Contacts of the helix formed by residues 114 - 139 (chain A) in PDB entry 1RP1
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 TYR 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR 3.7 1.2 + - - -
113A SER* 1.3 69.1 - - - +
115A THR* 1.3 63.0 + - + +
117A ALA* 3.1 3.1 + - + +
118A ALA* 2.8 35.8 + - + +
153A LEU* 4.0 19.7 - - + -
178A VAL* 3.6 24.8 - - + +
180A ALA* 2.7 46.2 + - + +
181A SER* 3.6 15.9 - - - -
182A PHE* 3.9 2.8 - - - -
248A LEU* 3.9 31.6 - - + -
249A ASP* 3.0 19.4 + - - +
252A TRP* 3.3 45.5 - + + +
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Residues in contact with THR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 6.4 1.6 - - - -
24A PRO* 6.2 3.6 - - + -
25A LEU* 4.4 22.7 - - + +
27A VAL* 4.5 17.5 - - - +
113A SER* 4.0 9.7 + - - -
114A TYR* 1.3 79.5 + - + +
116A GLN* 1.3 57.3 + - - +
118A ALA* 3.4 6.0 + - - +
119A ASN* 2.8 41.6 + - - +
181A SER* 4.8 11.7 - - - +
249A ASP* 4.3 5.6 + - - +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.1 25.3 - - + +
28A LEU 3.0 23.8 + - - +
29A PRO* 4.0 0.4 - - - +
30A TRP* 3.2 39.7 + - + +
112A THR* 3.9 13.0 - - + +
113A SER* 3.3 21.9 + - - +
114A TYR 3.1 0.2 - - - -
115A THR* 1.3 77.4 + - - +
117A ALA* 1.3 61.5 + - - +
119A ASN* 3.4 1.9 + - - +
120A ASN* 2.9 58.4 + - - +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 4.0 5.0 - - - -
109A GLY 3.8 15.3 - - - +
110A SER* 3.5 25.6 - - - +
112A THR* 3.9 2.0 - - + +
113A SER 2.9 18.2 + - - +
114A TYR* 3.7 7.4 - - - +
116A GLN* 1.3 76.1 - - - +
118A ALA* 1.3 62.5 + - - +
120A ASN* 3.3 10.4 + - - +
121A VAL* 3.4 15.8 + - - +
153A LEU* 3.8 18.4 - - + -
252A TRP* 4.8 2.2 - - + -
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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
----------------------------------------------------------
23A ARG* 4.6 6.4 + - - +
114A TYR* 2.8 23.7 + - + +
115A THR* 3.5 9.2 - - - +
117A ALA* 1.3 77.8 - - - +
119A ASN* 1.3 60.6 + - - +
121A VAL* 3.2 21.7 - - - +
122A ARG* 4.4 2.3 + - - +
153A LEU* 4.1 13.6 - - - +
181A SER* 4.4 15.5 - - - -
182A PHE* 3.7 26.5 - - + -
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TRP 4.0 7.4 + - - +
23A ARG* 3.0 25.0 + - - +
25A LEU 5.1 3.0 + - - -
27A VAL* 3.3 28.7 + - - +
28A LEU 4.5 1.3 - - - -
29A PRO* 3.6 17.6 - - + +
115A THR* 2.8 34.0 + - - +
116A GLN* 4.0 5.4 - - - +
118A ALA* 1.3 74.7 - - - +
120A ASN* 1.3 63.3 + - - +
121A VAL 3.0 4.9 - - - -
122A ARG* 3.0 50.2 + - - +
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 3.5 5.1 - - - +
30A TRP* 2.8 57.7 + - - -
34A ILE* 4.1 9.8 - - + +
106A TRP* 4.3 5.4 - - + -
109A GLY* 2.8 27.0 + - - +
112A THR* 4.3 0.2 - - - +
116A GLN* 2.9 36.8 + - - +
117A ALA 3.3 7.1 + - - +
119A ASN* 1.3 76.2 - - - +
121A VAL* 1.3 61.1 + - - +
122A ARG 3.1 0.4 - - - -
123A VAL* 3.2 6.6 + - - +
124A VAL* 3.2 25.1 + - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 3.9 4.2 - - + -
117A ALA 3.4 14.1 + - - +
118A ALA 3.2 14.6 - - - +
120A ASN* 1.3 75.8 - - - +
122A ARG* 1.3 64.3 + - + +
124A VAL* 3.4 2.7 + - - +
125A GLY* 2.9 29.3 + - - -
153A LEU* 3.7 29.4 - - + +
156A HIS* 3.7 15.9 - - + +
157A VAL* 3.6 42.0 - - + +
