69D LEU* 3.7 45.9 - - + +
70D ALA* 3.9 12.6 - - + -
73D LEU* 3.5 24.5 - - + -
93D ALA 2.9 14.6 + - - +
94D PHE* 3.3 19.3 - + - +
96D ASP* 1.3 75.5 - - - +
98D LEU* 1.3 63.7 + - + +
100D ALA* 3.5 3.7 + - - +
101D SER* 2.9 35.2 + - - -
439G LEU* 3.5 33.0 - - + -
442G PHE* 4.1 21.8 - + - -
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D PHE* 3.0 45.4 + - + +
95D ALA* 3.2 11.9 + - - +
97D PHE* 1.3 86.9 - - + +
99D PHE* 1.3 62.8 + - - +
101D SER* 3.4 4.3 + - - -
102D THR* 3.0 29.1 + - - -
579F PHE* 3.5 34.1 - - + -
583F HIS* 3.7 33.3 - - + +
439G LEU* 5.0 7.4 - - + -
443G SER* 5.0 4.5 - - - +
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE* 3.6 39.0 - + + -
250A MET* 3.7 26.7 - - + -
251A CYS* 5.2 3.6 - - - -
254A LEU* 5.2 6.1 - - + -
95D ALA 3.0 12.7 + - - +
96D ASP* 3.3 12.1 + - - +
98D LEU* 1.3 76.6 - - - +
100D ALA* 1.3 63.7 + - - +
102D THR* 3.2 8.3 + - - -
103D ILE* 3.1 47.1 + - + +
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Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 4.0 5.6 - - + -
250A MET* 3.6 38.7 - - + +
300A VAL* 5.5 0.3 - - - +
69D LEU* 3.8 27.6 - - + +
96D ASP 3.0 16.3 + - - +
97D PHE* 4.0 2.9 - - - +
99D PHE* 1.3 76.7 - - - +
101D SER* 1.3 63.0 + - - +
103D ILE* 3.3 2.9 + - - +
104D LEU* 3.0 24.1 + - - +
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Residues in contact with SER 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D SER* 5.0 3.6 + - - -
69D LEU* 3.9 13.8 - - - +
97D PHE* 2.9 24.3 + - - -
98D LEU* 3.7 6.3 - - - -
99D PHE 3.3 0.2 - - - -
100D ALA* 1.3 77.6 - - - +
102D THR* 1.3 62.3 + - - +
104D LEU* 3.3 4.3 + - - +
105D HIS* 3.0 37.6 + - - -
439G LEU* 3.2 35.1 - - - +
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Residues in contact with THR 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.0 17.9 + - - +
99D PHE* 3.2 8.3 + - - -
101D SER* 1.3 77.0 - - - +
103D ILE* 1.3 65.5 + - + +
105D HIS* 3.3 5.7 + - - +
106D LEU* 3.0 22.9 + - + +
583F HIS* 4.9 10.4 - - - -
586F MET* 3.9 31.6 - - + -
587F LEU* 5.5 6.9 - - + +
590F MET* 4.7 6.9 - - + +
606F LEU* 4.6 20.6 - - + -
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Residues in contact with ILE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A MET* 3.6 31.0 - - + -
254A LEU* 4.1 32.8 - - + -
300A VAL* 4.8 6.1 - - + -
304A LEU* 5.2 1.3 - - + -
99D PHE* 3.1 45.7 + - + +
100D ALA 3.9 1.3 - - - +
102D THR* 1.3 78.3 - - + +
104D LEU* 1.3 65.0 + - - +
106D LEU* 3.3 9.7 + - + +
107D VAL* 3.0 39.0 + - + +
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A MET* 5.2 0.2 - - - +
299A ILE* 5.0 7.4 - - + -
300A VAL* 5.0 13.0 - - + -
303A ILE* 4.3 23.8 - - + -
61D ILE 4.7 8.3 - - - +
62D SER* 4.4 5.2 - - - +
65D GLY* 3.7 35.2 - - - -
66D SER* 3.8 11.4 - - - +
69D LEU* 4.2 13.0 - - + -
100D ALA 3.0 17.2 + - - +
101D SER* 3.7 5.6 - - - +
103D ILE* 1.3 79.1 - - - +
105D HIS* 1.3 66.0 + - + +
107D VAL* 3.3 4.9 + - - +
108D VAL* 2.9 39.3 + - + +
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Residues in contact with HIS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D SER* 4.4 16.7 + - - -
