Contacts of the helix formed by residues 139 - 161 (chain A) in PDB entry 1G5J
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 VAL 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.5 34.5 - - + +
138A GLY* 1.3 79.4 - - - +
140A ASN* 1.3 81.7 + - - +
143A ARG* 2.8 28.2 + - - +
144A ILE* 3.8 2.7 - - + -
182A LEU* 3.5 31.6 - - + -
185A TRP* 3.7 32.5 - - + +
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 1.3 96.0 - - - +
141A TRP* 1.3 71.5 + - - +
142A GLY* 3.0 6.9 + - - +
143A ARG* 3.3 7.5 + - - +
144A ILE* 2.9 13.2 - - - +
185A TRP* 3.3 22.7 + - - +
189A ASN* 4.2 11.1 + - - +
199A TYR* 4.9 7.0 + - - +
320B VAL* 5.2 11.3 - - + +
324B LYS* 4.8 25.2 - - - +
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Residues in contact with TRP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASN* 1.3 77.4 - - - +
142A GLY* 1.3 62.6 + - - +
144A ILE* 3.2 10.7 + - + +
145A VAL* 3.0 27.9 + - - +
185A TRP* 3.0 35.4 - + - -
186A ILE* 3.8 20.0 - - + -
189A ASN* 2.9 40.1 - - + +
191A GLY 4.0 7.9 - - - -
192A TRP* 4.9 6.3 - + - -
194A THR* 3.7 17.0 - - + +
195A PHE* 3.5 42.1 - + + +
198A LEU* 3.4 30.9 - - + +
199A TYR* 3.5 43.5 + + + -
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL 4.7 0.2 - - - -
140A ASN 3.0 1.8 - - - -
141A TRP* 1.3 81.3 - - - +
143A ARG* 1.3 62.5 + - - +
146A ALA* 3.3 16.5 + - - +
199A TYR* 3.3 14.8 + - - -
316B SER* 5.2 2.2 - - - -
319B PHE* 3.3 20.3 - - - -
320B VAL* 3.4 28.8 - - - +
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.3 23.9 + - + +
135A PHE* 3.0 28.5 - - + -
137A ASP 4.5 7.9 + - - -
138A GLY* 2.7 38.1 + - - +
139A VAL* 2.8 26.0 + - - +
140A ASN* 5.2 5.7 - - - +
142A GLY* 1.3 73.6 - - - +
144A ILE* 1.3 56.1 + - - +
146A ALA* 3.4 7.0 + - - +
147A PHE* 2.8 24.9 + - - -
313B ARG* 3.4 31.3 + - - +
316B SER* 3.0 39.2 + - - +
317B ASP* 4.7 12.9 + - - +
320B VAL* 5.1 1.4 - - - +
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.3 2.5 - - + -
135A PHE* 4.1 4.3 - - - -
139A VAL* 3.8 1.8 - - + -
140A ASN 2.9 18.6 - - - +
141A TRP* 3.3 12.1 - - + +
142A GLY 3.1 0.4 - - - -
143A ARG* 1.3 76.9 - - - +
145A VAL* 1.3 66.3 + - + +
147A PHE* 2.9 15.2 + - + +
148A PHE* 3.1 28.6 + - + -
178A LEU* 4.5 9.4 - - + -
182A LEU* 3.4 25.4 - - + -
185A TRP* 3.2 36.1 - - + -
192A TRP* 3.4 34.1 - - + -
195A PHE* 6.0 0.9 - - + -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 4.4 1.4 - - - -
94A LEU* 3.1 37.7 - - + +
97A ALA* 3.3 21.5 - - + -
98A GLY* 2.8 39.9 - - - +
141A TRP 3.0 15.3 + - - +
142A GLY 3.4 3.8 + - - +
144A ILE* 1.3 78.5 - - + +
146A ALA* 1.3 63.2 + - - +
148A PHE* 3.2 14.4 + - - +
149A SER* 3.3 11.3 + - - -
195A PHE* 4.1 13.7 - - + -
199A TYR* 4.4 4.7 - - + -
319B PHE* 4.0 5.4 - - + -
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY* 5.6 0.2 - - - -
101A PHE* 3.6 42.0 - - + -
109A PHE* 4.9 2.0 - - + -
134A LEU* 5.9 1.8 - - + -
142A GLY 3.3 8.9 + - - +
143A ARG* 3.8 9.0 - - - +
144A ILE 3.2 0.6 - - - -
145A VAL* 1.3 80.3 - - - +
147A PHE* 1.3 52.7 + - - +
149A SER* 3.4 6.8 + - - +
150A PHE* 2.8 36.7 + - - +
312B LEU* 3.8 15.6 - - + +
316B SER* 5.8 1.3 - - - -
319B PHE* 4.5 0.2 - - - -
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.7 28.9 - + - -
130A VAL* 6.0 2.2 - - + -
131A VAL* 4.0 17.0 - - + -
134A LEU* 4.2 12.3 - - + +
135A PHE* 3.6 23.8 - + + -
143A ARG 2.8 15.2 + - - +
144A ILE* 2.9 14.1 + - + +