160A GLU* 4.3 6.1 - - + +
182A PHE* 4.5 7.0 - - + -
189A VAL 5.5 0.2 - - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.7 36.0 - - + +
12A SER 3.0 32.5 + - - +
13A ASP* 4.6 1.0 - - - +
17A TRP* 3.3 51.0 + - + +
23A ARG* 4.9 2.0 - - - +
27A VAL 3.8 11.5 + - - -
28A LEU* 4.5 0.8 - - - +
29A PRO* 3.8 19.3 - - + +
118A ALA 4.7 2.5 - - - +
119A ASN* 3.0 44.6 + - - +
121A VAL* 1.3 79.2 - - + +
123A VAL* 1.3 55.9 + - - +
125A GLY* 3.9 1.0 - - - -
126A ALA* 3.1 26.7 + - - +
160A GLU* 3.6 24.6 - - + +
164A ARG* 4.3 3.7 + - - +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.9 6.5 - - + -
8A ILE* 3.9 14.5 - - + +
11A PHE* 3.9 28.0 - - + -
29A PRO* 3.3 28.5 - - + -
30A TRP 3.6 8.7 - - - +
31A PRO* 4.1 12.8 - - + -
34A ILE* 3.6 21.3 - - + -
120A ASN 3.2 8.5 + - - +
122A ARG* 1.3 74.7 - - - +
124A VAL* 1.3 66.6 + - - +
126A ALA* 3.0 3.3 + - - +
127A GLN* 2.9 36.2 + - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 4.0 14.1 - - + -
36A THR* 4.1 10.5 - - + +
104A VAL* 4.1 20.0 - - + -
106A TRP* 3.8 46.9 - - + -
120A ASN 3.2 15.6 + - - +
121A VAL* 3.9 3.1 - - - +
123A VAL* 1.3 76.0 - - - +
125A GLY* 1.3 58.6 + - - +
127A GLN* 3.1 10.0 + - - +
128A VAL* 3.0 26.7 + - + +
157A VAL* 3.6 22.7 - - + -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL 2.9 15.0 + - - -
124A VAL* 1.3 76.7 - - - +
126A ALA* 1.3 57.2 + - - +
128A VAL* 3.4 2.6 + - - -
129A ALA* 2.9 23.9 + - - +
157A VAL* 3.4 29.5 - - - +
160A GLU* 3.8 8.1 - - - -
161A ALA* 3.4 17.1 - - - +
164A ARG* 4.5 0.7 - - - -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.8 18.2 - - + +
11A PHE* 3.8 22.2 - - + -
122A ARG 3.1 14.0 + - - +
123A VAL* 3.0 8.9 + - - +
125A GLY* 1.3 75.8 - - - +
127A GLN* 1.3 58.1 + - - +
129A ALA* 3.4 2.8 + - - +
130A GLN* 2.9 27.2 + - - +
164A ARG* 3.8 26.2 - - - +
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.1 16.6 - - + -
31A PRO* 3.4 28.3 + - - +
36A THR* 2.5 39.1 + - + +
38A PHE* 3.6 23.9 - - + -
54A PRO* 3.9 8.1 - - + +
123A VAL* 2.9 26.3 + - - +
124A VAL* 3.1 13.5 + - - +
126A ALA* 1.3 74.9 - - - +
128A VAL* 1.3 61.1 + - - +
130A GLN* 3.3 15.5 + - - +
131A MET* 3.0 22.0 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.0 22.9 - - + -
72A PHE* 4.4 10.5 - - + -
74A ILE* 4.5 6.3 - - + -
104A VAL* 4.3 19.7 - - + -
124A VAL 3.0 19.5 + - - +
125A GLY 3.7 7.0 - - - +
127A GLN* 1.3 74.8 - - - +
129A ALA* 1.3 64.3 + - - +
131A MET* 3.2 3.5 + - - +
132A LEU* 3.0 25.7 + - + +
148A LEU* 4.1 23.6 - - + -
157A VAL* 4.4 11.4 - - + -
161A ALA* 3.5 20.9 - - + -
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 2.9 17.3 + - - +
126A ALA 3.7 5.4 - - - +
128A VAL* 1.3 76.0 - - - +
130A GLN* 1.3 51.5 + - - +
132A LEU* 3.2 4.7 + - - +
133A SER* 2.8 35.4 + - - -
161A ALA* 3.8 4.2 - - - +
164A ARG* 3.6 29.2 - - + +
165A THR* 3.5 24.0 + - - +
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Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU 5.0 0.5 + - - +
7A GLN* 2.8 44.3 + - + +
8A ILE* 3.3 25.5 - - + +
54A PRO* 3.8 23.5 + - + +
126A ALA 2.9 15.0 + - - +
127A GLN* 3.3 13.2 + - - +
129A ALA* 1.3 74.4 - - - +
131A MET* 1.3 64.7 + - - +
133A SER* 2.9 20.6 + - - +
