Contacts of the helix formed by residues 79 - 110 (chain A) in PDB entry 6TOS
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 THR 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS 4.0 18.2 - - - +
77A MET* 2.8 8.1 + - - -
78A ARG* 1.3 81.8 - - - +
80A VAL* 1.3 58.5 + - - +
81A THR* 3.8 7.7 + - - -
82A ASN* 3.4 26.1 + - - +
83A TYR* 3.0 30.9 + - - -
158A ALA* 5.6 1.3 - - - -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 1.3 70.6 - - - +
81A THR* 1.4 65.4 + - - +
83A TYR* 3.4 7.7 + - - +
84A PHE* 3.2 47.5 + - + -
143A ASP* 3.4 34.8 - - - +
144A ARG* 5.8 1.6 - - - +
156A SER* 4.0 18.2 - - - +
157A THR 3.6 32.5 - - - +
158A ALA* 3.9 4.5 - - - +
161A ALA* 4.4 7.5 - - + +
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.3 7.8 + - - -
80A VAL* 1.4 77.7 - - - +
82A ASN* 1.4 54.5 + - - +
84A PHE* 3.1 8.2 + - - +
85A LEU* 2.8 42.5 + - + +
140A ILE* 4.0 13.9 - - + +
143A ASP* 4.5 2.6 + - - -
144A ARG* 3.8 27.7 + - - +
296A THR* 4.2 13.2 - - + +
299A MET* 5.1 0.4 - - + -
300A LEU* 3.7 39.0 - - + -
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.0 10.4 - - + +
77A MET* 2.8 56.5 + - - +
79A THR* 3.4 12.7 + - - +
81A THR* 1.4 76.4 - - - +
83A TYR* 1.4 61.5 + - - +
85A LEU* 3.3 15.6 + - - +
86A VAL* 2.9 33.0 + - - +
296A THR* 6.1 0.3 - - - +
299A MET* 4.9 3.3 - - - +
364A LYS* 6.3 0.4 - - - +
365A PHE* 3.5 23.4 - - + -
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.0 16.6 - - + -
78A ARG* 3.4 51.1 + - + +
79A THR 3.0 20.0 + - - +
80A VAL 3.8 5.4 - - - +
81A THR 3.3 0.4 - - - -
82A ASN* 1.4 74.7 - - - +
84A PHE* 1.3 60.8 + - - +
86A VAL* 3.5 8.3 + - + +
87A ASN 3.2 16.5 + - - -
158A ALA* 3.4 48.0 - - + +
161A ALA* 4.4 7.0 - - + -
162A LEU* 4.8 16.8 - - + -
165A ILE* 3.4 22.1 - - + +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.2 39.7 + - + -
81A THR* 3.1 4.1 + - - +
83A TYR* 1.3 72.8 - - - +
85A LEU* 1.4 59.2 + - - +
87A ASN* 3.0 4.4 + - - -
88A LEU 2.9 24.1 + - - -
136A THR* 3.0 25.2 - - + +
139A PHE* 3.9 22.9 - + + -
140A ILE* 3.4 34.5 - - + -
143A ASP* 5.0 1.6 - - + -
156A SER* 6.0 0.4 - - - -
161A ALA* 4.2 10.8 - - + -
164A SER* 3.8 23.3 - - - -
165A ILE* 3.6 28.5 - - + -
168A ILE* 3.9 19.5 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.2 3.4 - - + +
81A THR* 2.8 22.7 + - + +
82A ASN* 3.3 30.2 + - + +
84A PHE* 1.4 75.8 - - - +
86A VAL* 1.4 55.1 + - - +
88A LEU* 3.3 14.9 + - + +
89A SER* 3.0 30.1 + - - -
140A ILE* 3.8 19.7 - - + -
299A MET* 3.8 24.5 - - + -
300A LEU* 4.3 9.9 - - + -
303A VAL* 5.2 4.0 - - + -
358A TYR* 3.4 39.4 + - + +
365A PHE* 4.3 11.7 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.4 4.5 - - + +
68A CYS* 3.7 31.6 - - + +
71A VAL* 3.7 34.5 - - + -
82A ASN 2.9 19.1 + - - +
