Contacts of the helix formed by residues 101 - 136 (chain A) in PDB entry 2KSB
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 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 3.4 25.4 - - - -
98A TRP* 2.5 35.8 + - - -
99A TYR 3.3 4.2 - - - -
100A TYR* 1.3 78.8 - - - +
102A LEU* 1.4 61.0 + - - -
103A PHE 3.3 2.5 - - - -
104A TYR 2.9 10.4 + - - -
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Residues in contact with LEU 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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19A THR* 3.6 21.0 - - + +
98A TRP* 5.2 2.0 - - + -
101A GLY* 1.4 66.5 - - - -
103A PHE* 1.3 68.8 + - + +
105A CYS* 3.1 19.7 + - + +
106A LYS* 3.1 12.3 + - - +
172A GLU* 5.9 4.7 - - - +
371B PHE 4.9 2.5 - - - +
372B PHE* 2.7 59.9 - - + -
374B LEU* 5.6 3.8 - - + -
375B MET* 4.2 27.3 - - + +
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Residues in contact with PHE 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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100A TYR 5.5 0.2 - - - +
101A GLY 3.2 0.8 + - - -
102A LEU* 1.3 80.4 - - + +
104A TYR* 1.3 69.4 + - + +
106A LYS* 3.0 17.9 + - - +
107A PHE* 2.9 49.4 + + + -
374B LEU* 3.3 33.4 - - + -
375B MET* 4.2 15.0 - - + -
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Residues in contact with TYR 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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98A TRP* 2.9 2.2 - - + -
100A TYR* 2.9 62.4 - + + -
101A GLY 2.9 2.8 + - - +
103A PHE* 1.3 83.9 - - + +
105A CYS* 1.4 53.8 + - - +
107A PHE* 3.9 21.5 - + + -
108A HIS* 2.6 63.4 + + - +
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Residues in contact with CYS 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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98A TRP* 2.7 39.5 - - + +
101A GLY 3.0 0.4 + - - -
102A LEU* 3.1 15.4 + - + +
104A TYR* 1.4 74.4 - - - +
106A LYS* 1.3 54.7 + - - +
109A ASN* 2.7 33.0 + - - +
171A THR* 5.9 1.1 - - - -
172A GLU* 3.7 23.6 - - - -
173A THR* 4.0 3.6 - - + -
180A CYS* 2.0 47.0 - - - +
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Residues in contact with LYS 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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102A LEU 3.1 6.3 + - - +
103A PHE* 3.0 20.9 + - - +
104A TYR 3.0 0.2 - - - -
105A CYS* 1.3 77.9 - - - +
107A PHE* 1.3 81.7 + - - +
109A ASN* 3.3 3.9 + - - +
110A PHE* 2.9 28.8 + - + +
163A PHE* 6.0 4.2 - - - -
165A GLN* 5.3 2.5 - - + +
166A GLY* 4.0 35.4 + - - +
171A THR* 6.0 6.3 - - + -
375B MET* 4.2 26.0 - - - +
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Residues in contact with PHE 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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103A PHE* 2.9 56.2 + + + -
104A TYR* 3.0 27.3 + + + +
106A LYS* 1.3 91.6 - - + +
108A HIS* 1.3 69.7 + - + +
110A PHE* 3.2 3.2 + - - +
111A PHE* 3.2 45.6 + + + -
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Residues in contact with HIS 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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84A PHE 4.9 3.4 - - - -
85A ASN* 5.6 3.4 - - - -
88A VAL* 2.8 50.6 - - + +
89A ASN* 5.2 7.9 - - - +
