Contacts of the helix formed by residues 118 - 144 (chain B) in PDB entry 2P1A
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 ARG 118 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 4.1 18.1 + - + +
59B ASN* 5.3 4.0 + - - -
96B PHE* 3.2 22.4 - - + -
99B TYR* 3.4 49.6 + - + -
103B GLN* 3.2 49.8 + - - +
104B LEU* 3.3 5.8 + - - +
106B GLU* 3.0 26.2 + - - +
108B LYS* 3.8 42.9 - - + +
117B SER* 1.3 72.4 - - - +
119B PHE* 1.3 61.3 + - - +
121B TRP* 3.3 2.8 + - - +
122B LEU 3.0 17.2 + - - -
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 5.4 3.6 - - + -
2A PHE* 3.5 54.3 - + + -
5A SER* 3.9 15.3 - - - +
119A PHE* 3.9 21.5 - + - -
2B PHE 3.8 23.3 - - - -
3B VAL* 4.1 16.8 - - + -
6B ALA* 4.6 7.0 - - + -
96B PHE* 4.3 3.1 - - - -
104B LEU* 3.0 20.2 + - + +
117B SER* 4.1 3.1 - - - +
118B ARG* 1.3 74.1 - - - +
120B GLU* 1.3 66.8 + - - +
122B LEU* 3.1 20.7 + - + +
123B LEU* 3.2 42.3 + - + +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 3.6 30.2 + - - +
8A HIS* 6.0 4.3 - - - +
9A GLN* 4.0 2.2 - - - +
107B MSE 5.1 6.3 - - - +
115B SER 4.9 0.9 - - - +
116B TYR* 3.6 16.6 - - + +
117B SER* 3.0 45.3 + - - +
119B PHE* 1.3 76.4 - - - +
121B TRP* 1.3 58.4 + - - +
123B LEU* 3.2 10.8 + - - +
124B GLU* 3.0 29.5 + - + +
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Residues in contact with TRP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 3.0 33.8 + - + -
55B LEU* 5.9 0.2 - - - -
57B ILE* 3.8 22.0 - - + -
58B LEU* 3.7 38.4 - - + +
112B TRP* 3.6 24.7 - + - -
116B TYR* 3.5 54.2 - + + +
117B SER 2.9 16.7 + - - +
118B ARG 3.7 4.7 - - - +
119B PHE 3.2 0.2 - - - -
120B GLU* 1.3 72.5 - - - +
122B LEU* 1.3 65.7 + - - +
124B GLU* 3.1 20.9 + - + +
125B ILE* 3.0 45.9 + - + +
128B HIS* 5.8 2.5 - - - -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 4.3 13.0 - - + +
6B ALA* 3.5 31.0 - - + -
7B LEU* 3.9 25.6 - - + -
10B LEU* 4.9 4.3 - - + -
92B LEU* 4.5 13.9 - - + -
96B PHE* 3.8 45.5 - - + -
118B ARG 3.0 6.5 + - - -
119B PHE* 3.1 19.9 + - + +
121B TRP* 1.3 76.0 - - - +
123B LEU* 1.3 58.3 + - + +
125B ILE* 3.1 11.9 + - + +
126B VAL* 3.1 30.0 + - + +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 3.7 10.8 - - - +
6A ALA* 3.5 35.4 - - + +
9A GLN* 3.7 18.7 - - + +
123A LEU* 3.4 26.2 - - + -
126A VAL* 5.1 3.2 - - + +
6B ALA* 4.1 15.7 - - + -
119B PHE* 3.2 43.8 + - + +
120B GLU* 3.2 8.5 + - - +
122B LEU* 1.3 75.6 - - - +
124B GLU* 1.3 58.8 + - - +
126B VAL* 3.5 11.4 + - + +
127B ALA* 3.0 27.7 + - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 2.9 33.0 + - - +
12A VAL* 6.1 0.9 - - - +
130A TYR* 5.1 0.3 + - - -
54B ASP* 5.2 0.2 - - - -
116B TYR* 4.1 29.9 + - + -
120B GLU* 3.0 14.5 + - + +
121B TRP* 3.1 28.6 + - + +
123B LEU* 1.3 74.1 - - - +
125B ILE* 1.3 58.1 + - - +
127B ALA* 3.8 2.2 - - - +
128B HIS* 2.9 30.4 + - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.2 11.9 - - + -
50B ILE* 4.1 13.2 - - + +
51B CYS* 4.7 2.5 - - - -
54B ASP* 3.2 39.0 - - + +
92B LEU* 3.9 34.1 - - + -
96B PHE* 5.7 0.2 - - + -
121B TRP* 3.0 53.8 + - + +
122B LEU* 3.1 15.9 + - + +
124B GLU* 1.3 73.0 - - - +
126B VAL* 1.3 61.7 + - - +
128B HIS* 3.3 1.6 + - - +
129B PHE* 2.9 30.2 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 5.1 8.1 - - + +
126A VAL* 5.3 4.7 - - + -
127A ALA* 4.6 10.1 - - + +
6B ALA* 3.6 30.3 - - + +