83A TYR* 3.6 11.2 - - + +
84A PHE 3.3 0.2 - - - -
85A LEU* 1.4 74.4 - - - +
87A ASN* 1.4 58.6 + - - +
89A SER* 3.0 10.9 + - - -
90A LEU* 2.9 34.9 + - + +
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR 3.2 12.8 + - - +
84A PHE* 3.0 10.6 + - - +
86A VAL* 1.4 73.2 - - - +
88A LEU* 1.4 63.0 + - - +
90A LEU* 3.2 14.4 + - - +
91A ALA* 3.1 23.0 + - - +
132A VAL* 3.7 11.6 - - - +
136A THR* 2.8 25.8 + - - +
165A ILE* 3.4 36.0 - - + +
168A ILE* 4.2 8.9 - - - +
169A TRP* 2.7 28.9 + - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 2.9 12.7 + - - +
85A LEU* 3.5 15.9 - - + +
86A VAL 3.3 0.2 - - - -
87A ASN* 1.4 75.0 - - - +
89A SER* 1.3 57.6 + - - +
91A ALA* 3.5 4.1 + - - +
92A ASP* 3.0 47.3 + - - +
133A ALA* 3.8 39.3 - - + +
136A THR* 3.9 11.3 - - + +
137A LEU* 4.2 26.0 - - + -
303A VAL* 4.4 4.0 - - + -
307A PHE* 5.2 2.2 - - + -
354A ASN* 4.0 16.2 - - + +
358A TYR* 3.5 23.3 - - - +
419A NA 4.6 1.8 - - - -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 2.9 42.6 + - - +
67A VAL* 3.4 18.9 - - - +
68A CYS* 4.4 5.2 - - - -
85A LEU 3.0 14.0 + - - -
86A VAL* 3.3 14.1 - - - -
88A LEU* 1.3 77.0 - - - +
90A LEU* 1.4 50.8 + - - +
92A ASP* 3.4 2.1 + - - +
93A VAL* 2.8 39.4 + - - +
354A ASN* 5.9 0.5 - - - +
358A TYR* 4.8 4.3 + - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A CYS* 4.7 12.6 - - - -
86A VAL* 2.9 25.9 + - + +
87A ASN* 3.2 21.3 + - - +
89A SER* 1.4 72.8 - - - +
91A ALA* 1.3 54.0 + - - +
93A VAL* 3.2 11.3 + - + +
94A LEU* 2.8 34.1 + - - +
165A ILE* 6.1 1.1 - - + -
169A TRP* 4.3 16.6 - - + +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASN 3.1 6.8 + - - +
88A LEU 3.7 8.5 - - - +
90A LEU* 1.3 75.2 - - - +
92A ASP* 1.3 63.4 + - - +
94A LEU* 3.3 8.2 + - - +
95A ALA 3.2 11.3 + - - -
129A SER* 2.7 41.3 + - - +
132A VAL* 3.6 29.8 - - + -
133A ALA* 4.1 6.5 - - - +
169A TRP* 4.2 7.7 - - - -
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 4.2 11.4 - - - +
88A LEU* 3.0 27.4 + - - +
89A SER 3.8 4.0 - - - +
90A LEU 3.2 0.2 - - - -
91A ALA* 1.3 75.9 - - - +
93A VAL* 1.3 55.4 + - - +
95A ALA* 3.6 2.4 + - - +
96A THR* 2.7 37.1 + - - -
129A SER* 4.7 3.4 + - - -
133A ALA* 4.5 3.8 - - - +
351A SER* 3.2 29.0 + - - +
354A ASN* 3.1 29.5 + - - +
419A NA 2.4 25.5 - - - -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA 4.7 3.1 - - - +
61A LEU* 4.4 23.1 - - + +
64A ASN* 3.6 26.7 - - + -
65A THR* 5.0 3.4 - - - +
68A CYS* 6.3 1.3 - - - -
89A SER 2.8 24.2 + - - +
90A LEU* 3.2 11.4 + - + +
92A ASP* 1.3 69.6 - - - +
94A LEU* 1.3 65.9 + - - +
96A THR* 4.3 4.7 - - - -
97A ALA* 2.9 28.7 + - + +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 2.8 13.6 + - - +
91A ALA* 3.3 10.1 + - - +
93A VAL* 1.3 79.2 - - - +
95A ALA* 1.4 60.9 + - - +
97A ALA* 5.3 0.4 - - - -