98A TRP* 2.9 22.8 - + + -
100A TYR* 4.5 5.4 - + - -
104A TYR* 2.6 59.2 + + + +
105A CYS 4.0 1.6 - - - +
107A PHE* 1.3 78.7 - - + +
109A ASN* 1.3 55.9 + - - +
111A PHE* 5.5 1.1 - + - -
112A PRO* 2.8 36.0 - - + +
180A CYS* 4.7 7.0 - - + +
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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 CYS* 2.7 23.5 + - - +
106A LYS* 4.0 4.3 - - - +
108A HIS* 1.3 75.8 - - - +
110A PHE* 1.4 64.0 + - - +
112A PRO* 3.8 1.2 - - - +
113A ILE* 2.9 23.3 + - - +
165A GLN* 2.7 36.5 + - - +
171A THR* 5.7 0.7 - - - -
172A GLU 5.5 1.2 + - - +
180A CYS* 2.7 36.3 + - + +
181A MET* 3.2 32.7 - - - +
182A ILE 3.7 0.2 + - - -
291A MET* 5.2 0.2 - - - +
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Residues in contact with PHE 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 LYS* 2.9 23.0 + - + +
107A PHE* 3.2 4.9 + - + +
109A ASN* 1.4 77.7 - - - +
111A PHE* 1.3 92.9 + + + +
113A ILE* 2.7 26.8 - - - +
114A ALA* 2.9 12.0 + - + +
159A LEU* 3.0 30.1 - - + -
162A ALA* 2.9 52.3 - - + +
163A PHE* 3.1 27.8 - + - -
165A GLN* 5.0 2.0 - - - -
166A GLY* 5.9 1.6 - - - -
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Residues in contact with PHE 111 (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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80A SER* 4.9 16.8 + - - +
84A PHE* 5.0 24.7 - + + -
107A PHE* 3.2 37.4 + + + +
108A HIS* 5.5 0.9 - + - -
110A PHE* 1.3 101.1 - + - +
112A PRO* 1.3 77.2 - - + +
114A ALA* 3.2 6.8 + - + +
115A ALA* 3.0 21.3 + - - +
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Residues in contact with PRO 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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81A MET* 5.7 1.6 - - + +
85A ASN* 3.0 42.0 - - + +
89A ASN* 5.4 3.8 - - - +
108A HIS* 2.8 32.1 - - + +
109A ASN* 3.4 3.1 - - - +
111A PHE* 1.3 93.8 - - + +
113A ILE* 1.3 61.5 + - - +
115A ALA* 3.3 7.7 + - + +
116A VAL* 3.2 28.6 + - + +
179A VAL* 6.0 1.3 - - + -
180A CYS 5.5 0.7 - - - +
181A MET* 5.9 1.1 - - - -
291A MET* 5.2 10.8 - - + -
295A MET* 5.1 10.8 - - + -
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Residues in contact with ILE 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* 2.9 21.9 + - - +
110A PHE* 2.7 28.0 - - - +
112A PRO* 1.3 73.7 - - - +
114A ALA* 1.3 66.9 + - - +
116A VAL* 3.2 10.2 + - + +
117A PHE* 2.9 65.1 + - + -
162A ALA* 3.1 26.7 - - + +
165A GLN* 4.5 10.8 - - - +
181A MET* 3.7 36.8 - - + -
182A ILE* 5.5 4.5 - - + +
200A VAL* 5.9 0.9 - - + -
268A PHE* 5.7 2.7 - - + -
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Residues in contact with ALA 114 (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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110A PHE* 2.9 20.5 + - + +
111A PHE* 3.6 11.4 - - + +
113A ILE* 1.3 82.3 - - - +
115A ALA* 1.3 62.3 + - - +
117A PHE* 3.9 4.6 - - - +
118A ALA* 2.9 27.3 + - - +
155A TRP* 4.8 15.5 - - + -
158A ALA* 4.0 8.1 - - + +
159A LEU* 5.2 4.7 - - + -
162A ALA* 3.8 17.9 - - + -
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Residues in contact with ALA 115 (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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77A ALA* 4.2 26.7 - - + +