9B GLN* 4.5 10.1 - - + -
10B LEU* 4.3 19.5 - - + -
122B LEU* 3.1 18.1 + - + +
123B LEU* 3.6 15.3 - - + +
124B GLU 3.4 0.2 - - - -
125B ILE* 1.3 76.7 - - + +
127B ALA* 1.3 63.0 + - - +
129B PHE* 3.8 0.5 - - - +
130B TYR* 3.0 51.0 + - + -
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.5 24.9 - - + +
126A VAL* 4.8 2.4 - - + +
127A ALA* 6.0 0.4 - - - +
130A TYR* 3.4 41.9 - - + +
123B LEU 3.0 11.1 + - - +
124B GLU* 3.8 4.9 - - - +
126B VAL* 1.3 75.8 - - - +
128B HIS* 1.3 52.7 - - - +
130B TYR* 4.9 0.7 - - - -
131B HIS* 2.8 38.3 + - - +
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 4.1 8.3 + + - -
50B ILE* 3.5 24.2 - - + +
54B ASP* 2.9 36.0 + - - +
70B TYR* 5.4 4.2 + - - -
121B TRP* 5.8 3.2 - - - -
124B GLU 2.9 18.9 + - - +
125B ILE 3.4 4.9 - - - +
127B ALA* 1.3 74.2 - - - +
129B PHE* 1.3 58.1 + - - +
131B HIS* 3.4 3.9 + - - +
132B HIS* 3.0 64.9 + + - +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.9 20.2 - - + -
13B ALA* 3.3 40.4 - - + -
14B VAL* 4.0 20.6 - - + -
17B SER* 3.5 10.8 - - - -
47B LEU* 3.7 29.3 - - + +
50B ILE* 3.9 28.5 - - + +
51B CYS* 4.5 7.4 - - - -
85B MSE 3.9 28.0 - - + -
125B ILE 2.9 16.8 + - - +
126B VAL 3.8 3.1 - - - +
128B HIS* 1.3 78.0 - - - +
130B TYR* 1.3 57.3 + - - +
133B ARG* 2.8 34.0 + - + +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA* 3.5 52.7 - - + +
130A TYR* 4.5 1.6 - - + -
131A HIS* 3.5 19.4 + - + +
9B GLN* 2.5 42.2 + - + -
10B LEU* 4.6 1.3 - - - -
12B VAL* 3.8 10.8 - - + +
13B ALA* 3.5 23.6 + - + -
126B VAL* 3.0 38.7 + - + +
127B ALA 4.1 2.2 - - - +
129B PHE* 1.3 74.3 - - + +
131B HIS* 1.3 65.3 + - - +
133B ARG* 3.3 36.3 - - - +
134B GLY 2.9 19.2 + - - -
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 3.5 18.2 + + + +
133A ARG* 3.9 26.8 + - + -
134A GLY* 3.5 27.6 + - - -
137A HIS* 3.7 23.4 + + + -
127B ALA 2.8 23.0 + - - +
128B HIS* 3.6 6.1 - - - +
130B TYR* 1.3 76.5 - - - +
132B HIS* 1.3 75.0 + + + +
134B GLY* 3.0 12.5 + - - -
135B GLN* 3.1 42.4 + - - +
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B MSE 5.0 1.9 - - + +
46B HIS* 3.5 36.0 + + + -
47B LEU* 3.8 18.8 - - + -
50B ILE* 4.0 2.9 - - + -
128B HIS* 3.0 46.9 + + - +
131B HIS* 1.3 95.1 - + + +
133B ARG* 1.3 58.1 + - - +
135B GLN* 3.4 25.5 + - - +
136B ILE* 3.2 28.4 + - + +
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A HIS* 4.0 16.1 + - + +
12B VAL* 5.6 2.4 - - - +
13B ALA* 3.8 17.0 - - - -
16B THR* 3.1 28.4 + - - +
17B SER* 3.4 22.6 + - - +
20B MSE 4.0 15.8 - - + +
47B LEU* 3.6 16.2 - - + +
129B PHE* 2.8 22.2 + - + +
130B TYR* 3.3 37.9 - - - +
132B HIS* 1.3 72.7 - - - +
134B GLY* 1.3 56.3 + - - +
136B ILE* 3.6 4.6 + - - +
137B HIS* 2.9 27.6 + - + +
149B ILE* 3.2 46.0 - - + +
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A HIS* 3.4 34.3 + - - -
135A GLN* 3.3 19.4 - - - +
130B TYR 2.9 12.7 + - - -
131B HIS 3.0 5.1 + - - -
133B ARG* 1.3 74.3 - - - +
135B GLN* 1.3 62.6 + - - +
138B ILE 3.2 18.5 + - - -
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLY* 3.2 21.9 - - - +
137A HIS* 2.9 32.7 + - - -
138A ILE* 3.6 19.2 - - + +
43B MSE 3.7 24.1 - - + +
131B HIS* 3.1 37.3 + - - +
132B HIS* 3.4 28.3 + - - +
134B GLY* 1.3 72.7 - - - +
136B ILE* 1.3 63.8 + - - +
138B ILE* 3.3 6.8 - - - +
139B LEU* 3.3 25.3 + - - +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MSE 4.6 3.6 - - + -