98A ILE* 3.2 34.8 + - + +
99A CYS* 4.1 1.0 + - - -
125A LEU* 3.8 60.1 - - + +
128A VAL* 4.4 5.4 - - + -
129A SER* 4.3 7.6 - - - -
169A TRP* 4.0 29.2 - - + -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 3.2 5.3 + - - +
92A ASP* 3.9 6.3 - - - +
94A LEU* 1.4 75.3 - - - +
96A THR* 1.3 59.0 + - - +
99A CYS* 3.1 19.1 + - - +
100A LEU 2.9 26.7 + - - -
126A GLN* 4.1 10.3 - - - +
129A SER* 3.3 25.1 + - - +
347A VAL* 5.8 1.6 - - + -
348A TYR* 3.6 20.0 - - + -
351A SER* 4.9 3.1 - - - +
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Residues in contact with THR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.4 44.4 - - + +
60A ALA* 3.7 14.3 - - + +
61A LEU* 3.9 17.3 - - + -
92A ASP 2.7 22.4 + - - -
93A VAL* 3.4 4.0 + - - -
95A ALA* 1.3 75.8 - - - +
97A ALA* 1.3 61.7 + - - +
100A LEU* 3.2 30.4 - - + +
101A PRO* 3.6 0.3 - - - +
348A TYR* 4.8 3.1 + - - -
351A SER* 3.5 20.8 + - - -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.3 10.8 - - + -
61A LEU* 4.4 14.6 - - + -
93A VAL* 2.9 23.0 + - + +
94A LEU* 4.4 0.7 - - - +
96A THR* 1.3 76.4 - - - +
98A ILE* 1.3 72.2 + - + +
101A PRO* 3.4 20.1 - - - +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.2 27.8 + - + +
97A ALA* 1.3 90.9 - - + +
99A CYS* 1.3 66.3 + - - +
100A LEU 3.7 0.2 - - - -
101A PRO* 3.7 7.4 - - - +
102A ALA* 4.2 10.9 + - - +
118A LEU* 6.4 0.7 - - + -
121A VAL* 5.8 1.1 - - + -
122A ILE* 4.0 25.1 - - + +
125A LEU* 4.0 22.0 - - + -
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Residues in contact with CYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU 4.4 3.1 - - - -
95A ALA* 3.1 19.7 + - - +
98A ILE* 1.3 78.3 - - - +
100A LEU* 1.4 60.4 + - - +
102A ALA* 3.2 4.5 + - - +
103A SER* 3.0 25.1 + - - -
122A ILE* 3.8 19.7 - - + -
125A LEU* 4.1 11.4 - - - -
126A GLN* 3.3 56.3 - - + +
348A TYR* 3.5 6.9 + - - +
401A NRE 3.8 2.7 - - + +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.6 34.8 - - + +
56A VAL* 3.9 15.5 - - + -
57A PHE* 3.7 33.7 - - + -
95A ALA 2.9 12.8 + - - +
96A THR* 3.2 23.8 - - + +
99A CYS* 1.4 71.0 - - - +
101A PRO* 1.4 66.9 - - + +
103A SER* 3.3 2.8 + - - -
104A LEU* 3.0 24.7 + - + +
348A TYR* 3.6 41.2 - - + -
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Residues in contact with PRO 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.1 16.6 - - + -
96A THR 3.6 2.5 - - - +
97A ALA 3.4 27.4 - - - +
98A ILE 3.7 4.7 - - - +
99A CYS 3.6 3.6 - - - -
100A LEU* 1.4 96.4 - - + +
102A ALA* 1.4 61.0 + - - +
104A LEU* 3.4 9.2 + - + +
105A LEU* 3.2 28.6 + - + +
114A PHE* 4.7 4.5 - - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE 4.2 3.3 + - - +
99A CYS 3.2 9.9 + - - +
101A PRO* 1.4 74.2 - - - +
103A SER* 1.3 60.0 + - - +
105A LEU* 3.3 4.7 + - - +
