Contacts of the helix formed by residues 130 - 155 (chain A) in PDB entry 6GA6
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 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 3.4 14.2 - - + +
129A LYS* 1.3 79.2 - - + +
131A TYR* 1.3 66.3 + - - +
132A SER* 3.9 12.6 - - - +
133A TYR* 3.0 53.8 + - + -
134A ARG* 3.4 1.5 + - - +
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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
----------------------------------------------------------
71A PHE* 3.5 36.3 - + + -
72A GLY* 4.8 10.8 - - - +
129A LYS 3.4 5.6 + - - -
130A VAL* 1.3 72.5 - - - +
132A SER* 1.3 63.3 + - - +
134A ARG* 3.1 31.2 + - - +
135A PHE* 3.4 26.4 - + - -
195A GLY 3.0 27.1 + - - -
196A ALA* 3.4 8.0 + - - -
309A UND 3.9 19.5 - - + -
310A L2P 3.2 31.3 - - - -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.9 7.6 - - - +
131A TYR* 1.3 80.3 - - - +
133A TYR* 1.3 80.8 + - - +
135A PHE* 3.3 19.9 + - - +
136A VAL* 3.8 7.6 + - - +
309A UND 3.8 40.1 - - - +
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 3.7 10.8 - - + -
130A VAL* 3.0 40.1 + - + +
132A SER* 1.3 88.5 + - - +
134A ARG* 1.3 66.0 + - - +
135A PHE 3.1 2.9 - - - -
136A VAL* 3.0 25.7 + - + +
137A TRP* 3.1 24.5 + - + +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 4.1 0.8 - - - +
71A PHE* 3.3 30.1 - - - -
78A ILE* 3.7 3.8 - - - +
125A GLY* 3.2 23.9 + - - +
126A ALA* 2.8 37.6 + - - +
127A LEU 4.0 0.6 - - - -
128A THR* 2.8 37.0 + - + +
130A VAL 3.7 4.3 - - - +
131A TYR* 3.1 34.5 + - - +
133A TYR* 1.3 77.4 - - - +
135A PHE* 1.3 62.0 + - + +
137A TRP* 3.3 5.5 + - - +
138A TRP* 3.0 23.2 + - - +
189A TRP* 3.8 13.2 - - + -
194A GLU* 2.9 44.1 + - - +
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 3.4 61.2 - + - -
132A SER* 3.7 12.1 - - - +
133A TYR 3.1 0.8 - - - -
134A ARG* 1.3 77.4 - - + +
136A VAL* 1.3 65.0 + - - +
137A TRP 3.3 0.2 - - - -
138A TRP* 3.6 7.9 - - + +
139A ALA* 3.0 23.4 + - - +
189A TRP* 4.7 4.9 - + - -
190A LEU* 3.7 31.9 - - + -
195A GLY* 3.8 23.8 - - - -
196A ALA* 4.1 2.0 - - + -
309A UND 3.9 27.7 - - + +
310A L2P 3.8 34.3 - - + -
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER 4.0 10.3 - - - +
133A TYR* 3.0 25.5 + - + +
135A PHE* 1.3 78.2 - - - +
137A TRP* 1.3 70.1 + - + +
139A ALA* 3.2 7.4 + - + +
140A ILE* 3.1 37.7 + - + +
309A UND 4.6 16.6 - - + -
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Residues in contact with TRP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.5 48.0 + - + +
122A GLY* 5.7 0.2 - - - -
124A VAL* 3.4 28.1 - - + +
125A GLY* 3.5 15.7 - - - -
128A THR* 3.7 21.3 + - - +
133A TYR* 3.1 32.6 + - - +
134A ARG 3.7 0.9 - - - +
136A VAL* 1.3 81.1 - - + +
138A TRP* 1.3 66.0 + - - +
140A ILE* 3.3 20.1 + - + +
141A SER* 2.9 25.9 + - - -
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Residues in contact with TRP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLY* 6.0 0.7 - - - -
134A ARG 3.0 15.4 + - - +
135A PHE* 3.6 14.6 - - - +
136A VAL 3.3 0.2 - - - -
137A TRP* 1.3 76.3 - - - +
139A ALA* 1.3 66.0 + - + +
141A SER* 3.3 5.8 + - - -
142A THR* 2.9 56.7 + - + -