66D SER* 3.8 18.9 + - - -
101D SER* 3.0 35.9 + - - +
102D THR* 4.0 4.9 - - - +
104D LEU* 1.3 84.1 - - + +
106D LEU* 1.3 65.6 + - - +
108D VAL* 3.7 6.9 - - + +
109D MET* 3.0 29.5 + - - +
587F LEU* 5.2 8.7 - - + +
590F MET* 4.4 7.6 - - + -
432G ALA 5.6 0.9 + - - -
435G MET* 4.8 4.3 - - - +
436G MET* 3.8 49.3 + - + +
439G LEU* 4.1 17.7 - - + +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR 3.0 17.6 + - - +
103D ILE* 3.6 10.5 - - + +
105D HIS* 1.3 76.6 - - - +
107D VAL* 1.3 66.2 + - + +
109D MET* 3.8 0.9 - - - +
110D ASN* 3.0 22.8 + - + +
590F MET* 3.7 27.4 - - + -
593F TYR* 4.6 13.7 - - + -
599F MET* 4.2 21.3 - - + -
602F THR* 4.7 8.7 - - + +
603F LEU* 4.1 20.4 - - + -
606F LEU* 3.8 24.5 - - + -
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A VAL* 6.1 0.9 - - + -
303A ILE* 3.6 30.1 - - + +
304A LEU* 3.4 33.0 - - + -
307A GLN* 3.5 24.5 - - + +
103D ILE* 3.0 24.7 + - + +
104D LEU* 3.7 4.7 - - - +
106D LEU* 1.3 78.4 - - + +
108D VAL* 1.3 63.7 + - - +
110D ASN* 3.1 8.2 + - - +
111D PHE* 2.9 21.5 + - - +
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ILE* 3.6 22.0 - - + -
58D SER* 3.2 29.9 + - - +
62D SER* 3.8 32.3 - - - +
104D LEU* 2.9 25.7 + - + +
105D HIS* 3.7 9.4 - - + +
106D LEU 3.3 0.2 - - - -
107D VAL* 1.3 75.3 - - - +
109D MET* 1.3 71.9 + - - +
111D PHE* 2.9 16.6 + - - -
112D VAL* 2.9 13.9 + - - +
432G ALA* 4.4 11.9 - - + -
436G MET* 5.8 0.9 - - + -
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Residues in contact with MET 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D HIS 3.0 19.4 + - - +
106D LEU 4.1 0.9 - - - +
108D VAL* 1.3 87.7 - - - +
110D ASN* 1.3 59.4 + - - +
111D PHE 3.3 0.4 + - - -
112D VAL* 3.9 21.0 - - + +
590F MET* 3.7 14.1 - - + +
593F TYR* 3.5 27.4 + - + -
594F TRP* 3.5 45.0 - - + -
432G ALA* 4.4 11.2 - - + -
433G PHE* 3.6 23.8 - - + -
436G MET* 3.6 26.9 - - + -
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Residues in contact with ASN 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLN* 3.9 21.3 + - - +
106D LEU 3.0 18.3 + - - +
107D VAL* 3.1 10.6 + - - +
109D MET* 1.3 76.4 - - - +
111D PHE* 1.3 58.5 + - - +
112D VAL 5.3 0.6 - - - -
593F TYR* 2.8 25.8 + - + +
599F MET* 4.4 19.9 - - + +
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Residues in contact with PHE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 4.8 10.3 - - + -
306A MET* 3.9 36.8 - - + -
307A GLN* 3.3 32.3 - - - +
313A PHE* 3.7 28.5 - + - -
54D ASN* 4.0 22.9 + - + +
57D LEU* 3.8 25.4 - - + -
58D SER* 4.1 17.3 - - - -
61D ILE* 5.7 1.1 - - + -
107D VAL 2.9 8.6 + - - +
108D VAL* 2.9 7.4 + - - +
110D ASN* 1.3 79.4 - - - +
112D VAL* 1.3 67.2 + - - +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ASN* 5.0 4.5 - - - +
55D SER* 3.9 23.9 + - - +
58D SER* 3.2 28.2 + - - +
59D GLY 5.4 0.7 - - - +
108D VAL* 2.9 10.3 + - + +
109D MET* 3.9 27.1 - - + +
110D ASN 3.7 1.3 - - - -
111D PHE* 1.3 81.9 - - - +
594F TRP* 3.8 30.5 - - + +
428G TYR* 5.3 1.3 - - + -
429G TYR* 3.6 37.2 - - + +
432G ALA* 6.0 2.7 - - + -
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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