106A VAL* 3.1 30.8 + - - +
112A TRP* 4.1 3.1 - - + -
114A PHE* 3.7 26.9 - - + -
122A ILE* 3.8 25.8 - - + -
401A NRE 3.6 14.8 - - + -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 2.8 22.0 + - - -
99A CYS 3.0 17.2 + - - -
100A LEU 3.6 4.3 - - - -
102A ALA* 1.3 71.9 - - - +
104A LEU* 1.3 60.3 + - - +
106A VAL* 3.3 4.7 + - - +
107A ASP* 2.8 33.6 + - - +
344A HIS* 3.6 20.3 + - - +
348A TYR* 3.6 19.9 - - - -
401A NRE 3.4 16.0 - - - +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.1 11.9 - - + +
50A ILE* 4.2 16.4 - - + -
53A TYR* 3.8 48.4 - - + -
54A VAL* 5.0 10.5 - - + -
100A LEU* 3.0 15.4 + - + +
101A PRO* 3.5 14.1 - - + +
102A ALA 3.4 0.2 - - - -
103A SER* 1.3 76.5 - - - +
105A LEU* 1.4 60.2 + - + +
107A ASP* 3.4 2.8 + - - +
108A ILE* 3.1 55.7 + - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PRO* 3.2 17.1 + - + +
102A ALA 3.8 6.3 - - - +
103A SER 3.3 0.2 - - - -
104A LEU* 1.4 76.2 - - + +
106A VAL* 1.4 60.1 + - - +
108A ILE* 3.3 14.9 + - + +
109A THR* 2.9 45.1 + - + +
111A SER 4.7 1.3 - - - +
113A LEU* 3.9 26.5 - - + -
114A PHE* 3.6 34.3 - - + -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 3.1 15.4 + - - +
103A SER* 3.3 8.3 + - - +
105A LEU* 1.4 73.6 - - - +
107A ASP* 1.3 66.4 + - - +
110A GLU* 2.7 50.5 + - - +
111A SER 3.8 17.0 - - - +
112A TRP* 3.6 33.9 - - + -
114A PHE* 5.4 1.6 - - + -
344A HIS* 5.9 4.5 - - + -
401A NRE 4.9 7.4 - - + -
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 5.0 6.6 + - - -
49A LEU* 3.9 16.2 - - + +
53A TYR* 2.6 25.7 + - - +
103A SER* 2.8 19.8 + - - +
104A LEU 3.4 6.0 + - - +
106A VAL* 1.3 77.7 - - - +
108A ILE* 1.4 58.0 + - - +
110A GLU* 3.6 16.6 - - - +
340A PHE* 5.7 0.2 - - - +
341A THR* 3.3 45.6 + - + +
344A HIS* 3.2 24.9 + - - -
----------------------------------------------------------
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 6.3 1.1 - - + -
49A LEU* 3.9 19.7 - - + -
50A ILE* 4.0 23.3 - - + -
104A LEU* 3.1 40.1 + - + +
105A LEU* 3.8 15.7 - - + +
106A VAL 3.2 0.6 - - - -
107A ASP* 1.4 78.7 - - - +
109A THR* 1.3 73.9 + - + +
110A GLU* 3.7 2.9 - - - +
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 2.9 26.5 + - + +
108A ILE* 1.3 89.2 - - + +
110A GLU* 1.3 68.9 + - - +
111A SER* 2.9 33.1 + - - -
113A LEU* 4.2 21.8 - - + +
199A PHE* 6.1 0.2 - - - -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 2.7 44.6 + - - +
107A ASP* 3.6 21.0 - - - +
108A ILE 5.0 2.5 - - - +
109A THR* 1.3 73.6 - - - +
111A SER* 1.3 56.6 + - - +
199A PHE* 4.3 10.4 - - - -
201A VAL* 4.9 8.3 - - - +
337A TYR* 3.5 67.5 - - + +
341A THR* 4.3 4.3 + - - -
404A CIT 4.2 7.8 - - - +
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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