Contacts of the helix formed by residues 88 - 113 (chain A) in PDB entry 6WNX
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 PRO 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A MET* 4.2 3.4 - - + -
86A GLY 3.1 8.0 - - - +
87A PRO* 1.4 90.0 - - + +
89A ASN* 1.3 65.5 + - - +
90A SER* 3.3 23.1 - - - +
91A PHE* 3.2 17.4 + - + +
92A TYR* 3.3 9.5 - - - -
126D ASN* 3.5 26.7 - - - +
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 5.2 0.8 + - - -
45A ILE* 4.1 2.7 + - - +
46A SER* 3.2 45.9 - - - +
49A MET* 3.5 38.3 - - + +
50A LEU 3.6 0.2 + - - -
51A TRP* 3.6 38.0 + - - +
52A LYS 4.3 2.1 + - - -
88A PRO* 1.3 70.4 - - - +
90A SER* 1.3 66.5 + - - +
91A PHE 2.8 2.4 + - - -
92A TYR* 2.8 17.0 + - - -
93A ARG* 2.9 17.2 + - - +
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO* 3.3 11.5 - - - +
89A ASN* 1.3 78.5 - - - +
91A PHE* 1.3 54.3 + - - +
93A ARG* 3.5 13.3 - - - +
94A SER* 2.7 36.2 + - - -
126D ASN* 3.2 24.2 + - - -
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 5.3 0.9 - - + -
77A TYR* 3.9 41.7 - + + -
87A PRO* 3.8 13.2 - - + -
88A PRO* 3.2 24.4 + - + +
89A ASN 2.8 5.1 + - - -
90A SER* 1.3 75.4 + - - +
92A TYR* 1.3 90.9 - + - +
94A SER* 3.2 8.9 + - - -
95A LEU* 3.0 49.4 + - + +
125D GLU* 5.5 11.2 - - + -
126D ASN* 5.1 5.2 - - - +
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A MET* 4.7 2.9 - - - -
51A TRP* 3.9 6.3 - - + +
52A LYS* 3.6 60.4 - - + +
55A ILE* 3.6 16.3 - - + +
77A TYR* 2.7 34.1 + - + -
78A LEU* 4.0 10.5 - - + -
87A PRO* 3.3 39.4 + - + +
88A PRO 3.3 20.0 - - - -
89A ASN* 2.8 12.4 + - - +
91A PHE* 1.3 93.9 - + - +
93A ARG* 1.3 65.9 + - - +
95A LEU* 4.1 6.3 - - + -
96A TYR* 3.3 19.8 + - - +
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 3.1 28.1 + - - -
42A GLN* 5.4 5.7 - - - +
51A TRP* 3.6 40.3 - - + +
89A ASN* 2.9 17.1 + - - +
90A SER* 3.5 15.3 - - - +
92A TYR* 1.3 79.0 - - - +
94A SER* 1.3 61.2 + - - +
96A TYR* 3.9 2.6 + - - +
97A PRO* 3.2 18.2 - - - +
135B VAL* 3.7 12.9 - - - +
138B GLU* 2.6 40.1 + - - +
139B ASN* 2.7 29.9 + - - -
141B TRP* 5.6 0.5 + - - -
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER* 2.7 20.0 + - - -
91A PHE* 3.2 10.0 + - - -
93A ARG* 1.3 76.2 - - - +
95A LEU* 1.3 61.8 + - - +
97A PRO* 3.4 16.2 - - - +
98A LYS* 3.4 19.1 - - - +
125D GLU* 3.2 27.8 + - - -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 4.0 17.0 - - + -
74A TRP* 4.1 40.2 - - + +
77A TYR* 5.8 0.4 - - + -
78A LEU* 5.9 0.9 - - + -
91A PHE* 3.0 39.8 + - + +
92A TYR* 3.6 10.1 - - + +
93A ARG 3.3 0.2 - - - -
94A SER* 1.3 76.7 - - - +
96A TYR* 1.3 67.7 + - - +
98A LYS* 2.7 31.7 + - + +
99A ILE* 2.9 31.0 + - + -
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Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 3.5 26.7 - - + +
51A TRP* 3.8 27.4 - + + -
54A LEU* 3.4 23.1 - - + +
55A ILE* 3.7 20.8 - - + +