146A ALA* 1.3 77.4 - - - +
148A PHE* 1.3 71.4 + + - +
150A PHE* 3.0 24.5 + + + +
151A GLY 3.3 5.0 + - - -
174A MET* 3.3 49.5 - - + +
177A TYR* 4.0 16.8 - + + -
178A LEU* 5.5 2.7 - - + -
182A LEU* 5.2 5.4 - - + -
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Residues in contact with PHE 148 (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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9A ASN 4.5 0.4 - - - -
12A LEU* 3.3 40.6 - - + -
13A VAL* 3.1 46.2 - - + -
16A PHE* 3.7 26.2 - - + -
17A LEU* 4.7 0.7 - - - +
94A LEU* 3.0 24.9 - - + -
144A ILE* 3.1 32.3 + - + -
145A VAL 3.2 7.6 + - - +
147A PHE* 1.3 87.8 - + - +
149A SER* 1.3 63.5 + - - +
152A GLY* 3.2 16.6 + - - -
174A MET* 3.3 16.3 - - + +
178A LEU* 4.7 10.5 - - + -
192A TRP* 4.2 12.3 - + - -
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Residues in contact with SER 149 (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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16A PHE* 3.3 26.2 - - - -
19A TYR* 5.3 0.2 - - - -
20A LYS* 2.8 27.7 + - - -
98A GLY* 4.2 13.9 + - - -
101A PHE* 5.9 0.7 - - - -
102A GLU* 5.0 0.7 - - - +
109A PHE* 3.8 22.2 - - - -
145A VAL 3.3 6.8 + - - -
146A ALA* 3.8 8.1 - - - -
148A PHE* 1.3 75.7 - - - +
150A PHE* 1.3 69.9 + - - +
152A GLY* 2.9 10.7 + - - +
153A ALA 3.1 10.6 + - - -
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Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 4.0 10.1 - + - -
127A PHE* 6.0 4.0 - + - -
130A VAL* 3.3 30.1 - - + -
134A LEU* 4.0 14.8 - - + -
146A ALA 2.8 12.3 + - - +
147A PHE* 3.0 20.4 - + + +
149A SER* 1.3 80.4 - - - +
151A GLY* 1.3 63.5 + - - +
152A GLY 3.1 0.2 + - - -
153A ALA* 3.4 2.8 + - - +
154A LEU* 3.2 32.4 + - + +
308B TYR* 3.0 59.9 + + + -
309B GLY* 4.7 0.4 - - - -
312B LEU* 3.5 42.0 - - + -
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Residues in contact with GLY 151 (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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17A LEU* 3.7 7.5 - - - +
127A PHE* 5.1 4.5 - - - -
147A PHE* 3.3 7.9 + - - -
148A PHE 3.4 0.4 + - - -
150A PHE* 1.3 82.0 - - - +
152A GLY* 1.3 57.4 + - - +
154A LEU* 3.6 9.0 - - - +
155A CYS* 2.8 31.7 + - - +
170A ILE* 4.2 10.6 - - - +
174A MET* 3.9 19.7 - - - -
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Residues in contact with GLY 152 (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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16A PHE* 5.4 0.7 - - - -
17A LEU* 3.4 19.0 - - - +
20A LYS* 3.6 21.0 - - - +
148A PHE 3.2 10.1 + - - -
149A SER* 2.9 10.7 + - - -
151A GLY* 1.3 75.5 - - - +
153A ALA* 1.3 60.0 + - - -
155A CYS* 3.0 14.4 + - - +
156A VAL* 3.3 16.1 + - - +
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Residues in contact with ALA 153 (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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20A LYS* 3.7 18.0 - - + +
109A PHE* 3.8 42.0 - - + +
112A LEU* 4.5 5.8 - - + -
149A SER 3.1 6.9 + - - +
150A PHE 4.1 1.8 - - - +
152A GLY* 1.3 73.6 - - - +
154A LEU* 1.3 62.9 + - - +
156A VAL* 3.6 3.5 + - - +
157A GLU* 2.9 36.9 + - - +
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Residues in contact with LEU 154 (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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112A LEU* 3.5 30.9 - - + +
113A THR* 5.0 1.3 - - + -