40B LEU* 3.9 14.5 - - + +
43B MSE 3.4 50.0 - - + +
44B TYR* 3.4 37.0 - - + -
47B LEU* 3.8 28.3 - - + -
132B HIS* 3.2 12.9 + - + +
133B ARG* 3.7 6.7 - - - +
135B GLN* 1.3 79.9 - - - +
137B HIS* 1.3 63.2 + - - +
139B LEU* 3.1 4.3 + - - +
140B LEU* 2.9 32.5 + - + +
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A HIS* 3.9 14.6 - + + -
135A GLN* 2.9 28.3 + - - -
20B MSE 4.1 16.4 - - + -
133B ARG* 2.9 20.5 + - + +
134B GLY 3.7 4.7 - - - +
135B GLN 3.4 0.4 - - - -
136B ILE* 1.3 76.7 - - - +
138B ILE* 1.3 57.2 + - + +
140B LEU* 3.4 4.6 + - - +
141B CYS* 3.1 48.8 + - - -
146B ASP* 4.9 2.6 + - - -
147B PRO* 4.1 22.2 + - + +
149B ILE* 4.1 25.6 - - + +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 3.7 36.3 - - - +
43A MSE 4.8 3.6 - - - -
135A GLN* 3.5 35.9 - - + +
138A ILE* 3.0 36.8 - - + -
139A LEU* 3.8 25.1 - - + -
134B GLY 3.2 9.2 + - - +
135B GLN 3.3 4.7 - - - +
137B HIS* 1.3 77.9 + - + +
139B LEU* 1.3 62.1 + - - +
141B CYS* 3.4 6.0 + - + +
142B GLU* 3.0 38.1 + - + +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.8 28.7 - - + -
139A LEU* 5.2 6.7 - - + -
34B ILE* 4.1 25.8 - - + +
36B SER* 5.2 1.1 - - - +
40B LEU* 3.5 28.9 - - + +
43B MSE 4.9 4.7 - - - -
135B GLN 3.3 14.6 - - - +
136B ILE 3.1 3.2 + - - +
138B ILE* 1.3 81.4 - - + +
140B LEU* 1.3 57.4 + - - +
142B GLU* 4.4 0.4 - - - -
143B HIS* 3.0 56.3 + - + +
144B MSE 4.3 0.2 + - - -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MSE 3.7 30.3 - - + -
24B TYR* 3.6 49.1 - - + +
29B LEU* 4.2 13.9 - - + -
40B LEU* 3.5 25.6 - - + -
44B TYR* 4.4 3.1 - - + -
136B ILE* 2.9 30.6 + - + +
137B HIS 3.5 6.5 - - - +
138B ILE 3.2 0.2 - - - -
139B LEU* 1.3 76.6 - - - +
141B CYS* 1.3 58.5 + - - +
144B MSE 2.9 39.7 + - + +
145B LYS 3.4 3.2 - - - +
147B PRO* 4.4 3.6 - - + -
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Residues in contact with CYS 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 3.4 31.1 + - - +
137B HIS* 3.1 44.2 + - - -
138B ILE* 3.4 10.1 + - + +
140B LEU* 1.3 74.7 - - - +
142B GLU* 1.3 60.3 + - - +
144B MSE 3.9 6.9 - - - +
146B ASP* 3.8 38.3 + - - +
147B PRO* 4.1 4.5 - - - -
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 5.1 0.5 - - - +
35A GLN 4.3 3.6 - - - +
36A SER* 2.8 39.2 + - - -
37A LYS* 3.8 7.7 + - - +
38A ARG* 3.3 27.4 + - - +
139A LEU* 4.4 22.4 - - + +
138B ILE* 3.0 26.1 + - + +
139B LEU* 4.4 0.2 - - - -
141B CYS* 1.3 78.3 - - - +
143B HIS* 1.3 83.7 + - + +
144B MSE 3.8 0.7 - - - -
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Residues in contact with HIS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 6.0 2.2 - - + -
32B ALA* 4.7 2.7 - - + -
33B PRO* 3.8 39.6 - - + +
34B ILE* 3.5 42.0 + - + +
139B LEU* 3.0 40.3 + - + +
142B GLU* 1.3 97.2 + - + +
144B MSE 1.3 70.6 + - - +
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Residues in contact with MSE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.8 26.5 - - + -
28B ASP* 3.7 50.0 - - + +
29B LEU* 6.1 0.4 - - + -
31B ILE* 6.4 1.3 - - - -
32B ALA* 4.1 19.7 - - + -
40B LEU* 4.5 10.3 - - + -
140B LEU* 2.9 21.9 + - + +
141B CYS 3.9 9.2 - - - +
142B GLU 4.8 0.3 - - - -
143B HIS* 1.3 85.2 - - - +
145B LYS* 1.3 70.8 + - + +
146B ASP 3.8 0.7 + - - -
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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