58A MET* 3.1 31.2 - - + +
65A TRP* 3.5 23.8 - + - -
92A TYR 3.3 7.9 + - - +
93A ARG 4.2 0.2 - - - +
95A LEU* 1.3 79.7 - - - +
97A PRO* 1.3 70.4 - - + +
99A ILE* 3.1 12.0 + - - +
100A ILE* 3.1 38.3 + - + +
141B TRP* 3.6 16.8 - + - -
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Residues in contact with PRO 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG 3.2 15.3 - - - +
94A SER* 3.4 17.9 - - - +
96A TYR* 1.3 96.8 - - + +
98A LYS* 1.3 54.6 + - + +
100A ILE* 3.4 9.3 + - + +
101A GLN* 2.9 28.2 + - - +
138B GLU 5.4 1.3 - - - +
141B TRP* 3.6 52.5 - - + +
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A SER* 3.4 21.1 - - - +
95A LEU* 2.7 27.1 + - + +
97A PRO* 1.3 71.5 - - + +
99A ILE* 1.3 56.4 + - - -
101A GLN* 3.7 7.7 - - - +
102A ASP* 2.9 27.5 + - - +
125D GLU* 3.2 38.3 + - - +
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 4.4 8.7 - - + -
65A TRP* 3.6 42.2 - - + -
68A LEU* 4.3 7.9 - - + -
74A TRP* 3.3 51.8 - - + +
95A LEU* 2.9 35.0 + - + +
96A TYR* 3.1 6.5 + - - +
98A LYS* 1.3 74.1 - - - +
100A ILE* 1.3 53.5 + - - +
102A ASP* 3.1 9.4 - - - +
103A ILE* 2.8 41.4 + - + +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TRP* 3.6 27.1 - - + -
96A TYR* 3.1 37.4 + - + +
97A PRO* 3.4 9.2 + - + +
99A ILE* 1.3 75.9 - - - +
101A GLN* 1.3 52.6 + - - +
103A ILE* 3.1 13.9 + - + +
104A GLU* 2.8 57.0 + - - +
141B TRP* 4.2 19.1 - - + +
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Residues in contact with GLN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO 2.9 18.1 + - - +
98A LYS* 3.7 8.7 - - - +
99A ILE 3.3 0.2 - - - -
100A ILE* 1.3 71.8 - - - +
102A ASP* 1.3 69.5 + - - +
104A GLU* 3.0 19.2 + - - +
105A THR* 3.0 37.3 + - + +
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.8 12.8 - - + +
72A ARG* 3.0 51.3 + - - +
74A TRP* 5.3 1.7 + - - -
98A LYS 2.9 16.3 + - - +
99A ILE* 3.1 14.6 - - - +
101A GLN* 1.3 72.1 - - - +
103A ILE* 1.3 63.8 + - - +
105A THR* 2.7 26.6 + - - -
106A ILE* 3.0 19.8 + - - +
407A LEU* 4.1 0.5 - - - +
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.0 26.2 - - + -
65A TRP* 3.4 42.0 - - + +
68A LEU* 3.6 18.8 - - + -
99A ILE* 2.8 25.3 + - + +
100A ILE* 3.4 13.7 - - + +
102A ASP* 1.3 72.4 - - - +
104A GLU* 1.3 65.2 + - + +
106A ILE* 3.1 13.1 + - - +
107A GLU* 3.1 37.0 + - - +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 2.8 43.9 + - - +
101A GLN* 3.0 19.4 + - - +
103A ILE* 1.3 76.3 - - + +
105A THR* 1.3 58.2 + - + +
107A GLU* 3.3 12.7 + - - +
108A SER* 2.9 28.1 + - - -
111A ARG* 4.6 3.7 + - - +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLN* 3.0 35.7 + - + +
102A ASP* 2.7 22.7 + - - -
104A GLU* 1.3 71.9 - - - +
106A ILE* 1.3 66.4 + - - +
108A SER* 3.3 8.1 + - - -
109A ASN* 3.0 34.8 + - - +
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Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.9 6.5 - - + -