134A MET* 3.0 13.6 + - + +
700A SER* 3.8 16.4 - - - +
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Residues in contact with MET 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 3.5 37.0 - - + -
52A LEU* 3.6 27.8 - - + -
53A LEU 4.4 2.9 - - - +
54A PRO* 3.6 32.8 - - + +
59A ILE* 4.4 17.9 - - - -
72A PHE* 3.9 23.8 - - + -
102A ILE* 5.2 1.6 - - + -
127A GLN 3.0 13.1 + - - +
128A VAL 3.5 7.9 - - - +
130A GLN* 1.3 75.4 - - - +
132A LEU* 1.3 58.9 + - - +
134A MET* 3.4 7.3 + - - +
135A LEU* 3.0 34.6 + - + +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.8 29.8 - - + -
128A VAL* 3.0 28.7 + - + +
129A ALA* 3.5 7.6 - - - +
131A MET* 1.3 75.6 - - - +
133A SER* 1.3 64.6 + - - +
135A LEU* 3.4 10.0 + - + +
136A SER* 3.0 24.3 + - - -
141A TYR 4.8 0.9 - - - +
143A PRO* 5.0 8.7 - - + +
146A VAL* 3.9 22.0 - - + -
148A LEU* 4.4 8.1 - - + -
161A ALA* 4.8 1.1 - - + -
165A THR* 3.8 34.8 - - + +
169A LEU* 4.1 17.9 - - + -
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 2.8 19.0 + - - -
130A GLN* 2.9 22.2 + - - +
132A LEU* 1.3 73.7 - - - +
134A MET* 1.3 56.2 + - - +
136A SER* 3.5 5.7 + - - -
137A ALA* 2.8 32.0 + - - +
165A THR* 5.5 1.7 - - - +
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Residues in contact with MET 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 4.8 4.0 - - - +
54A PRO 3.6 20.0 - - - +
55A ASP 4.6 1.6 - - - -
56A PRO* 3.6 28.7 - - + -
59A ILE* 3.9 10.5 - - + -
130A GLN* 3.0 17.9 + - + +
131A MET* 3.6 8.7 - - - +
133A SER* 1.3 76.6 + - - +
135A LEU* 1.3 74.4 + - + +
137A ALA* 4.4 2.7 - - - -
138A ASN* 2.8 44.8 + - + +
139A TYR* 3.3 35.4 - - + -
700A SER 5.7 0.2 - - - -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.9 33.0 - - + -
64A PHE* 4.0 34.3 - - + -
70A THR* 5.5 0.4 - - - +
72A PHE* 4.7 7.6 - - + -
102A ILE* 5.4 0.9 - - + -
131A MET* 3.0 34.1 + - + +
132A LEU* 3.4 20.4 + - + +
134A MET* 1.3 85.9 - - + +
136A SER* 1.3 64.5 + - - +
139A TYR* 3.0 24.3 + - + +
140A SER 3.3 4.9 + - - -
141A TYR* 3.3 29.8 + - + +
146A VAL* 5.3 0.2 - - + -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU 3.0 17.8 + - - -
133A SER* 3.5 8.5 - - - -
135A LEU* 1.3 74.9 - - - +
137A ALA* 1.3 59.4 + - - +
140A SER* 2.9 28.6 + - - +
141A TYR 3.3 17.6 + - - +
142A SER* 5.5 0.5 - - - -
143A PRO* 4.7 13.0 - - - +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER 2.8 22.2 + - - +
134A MET* 4.0 4.3 - - - +
136A SER* 1.3 77.8 + - - +
138A ASN* 1.3 65.1 + - - +
139A TYR 3.6 0.2 + - - -
140A SER* 4.2 5.2 + - - -
500A NAG 4.2 23.5 + - - +
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.2 27.1 - - + +
134A MET* 2.8 29.9 + - + +
137A ALA* 1.3 73.0 + - - +
139A TYR* 1.3 75.1 + - + +
140A SER* 3.8 0.4 - - - -
500A NAG 1.5 63.0 + - - +
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 2.9 29.5 + - + +
57A SER* 4.6 1.0 - - - -
59A ILE* 3.5 27.1 - - + -
60A GLY* 3.4 17.7 + - - -
66A THR* 4.2 30.5 - - + +
134A MET* 3.3 35.4 - - + -
135A LEU* 3.0 14.7 + - + +
138A ASN* 1.3 83.4 - - + +
140A SER* 1.3 74.5 + - - +
141A TYR* 3.0 8.3 + - + +
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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