80A SER* 5.5 4.5 - - - -
81A MET* 4.8 16.2 - - + +
85A ASN* 5.0 4.5 - - - +
111A PHE 3.0 12.7 + - - +
112A PRO* 3.6 12.3 - - + +
113A ILE 3.1 0.2 - - - -
114A ALA* 1.3 78.1 - - - +
116A VAL* 1.3 62.0 + - - +
118A ALA* 3.4 5.4 + - - +
119A SER* 3.1 27.0 + - - -
155A TRP* 5.6 3.8 - - - -
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Residues in contact with VAL 116 (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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81A MET* 5.3 3.8 - - + -
112A PRO* 3.2 16.2 - - + +
113A ILE* 3.2 13.6 + - + +
115A ALA* 1.3 73.3 - - + +
117A PHE* 1.3 74.4 + - + +
119A SER* 3.3 13.0 + - - -
120A ILE* 3.3 12.7 + - + +
181A MET* 6.1 2.2 - - - -
205A TYR* 5.7 1.1 - - + -
257A PHE* 4.3 4.3 - - + -
261A TRP* 3.0 63.9 - - + +
265A HIS* 4.4 15.7 - - + +
291A MET* 6.4 0.7 - - + -
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Residues in contact with PHE 117 (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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113A ILE* 2.9 60.0 + - + +
114A ALA* 3.9 3.8 - - - +
116A VAL* 1.3 81.0 - - + +
118A ALA* 1.3 63.5 + - - +
120A ILE* 3.1 2.6 - - - +
121A TYR* 3.0 29.3 + - + -
154A ILE* 4.6 0.2 - - - -
158A ALA* 3.6 27.4 - - + -
161A LEU* 3.5 24.0 - - + -
162A ALA* 3.5 11.0 - - - -
200A VAL* 3.8 12.3 - - + -
204A ILE* 2.9 57.9 - - + -
265A HIS* 5.9 4.7 - + - -
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Residues in contact with ALA 118 (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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73A ASN* 4.8 3.7 + - - +
77A ALA* 4.9 5.4 - - + -
114A ALA 2.9 19.3 + - - +
115A ALA* 3.7 5.8 - - - +
117A PHE* 1.3 78.0 - - - +
119A SER* 1.3 57.0 + - - +
122A SER* 2.8 31.6 + - - -
154A ILE* 3.3 23.4 - - + +
155A TRP* 4.6 25.8 - - + -
158A ALA* 4.1 7.2 - - + +
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Residues in contact with SER 119 (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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74A LEU* 5.3 7.8 - - - +
77A ALA* 4.0 6.5 - - - +
78A GLU* 3.8 18.5 + - - -
115A ALA* 3.1 15.8 + - - +
116A VAL* 3.7 9.7 - - - -
117A PHE 3.2 0.4 - - - -
118A ALA* 1.3 74.3 - - - +
120A ILE* 1.3 66.3 + - - +
122A SER* 3.0 6.9 + - - -
123A MET* 2.9 29.4 + - - +
257A PHE* 3.7 19.5 - - - -
261A TRP* 5.6 0.7 - - - -
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Residues in contact with ILE 120 (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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116A VAL* 3.3 5.1 + - + +
117A PHE 3.1 12.6 - - - +
119A SER* 1.3 77.3 - - - +
121A TYR* 1.3 70.5 + - + +
123A MET* 3.1 5.7 + - - +
124A THR* 3.1 15.1 + - - +
204A ILE* 3.6 29.4 - - + +
205A TYR* 4.4 18.2 - - + +
208A PRO* 3.4 24.5 - - + -
209A LEU* 3.9 4.0 - - + +
212A ILE* 3.0 27.6 - - + -
257A PHE* 3.5 34.1 - - + -
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Residues in contact with TYR 121 (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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117A PHE* 3.0 21.7 + - + -
120A ILE* 1.3 85.0 - - + +
122A SER* 1.3 59.1 + - - +
124A THR* 2.6 29.6 + - - -
125A ALA* 3.2 5.7 + - - +
154A ILE* 2.9 37.2 - - + +
157A LEU* 4.3 30.6 - - + +
