Contacts of the helix formed by residues 100 - 124 (chain A) in PDB entry 3V3Q
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 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU 3.8 1.0 + - - -
99A LEU* 1.3 74.8 - - - +
101A PRO* 1.3 70.9 - - - +
102A ALA 3.7 0.2 + - - -
103A ASP* 2.8 39.5 + - - +
104A GLN* 2.9 11.4 + - - +
188A GLN* 2.6 33.3 + - - -
189A GLU* 4.3 11.3 + - - -
192A ARG* 4.3 6.3 - - - +
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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
----------------------------------------------------------
99A LEU 3.6 2.7 - - - +
100A SER* 1.3 85.8 - - - +
102A ALA* 1.3 63.2 + - - +
104A GLN* 3.3 11.9 + - + +
105A ASP* 3.0 31.9 + - - +
188A GLN* 5.5 0.4 - - - +
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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
----------------------------------------------------------
100A SER* 3.2 1.2 + - - -
101A PRO* 1.3 80.2 - - - +
103A ASP* 1.3 59.5 + - - +
105A ASP* 3.5 8.4 + - - +
106A LEU* 3.0 29.5 + - - +
188A GLN* 3.9 24.7 - - + +
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 4.3 10.0 - - + +
100A SER* 2.8 34.0 + - - +
102A ALA* 1.3 74.9 - - - +
104A GLN* 1.3 59.1 + - - +
106A LEU* 3.3 3.7 + - - +
107A LEU* 3.0 36.5 + - - +
186A GLY 4.3 1.4 - - - +
187A LEU* 3.6 21.1 - - + +
188A GLN* 2.7 29.6 + - - +
189A GLU* 2.8 35.7 + - - +
193A VAL* 4.9 4.3 - - + +
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Residues in contact with GLN 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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91A GLU* 4.9 6.4 - - - +
96A PHE* 3.5 50.7 - - + +
97A ALA* 3.0 28.0 + - - +
99A LEU* 2.7 27.2 + - + +
100A SER 2.9 12.0 + - - +
101A PRO* 3.6 13.1 - - + +
103A ASP* 1.3 75.9 - - - +
105A ASP* 1.3 64.2 + - - +
106A LEU 3.3 0.2 + - - -
107A LEU 3.4 0.2 + - - -
108A LEU* 3.1 33.2 + - + +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.9 18.6 + - - +
101A PRO* 3.0 20.3 + - - +
102A ALA* 3.6 12.0 - - - +
104A GLN* 1.3 76.0 - - - +
106A LEU* 1.3 58.0 + - - +
108A LEU* 3.5 5.7 - - - +
109A GLU* 2.7 56.0 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 3.0 17.3 + - - +
103A ASP* 3.9 3.8 - - - +
105A ASP* 1.3 76.8 - - - +
107A LEU* 1.3 57.8 + - - +
109A GLU* 4.1 8.2 - - + +
110A SER* 2.5 54.1 + - - +
184A ARG* 4.1 10.5 - - + -
185A HIS 3.8 15.0 - - - +
186A GLY* 3.7 10.3 - - - +
187A LEU* 3.7 41.7 - - + +
263A ASP* 6.1 0.7 - - - +
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Residues in contact with LEU 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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96A PHE* 3.7 27.4 - - + -
99A LEU* 4.0 19.3 - - + -
103A ASP 3.0 20.0 + - - +
104A GLN 3.9 3.1 - - - +
105A ASP 3.3 0.2 - - - -
106A LEU* 1.3 76.9 - - - +
108A LEU* 1.3 56.4 + - - +
110A SER* 3.8 3.8 - - - -
111A ALA* 3.0 31.5 + - - +
180A LEU* 3.5 24.0 - - + +
181A ILE* 4.6 5.2 - - + -
182A THR 3.3 27.1 - - - +
184A ARG* 3.9 14.3 + - + -
187A LEU* 4.1 11.9 - - + -
193A VAL* 4.1 20.0 - - + -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.7 9.7 - - + +
86A ILE* 4.2 18.2 - - + +
87A ARG* 3.9 45.1 - - + +
90A ALA* 3.5 28.5 - - + -
96A PHE* 4.0 12.8 - - + -
104A GLN* 3.1 27.9 + - + +
105A ASP* 3.5 5.4 - - - +
107A LEU* 1.3 73.3 - - - +
109A GLU* 1.3 60.7 + - + +
111A ALA* 3.3 0.5 + - - +
112A PHE* 2.8 34.3 + - - +
115A LEU* 5.2 0.9 - - - +
180A LEU* 3.8 16.1 - - + +