116A LEU* 6.0 1.1 - - + -
118A ILE* 4.1 26.7 - - + -
126A SER* 5.9 4.5 - - - -
127A PHE* 5.4 10.5 - - + +
130A VAL* 5.6 4.9 - - + -
150A PHE* 3.2 27.1 + - + +
151A GLY* 3.6 8.3 - - - +
152A GLY 3.1 0.4 - - - -
153A ALA* 1.3 78.5 - - - +
155A CYS* 1.3 53.4 + - - +
157A GLU* 3.5 6.0 - - + +
158A SER* 2.6 33.0 + - - +
170A ILE* 4.5 16.2 - - + -
308B TYR* 4.2 21.3 - - + -
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Residues in contact with CYS 155 (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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17A LEU* 4.2 9.2 - - + -
21A LEU* 3.8 32.1 - - - -
28A TRP* 4.1 3.4 - - - -
31A PHE* 6.1 0.2 - - - -
151A GLY 2.8 17.0 + - - +
152A GLY 3.0 4.5 + - - +
154A LEU* 1.3 74.2 - - - +
156A VAL* 1.3 63.9 + - - +
157A GLU 3.0 1.3 - - - -
158A SER* 2.9 19.0 + - - -
159A VAL* 2.7 23.4 + - - +
167A VAL* 3.7 38.8 - - + +
170A ILE* 4.9 7.6 - - + +
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Residues in contact with VAL 156 (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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20A LYS* 3.8 21.1 - - + +
21A LEU* 3.3 25.6 - - + -
24A LYS* 3.3 45.8 - - + -
26A TYR* 3.9 14.3 + - + -
152A GLY 3.3 13.2 + - - +
153A ALA* 3.6 6.5 + - - +
155A CYS* 1.3 75.1 - - - +
157A GLU* 1.3 64.7 + - - +
159A VAL* 3.3 9.2 - - - +
160A ASP* 3.1 23.7 + - - +
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Residues in contact with GLU 157 (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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24A LYS* 5.3 8.5 + - - +
109A PHE 5.3 1.6 - - - +
110A SER 3.9 11.8 - - - +
111A ASP* 3.3 22.2 - - - +
112A LEU* 3.8 26.0 - - + +
113A THR* 3.5 23.6 + - + +
153A ALA* 2.9 34.9 + - - +
154A LEU* 3.5 10.5 - - + +
155A CYS 3.0 0.2 - - - -
156A VAL* 1.3 83.8 - - - +
158A SER* 1.3 63.9 + - - +
160A ASP* 3.4 20.9 - - - +
161A LYS* 3.6 7.4 + - - +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 4.0 1.9 - - - +
118A ILE* 4.3 12.3 - - - +
154A LEU* 2.6 18.8 + - - +
155A CYS* 2.9 10.9 + - - -
157A GLU* 1.3 73.1 - - - +
159A VAL* 1.3 56.0 + - - -
160A ASP 3.0 1.3 - - - -
161A LYS* 2.6 29.3 + - - +
163A MET* 3.1 45.3 + - - +
166A LEU* 4.3 14.3 - - - +
167A VAL* 5.1 1.7 - - - +
170A ILE* 4.7 2.9 - - - +
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.4 1.6 - - + -
26A TYR* 3.8 20.9 - - + -
31A PHE* 3.3 22.9 - - + -
155A CYS* 2.7 33.4 + - - +
156A VAL* 3.3 20.6 - - - +
158A SER* 1.3 73.3 - - - +
160A ASP* 1.3 59.3 + - - +
162A GLU* 3.1 14.6 + - - -
163A MET 3.1 8.1 + - - -
164A GLN* 3.1 32.3 - - + +
167A VAL* 3.3 18.6 - - + -
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Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 5.2 11.0 + - + -
26A TYR* 2.6 25.4 + - - +
156A VAL* 3.1 21.1 + - + +
157A GLU* 3.4 16.8 - - - +
158A SER 2.9 0.4 + - - -
159A VAL* 1.3 76.6 - - - +
161A LYS* 1.3 65.3 + - + +
162A GLU 3.2 3.0 + - - -
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Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 5.3 5.7 + - - -
113A THR* 3.1 28.2 + - - -
114A SER* 4.8 10.7 + - - +
157A GLU 3.6 6.5 + - - +
158A SER 2.6 16.1 + - - +
160A ASP* 1.3 79.9 - - - +
162A GLU* 1.3 64.7 + - - +
163A MET* 2.9 35.5 - - + +
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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