158A ALA* 5.7 1.3 - - - -
203A LEU* 3.0 23.9 + - - +
204A ILE* 2.9 40.1 - - + +
207A LEU* 5.7 1.7 - - + +
208A PRO* 3.2 17.5 - - + +
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Residues in contact with SER 122 (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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70A PHE* 3.8 13.5 + - - +
73A ASN* 3.9 18.2 + - - +
74A LEU* 2.9 32.4 - - - +
118A ALA 2.8 19.3 + - - -
119A SER* 3.0 5.4 + - - -
121A TYR* 1.3 76.8 - - - +
123A MET* 1.3 61.9 + - - +
125A ALA* 3.0 9.7 + - - +
126A VAL* 3.0 22.9 + - - +
151A ILE* 4.9 1.0 - - - +
154A ILE* 3.9 5.6 - - - +
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Residues in contact with MET 123 (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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71A LEU* 6.2 0.2 - - + -
74A LEU* 3.1 33.2 - - + -
119A SER* 2.9 20.5 + - - +
120A ILE* 3.1 11.2 + - - +
122A SER* 1.3 76.5 - - - +
124A THR* 1.3 62.4 + - - +
126A VAL* 3.3 25.6 + - + +
127A ALA* 3.0 20.8 + - - +
212A ILE* 3.8 15.9 - - + +
250A MET 5.3 0.4 - - - +
253A VAL* 3.5 32.8 - - + +
254A VAL* 4.3 21.8 - - + +
257A PHE* 4.9 16.6 - - + -
300A TYR* 5.9 0.2 - - - -
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Residues in contact with THR 124 (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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120A ILE 3.1 10.9 + - - +
121A TYR* 2.6 23.8 + - + +
123A MET* 1.3 73.7 - - - +
125A ALA* 1.3 66.1 + - - +
127A ALA* 2.9 13.5 + - - +
128A PHE* 2.9 14.4 + - - +
208A PRO* 3.2 24.2 - - + +
211A VAL* 3.6 17.1 - - + +
212A ILE* 3.0 35.0 - - + -
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Residues in contact with ALA 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 4.3 24.4 - - + -
121A TYR 3.2 6.0 + - - +
122A SER* 3.0 12.4 + - - +
124A THR* 1.3 81.3 + - - +
126A VAL* 1.3 58.5 + - - +
128A PHE* 3.1 8.1 + - - +
129A ASP* 2.8 31.8 + - - +
150A VAL* 4.6 13.7 - - + -
151A ILE* 6.1 0.7 - - + -
154A ILE* 6.4 1.3 - - + -
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Residues in contact with VAL 126 (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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67A THR* 4.9 2.0 - - + -
70A PHE* 4.0 24.0 - - + -
71A LEU* 5.1 5.8 - - + -
74A LEU* 4.7 1.6 - - + -
122A SER* 3.0 16.3 + - - +
123A MET* 3.4 28.9 - - + +
125A ALA* 1.3 75.8 - - - +
127A ALA* 1.3 57.6 + - - +
129A ASP* 2.6 33.9 - - - +
130A ARG* 2.9 9.8 + - + +
250A MET* 3.1 45.3 - - + -
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Residues in contact with ALA 127 (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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123A MET 3.0 11.7 + - - +
124A THR 2.9 10.8 + - - +
126A VAL* 1.3 77.5 - - - +
128A PHE* 1.3 63.7 + - - +
130A ARG* 3.1 9.4 + - - +
131A TYR* 2.9 21.0 + - - +
211A VAL* 6.5 0.2 - - + -
212A ILE* 4.2 23.3 - - + +
215A ALA* 3.8 23.3 - - + +
216A TYR* 5.2 1.6 - - - +
219A VAL* 5.0 2.3 - - - +
254A VAL* 6.3 0.7 - - + -
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Residues in contact with PHE 128 (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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124A THR 2.9 11.0 + - - +