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Residues in contact with GLU 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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83A LEU* 5.8 0.4 - - + -
87A ARG* 5.1 7.3 + - - +
105A ASP* 2.7 44.7 + - - +
106A LEU* 4.1 6.9 - - + +
108A LEU* 1.3 74.8 - - + +
110A SER* 1.3 58.6 + - - +
256A ILE* 4.3 13.1 - - + +
259A LYS* 2.9 40.6 + - - +
260A ILE* 3.6 39.9 - - + +
263A ASP* 3.9 6.5 - - + +
301A TMY 2.9 26.3 - - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 2.5 41.5 + - - +
107A LEU 3.9 0.9 - - - -
109A GLU* 1.3 79.0 - - - +
111A ALA* 1.3 58.1 + - - +
184A ARG* 3.5 38.1 + - - +
301A TMY 2.9 30.8 + - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 3.0 16.5 + - - +
108A LEU 4.3 0.2 - - - +
110A SER* 1.3 76.9 - - - +
112A PHE* 1.3 67.7 + - - +
113A LEU 3.3 2.5 - - - -
114A GLU* 3.1 4.7 + - - +
115A LEU* 2.8 43.1 + - + +
179A VAL* 3.9 15.7 - - + +
180A LEU* 4.0 4.9 - - - -
184A ARG* 3.8 12.8 - - - +
301A TMY 3.3 9.2 - - - -
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Residues in contact with PHE 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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79A LEU* 3.2 33.2 - - + -
82A SER* 3.4 23.3 - - - -
83A LEU* 3.5 34.8 - - + -
86A ILE* 4.0 9.2 - - + -
108A LEU 2.8 18.0 + - - +
109A GLU 4.0 2.7 - - - +
111A ALA* 1.3 75.8 - - - +
113A LEU* 1.3 75.7 + - + +
115A LEU* 3.0 7.7 + - - +
116A PHE* 2.7 48.0 + + + +
257A ILE* 3.8 17.3 - - + -
260A ILE* 4.1 18.8 - - + -
301A TMY 3.3 15.9 + - - -
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Residues in contact with LEU 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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79A LEU* 5.1 3.1 - - + -
112A PHE* 1.3 89.3 - - + +
114A GLU* 1.3 63.9 + - - +
116A PHE* 3.4 5.1 + - + +
117A ILE* 3.0 38.3 + - + +
151A TRP* 4.2 23.6 - - + -
235A CYS* 4.1 14.1 - - - +
238A GLY* 4.6 1.1 - - - -
239A LEU* 3.9 37.2 - - + +
242A ILE* 4.9 15.0 - - + -
260A ILE* 5.3 0.9 - - + -
301A TMY 2.4 54.1 - - + -
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Residues in contact with GLU 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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111A ALA 3.3 2.9 - - - +
113A LEU* 1.3 76.1 - - - +
115A LEU* 1.3 57.7 + - - +
117A ILE* 3.8 1.7 - - - +
118A LEU* 2.9 30.7 + - - +
179A VAL* 3.4 29.6 - - + +
184A ARG* 4.1 6.8 + - - -
228A LEU* 4.2 12.0 - - - +
231A LEU* 3.7 34.2 - - + +
232A ARG 5.7 0.2 + - - -
235A CYS* 3.9 9.8 - - - -
301A TMY 2.6 55.0 + - - +
303A GOL 5.8 0.9 - - - -
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Residues in contact with LEU 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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86A ILE* 3.7 35.4 - - + -
89A TRP* 3.8 17.3 - - + -
108A LEU 5.2 0.7 - - - +
111A ALA* 2.8 37.3 + - + +
112A PHE* 3.7 4.3 - - - +
114A GLU* 1.3 74.0 - - - +
116A PHE* 1.3 68.5 + - - +
118A LEU* 4.4 4.3 - - + +
119A ARG* 2.9 36.9 + - - +
176A SER* 3.4 36.1 - - - +
179A VAL* 3.8 15.3 - - + -
180A LEU* 4.1 10.5 - - + +
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Residues in contact with PHE 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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78A LEU 4.2 6.7 - - - -
79A LEU* 3.6 23.6 - - + -
82A SER* 3.3 38.6 - - - +
86A ILE* 4.0 3.0 - - - +
112A PHE* 2.7 32.8 + + + +
113A LEU* 3.7 6.1 - - + +
115A LEU* 1.3 73.7 - - - +
117A ILE* 1.3 69.9 + - + +
119A ARG* 4.3 2.1 - - - +
120A LEU* 3.1 54.5 + - + +
133A PHE* 4.5 13.0 - + - -