186A PRO* 3.0 31.5 + - + +
187A VAL* 5.5 0.7 - - + -
189A TRP* 3.3 29.3 - + + -
190A LEU* 3.9 29.7 - - + +
301A RET 3.2 31.8 - - + +
303A TRD 4.5 13.9 - - + -
309A UND 5.9 0.2 - - + -
310A L2P 3.6 52.7 - - + -
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE 3.0 17.6 + - - +
136A VAL* 3.5 5.4 - - + +
137A TRP 3.2 0.2 - - - -
138A TRP* 1.3 89.8 - - + +
140A ILE* 1.3 58.1 + - + +
142A THR* 3.3 2.2 + - - -
143A ALA* 2.9 28.6 + - - +
309A UND 3.8 29.2 - - + -
310A L2P 3.7 21.5 - - + +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 4.8 4.3 - - + -
121A THR* 4.1 20.0 - - + +
136A VAL* 3.1 28.6 + - + +
137A TRP* 3.8 28.5 - - + +
139A ALA* 1.3 76.2 - - + +
141A SER* 1.3 64.3 + - - +
143A ALA* 3.2 9.1 + - - +
144A ALA* 3.1 19.8 + - - +
302A L2P 4.2 35.1 - - + +
310A L2P 5.8 0.2 - - - -
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A MET* 2.7 30.6 + - - +
121A THR* 3.1 21.5 + - - -
122A GLY* 4.0 7.6 + - - -
137A TRP 2.9 15.6 + - - -
138A TRP 3.7 0.4 - - - -
140A ILE* 1.3 76.0 - - - +
142A THR* 1.3 57.1 + - - +
144A ALA* 3.1 6.1 + - - +
145A MET* 2.9 23.4 + - - +
301A RET 3.1 31.1 - - - +
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TRP* 2.9 46.1 + - + -
139A ALA* 3.7 6.3 - - - -
141A SER* 1.3 74.1 - - - +
143A ALA* 1.3 58.6 + - - +
145A MET* 3.1 5.8 + - + +
146A LEU* 2.8 37.7 + - + +
186A PRO* 3.8 1.7 - - + +
301A RET 3.6 18.2 - - - +
303A TRD 4.4 26.9 - - + -
310A L2P 4.5 15.9 - - + -
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Residues in contact with ALA 143 (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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139A ALA 2.9 14.2 + - - +
140A ILE* 3.2 12.1 + - - +
142A THR* 1.3 77.9 - - - +
144A ALA* 1.3 60.9 + - - +
146A LEU* 3.3 8.3 + - - +
147A TYR* 3.0 21.7 + - - +
302A L2P 4.3 14.8 - - + -
310A L2P 3.8 28.2 - - + +
315A UND 3.9 18.7 - - + +
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Residues in contact with ALA 144 (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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114A ALA* 3.7 23.0 - - - +
117A ILE* 4.2 7.0 - - + -
118A MET* 3.9 13.5 - - + +
140A ILE 3.1 12.9 + - - +
141A SER 3.1 8.7 + - - +
143A ALA* 1.3 73.1 - - - +
145A MET* 1.3 65.0 + - - +
147A TYR* 3.3 6.7 + - - +
148A ILE* 3.1 28.1 + - - +
302A L2P 3.9 21.4 - - + +
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Residues in contact with MET 145 (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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118A MET* 3.5 27.0 - - + -
141A SER 2.9 9.4 + - - +
142A THR* 3.1 9.8 + - + +
144A ALA* 1.3 76.9 - - - +
146A LEU* 1.3 64.4 + - + +
148A ILE* 3.0 6.8 + - + +
149A LEU* 2.8 60.2 + - + +
182A TRP* 3.7 29.4 - - + +
183A SER* 4.1 5.4 - - - -
186A PRO* 3.8 16.8 - - + -
301A RET 3.9 13.0 - - + -
303A TRD 3.8 33.0 - - + -
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Residues in contact with LEU 146 (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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142A THR* 2.8 25.5 + - + +
143A ALA* 3.3 8.3 + - - +