125A ALA* 3.6 9.9 - - - +
127A ALA* 1.3 75.8 - - - +
129A ASP* 1.3 59.9 + - - +
131A TYR* 3.0 15.0 + + + +
132A MET* 2.8 74.0 + - + +
215A ALA* 4.6 7.2 - - + +
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Residues in contact with ASP 129 (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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66A VAL* 5.2 8.5 - - + -
67A THR* 4.1 6.8 + - - -
70A PHE* 3.7 29.6 - - + -
125A ALA 2.8 11.7 + - - +
126A VAL* 2.6 43.4 + - - +
128A PHE* 1.3 78.7 - - - +
130A ARG* 1.3 88.8 + - - +
132A MET* 3.2 9.4 + - - +
133A ALA* 2.8 29.8 + - - +
142A LEU* 6.4 1.8 - - + -
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Residues in contact with ARG 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 6.2 0.8 - - - +
67A THR* 3.2 11.7 + - - -
126A VAL* 2.9 8.8 + - + +
127A ALA* 3.1 11.6 + - - +
129A ASP* 1.3 94.9 + - - +
131A TYR* 1.3 63.0 + - - +
133A ALA* 3.2 29.0 + - - +
134A ILE* 2.9 34.3 + - + +
219A VAL* 4.7 7.4 - - + -
243A LYS* 5.1 17.3 + - - +
246A VAL* 3.8 8.8 - - - +
247A VAL* 3.7 38.0 - - + +
250A MET* 2.9 60.3 - - + +
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Residues in contact with TYR 131 (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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127A ALA 2.9 13.5 + - - +
128A PHE* 3.0 21.5 + + + +
130A ARG* 1.3 77.5 - - - +
132A MET* 1.3 86.4 + - + +
134A ILE* 3.3 3.3 + - + +
135A ILE* 2.7 64.7 + - + +
215A ALA* 5.0 3.8 - - + -
218A VAL* 2.9 54.7 - - + +
219A VAL* 4.2 9.9 - - + -
222A THR* 5.8 0.7 - - + -
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Residues in contact with MET 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 2.8 53.6 + - + +
129A ASP* 3.2 9.8 + - - +
131A TYR* 1.3 119.2 - - + +
133A ALA* 1.3 55.9 + - - +
135A ILE* 2.7 33.1 - - + +
136A HIS* 2.8 49.2 + - + +
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Residues in contact with ALA 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASP 2.8 11.9 + - - +
130A ARG* 3.2 33.0 + - - +
132A MET* 1.3 76.9 - - - +
134A ILE* 1.3 65.9 + - + +
136A HIS 3.9 14.1 - - - -
137A PRO* 3.9 9.2 - - - +
243A LYS* 6.1 4.5 - - + -
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Residues in contact with ILE 134 (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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130A ARG* 2.9 29.6 + - + +
131A TYR* 3.8 3.6 - - + +
133A ALA* 1.3 82.6 - - + +
135A ILE* 1.4 64.3 + - + +
137A PRO* 3.9 4.9 - - - +
219A VAL* 3.0 44.2 - - + -
222A THR* 2.9 46.0 - - + +
223A LEU* 4.0 30.5 - - + +
247A VAL* 5.0 5.2 - - + -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 2.7 69.6 + - + +
132A MET* 2.7 41.3 - - + +
134A ILE* 1.4 77.1 - - + +
136A HIS* 1.3 83.6 + - + +
137A PRO* 2.8 11.3 - - - +
222A THR* 4.6 15.7 - - + -
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Residues in contact with HIS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MET* 2.8 66.1 + - + +
133A ALA* 3.9 3.2 - - - +
135A ILE* 1.3 101.2 - - + +
137A PRO* 1.3 65.4 - - - +
138A LEU* 3.0 10.9 + - + +
141A ARG* 2.9 62.2 + - + +
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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