148A PHE* 4.2 14.8 - + - -
151A TRP* 3.6 33.2 - + - -
155A ILE* 4.6 4.5 - - + -
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Residues in contact with ILE 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 LEU* 3.0 29.7 + - + +
114A GLU 3.8 2.2 - - - +
116A PHE* 1.3 80.8 - - + +
118A LEU* 1.3 64.9 + - - +
120A LEU* 3.3 4.0 + - - +
121A ALA* 3.0 23.7 + - - +
151A TRP* 3.8 25.1 - - + +
155A ILE* 4.2 14.7 - - + +
158A PHE* 4.3 6.7 - - + -
231A LEU* 3.7 16.2 - - + -
234A LEU* 3.8 30.5 - - + +
235A CYS* 3.8 38.6 - - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU 2.9 22.5 + - - +
115A LEU* 3.9 4.7 - - + +
117A ILE* 1.3 72.8 - - - +
119A ARG* 1.3 63.3 + - + +
121A ALA* 3.6 1.7 + - - +
122A TYR* 3.1 23.9 + - - +
158A PHE* 4.0 22.0 - - + -
162A LEU* 3.9 23.7 - - + +
172A PHE* 3.8 17.3 - - + -
175A LEU* 5.0 3.6 - - + +
176A SER* 4.3 18.8 - - - +
179A VAL* 3.8 29.4 - - + -
231A LEU* 4.3 14.1 - - + +
303A GOL 5.3 4.9 - - - +
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Residues in contact with ARG 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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41A HIS* 4.3 8.3 + - - -
44A SER* 2.7 51.7 + - - -
82A SER* 5.7 0.2 + - - -
85A VAL* 3.6 13.1 + - - +
86A ILE* 3.8 27.2 - - - +
89A TRP* 4.3 17.9 - - - +
115A LEU* 2.9 32.7 + - - +
116A PHE* 4.4 2.0 - - - +
118A LEU* 1.3 76.9 - - + +
120A LEU* 1.3 62.1 + - - +
122A TYR* 3.4 1.4 + - - +
123A ARG* 3.2 47.0 + - - +
134A CYS* 4.3 1.2 - - - +
172A PHE* 4.1 22.2 - - + -
176A SER* 5.0 8.0 + - - -
302A TMY 4.5 0.5 + - - -
304A GOL 3.3 21.5 + - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 3.1 49.4 + - + +
117A ILE 3.3 2.9 + - - +
119A ARG* 1.3 75.1 - - - +
121A ALA* 1.3 64.3 + - - +
123A ARG* 3.5 10.6 + - - +
124A SER* 2.6 40.9 + - - +
131A LEU* 4.0 13.7 - - + -
132A ILE 3.2 29.4 - - - +
133A PHE* 3.7 29.4 - - + -
152A ILE* 4.4 3.8 - - + -
155A ILE* 4.1 22.4 - - + -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE 3.0 17.0 + - - +
118A LEU 3.9 3.1 - - - +
120A LEU* 1.3 77.3 - - - +
122A TYR* 1.3 64.1 + - - +
123A ARG 3.5 0.2 + - - -
124A SER* 3.6 1.7 + - - -
155A ILE* 4.1 11.6 - - + +
158A PHE* 3.6 28.7 - - + -
159A SER* 2.6 45.8 + - - +
162A LEU* 4.4 3.1 - - + +
163A HIS* 3.2 7.1 + - - -
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Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 4.4 6.1 - + - -
118A LEU 3.1 19.2 + - - +
119A ARG 3.4 3.8 + - - +
120A LEU 3.2 0.4 - - - -
121A ALA* 1.3 77.9 - - - +
123A ARG* 1.3 57.0 + - - +
162A LEU* 4.1 8.7 - - + -
163A HIS* 2.9 13.2 - - - -
167A VAL* 2.4 33.9 + - + -
168A ASP* 3.3 14.9 - - - -
169A VAL* 3.5 8.9 + - + +
172A PHE* 3.5 54.3 - + + -
302A TMY 2.8 101.2 - + + +
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 4.1 2.8 - - - +
119A ARG* 3.2 36.7 + - - +
120A LEU* 3.5 18.9 - - - +
122A TYR* 1.3 74.8 - - - +
124A SER* 1.3 61.8 + - - +
125A LYS* 2.9 18.4 + - - +
132A ILE* 2.9 49.3 + - + +
133A PHE* 3.6 17.2 - - - +
134A CYS* 3.6 18.4 - - - +
302A TMY 2.7 40.5 - - + +
304A GOL 2.9 44.3 + - - -
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 2.6 23.8 + - - +
121A ALA* 3.6 1.3 + - - -
122A TYR 3.5 1.8 - - - -
123A ARG* 1.3 77.0 - - - +
125A LYS* 1.3 73.5 + - - +
126A PRO* 3.6 2.9 - - - -
130A LYS 3.2 11.0 - - - -
131A LEU* 3.4 18.2 - - - +
132A ILE* 3.3 24.3 + - - -
156A LEU* 4.3 4.9 - - - -
159A SER* 4.0 12.1 - - - -
163A HIS* 2.9 22.3 + - - -
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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