68A LEU* 4.0 8.7 - - + -
102A ASP* 3.0 26.5 + - - +
103A ILE* 3.1 14.8 + - - +
105A THR* 1.3 76.8 + - - +
107A GLU* 1.3 66.6 + - + +
109A ASN* 2.9 16.0 + - - +
110A TRP* 3.1 25.0 + - + +
342A ARG* 5.7 0.7 - - - +
389A GLU 3.8 21.8 - - - +
390A PHE* 4.0 21.5 - - + -
406A PHE* 4.0 17.9 - - + +
407A LEU* 3.6 32.8 - - + +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.5 1.0 - - - +
103A ILE* 3.1 33.5 + - - +
104A GLU* 3.7 13.3 - - - +
106A ILE* 1.3 76.9 - - + +
108A SER* 1.3 57.7 + - - +
110A TRP* 3.2 10.5 + - - +
111A ARG* 2.9 53.9 + - - +
341A LYS* 2.9 35.8 + - - -
342A ARG* 4.5 16.3 + - - +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLU 2.9 16.8 + - - -
105A THR* 3.5 11.2 - - - -
106A ILE 3.1 0.2 - - - -
107A GLU* 1.3 76.0 - - - +
109A ASN* 1.3 53.4 + - - +
111A ARG* 3.2 21.8 + - - +
112A CYS* 2.8 47.1 + - - -
114A ARG* 3.2 19.2 + - - -
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Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR* 3.0 26.2 + - - +
106A ILE* 2.9 11.2 + - - +
108A SER* 1.3 73.2 - - - +
110A TRP* 1.3 55.7 + - - +
113A GLY* 2.7 30.1 + - - -
114A ARG* 2.9 49.5 + - - +
406A PHE* 2.6 32.8 + - + +
407A LEU 4.6 3.6 + - - -
409A VAL* 3.4 21.5 - - - +
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Residues in contact with TRP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 3.1 32.4 + - + +
107A GLU* 3.2 6.7 + - - +
109A ASN* 1.3 76.3 - - - +
111A ARG* 1.3 61.2 + - + +
113A GLY* 3.3 12.1 + - - -
342A ARG* 3.6 52.5 - - - +
344A VAL* 4.6 1.8 - - + -
354A VAL* 4.0 19.5 - - + +
372A LEU* 5.2 3.4 - - + +
373A ARG* 3.9 14.2 - - - +
387A PHE* 3.8 11.7 - + - -
388A ASP 3.4 25.6 - - - -
389A GLU 3.1 18.9 + - - -
391A GLN 3.8 9.4 - - - -
392A ILE* 3.7 37.7 - - + -
406A PHE* 3.6 45.5 - + + +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU 4.6 2.8 + - - -
107A GLU* 2.9 43.6 + - - +
108A SER* 3.6 26.0 + - - +
110A TRP* 1.3 75.3 - - + +
112A CYS* 1.3 63.2 + - - +
342A ARG* 6.3 0.9 - - - +
372A LEU* 3.5 37.6 - - + +
373A ARG* 3.3 22.3 + - - -
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Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A SER* 2.8 33.7 + - - +
109A ASN 4.5 0.2 - - - +
111A ARG* 1.3 80.9 - - - +
113A GLY* 1.3 65.0 + - - +
114A ARG* 3.2 29.6 + - + +
373A ARG* 3.4 24.1 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN 2.7 12.7 + - - -
110A TRP 3.3 8.2 + - - -
111A ARG 3.3 0.6 - - - -
112A CYS* 1.3 78.3 - - - +
114A ARG* 1.3 57.2 + - - -
115A HIS* 3.3 20.8 + - - -
373A ARG* 3.6 22.6 + - - +
375A LEU* 4.6 4.8 - - - +
406A PHE* 4.3 7.4 - - - -
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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) + - + + + + + -
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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