145A MET* 1.3 85.2 - - + +
147A TYR* 1.3 57.7 + - - +
149A LEU* 3.3 4.5 + - + +
150A TYR* 2.9 28.9 + - - +
303A TRD 3.7 58.2 - - + +
310A L2P 4.0 27.8 - - + -
315A UND 4.7 11.7 - - + -
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Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA* 3.7 20.3 - - + +
111A LEU* 5.0 1.3 - - - -
114A ALA* 3.7 17.0 - - + -
143A ALA 3.0 9.1 + - - +
144A ALA 3.5 7.6 - - - +
145A MET 3.2 0.2 - - - -
146A LEU* 1.3 73.9 - - - +
148A ILE* 1.3 68.9 + - - +
150A TYR* 3.2 4.1 + + - +
151A VAL* 3.0 47.4 + - + +
302A L2P 3.0 81.0 - - + +
315A UND 4.0 53.0 - - + +
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.1 20.0 - - + -
111A LEU* 3.8 25.4 - - + +
114A ALA* 3.9 14.8 - - + -
115A ASP* 3.5 42.6 - - + +
118A MET* 4.1 18.2 - - + -
144A ALA 3.1 14.2 + - - +
145A MET* 3.0 7.7 + - + +
147A TYR* 1.3 75.3 - - - +
149A LEU* 1.3 69.3 + - + +
151A VAL* 3.2 4.3 + - - +
152A LEU* 3.0 30.0 + - + +
182A TRP* 4.6 7.6 - - + -
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Residues in contact with LEU 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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145A MET* 2.8 42.0 + - + +
146A LEU* 3.8 4.7 - - + +
148A ILE* 1.3 81.1 - - + +
150A TYR* 1.3 62.8 + - - +
152A LEU* 3.3 13.4 + - + +
153A PHE* 3.2 29.7 + - - -
178A THR* 5.2 0.7 - - + +
179A VAL* 4.0 31.6 - - + +
182A TRP* 5.0 11.0 - - + -
183A SER* 3.5 24.5 - - - +
303A TRD 3.5 36.1 - - + -
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU 2.9 18.1 + - - +
147A TYR* 3.2 8.5 + + - +
149A LEU* 1.3 76.8 - - - +
151A VAL* 1.3 65.4 + - + +
153A PHE 3.1 1.2 + - - -
154A PHE* 2.7 83.7 + + + +
303A TRD 4.0 18.5 - - + +
315A UND 3.8 57.1 - - + +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.8 29.2 - - + -
110A ALA* 5.8 0.9 - - + -
111A LEU* 4.0 21.5 - - + -
147A TYR* 3.0 53.3 + - + +
148A ILE 3.7 7.2 - - - +
150A TYR* 1.3 83.8 - - + +
152A LEU* 1.3 63.6 + - - +
154A PHE 4.9 0.2 - - - -
155A GLY* 3.0 25.2 + - - +
156A PHE* 3.2 11.4 + - + +
302A L2P 6.2 1.8 - - - -
315A UND 5.5 2.2 - - + -
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Residues in contact with LEU 152 (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 5.8 - - + -
97A LEU* 4.2 20.6 - - + -
111A LEU* 4.4 13.0 - - + -
148A ILE* 3.0 33.5 + - + +
149A LEU* 3.7 17.0 - - + +
150A TYR 3.3 0.2 - - - -
151A VAL* 1.3 75.9 - - - +
153A PHE* 1.3 61.4 + - + +
156A PHE* 3.5 42.9 - - + +
157A THR* 3.4 12.8 + - - -
171A PHE* 3.8 2.8 - - + -
175A ARG* 3.5 19.5 - - + -
178A THR* 4.1 26.2 - - + -
179A VAL* 4.7 4.9 - - + -
182A TRP* 6.1 0.2 - - + -
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU 3.2 20.2 + - - +
150A TYR 3.1 1.0 + - - -
151A VAL 3.1 0.6 - - - -
152A LEU* 1.3 82.6 - - - +
154A PHE* 1.3 89.0 + + + +
155A GLY 3.4 3.3 + - - -
157A THR* 3.4 22.0 + - - +
158A SER* 4.8 3.1 + - - -
175A ARG* 3.6 39.0 - - - -
176A ASN* 4.3 7.2 - - - -
179A VAL* 3.3 41.1 - - + -
303A TRD 4.1 15.5 - - + -
307A OCT 5.6 5.4 - - + -
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Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TYR* 2.7 71.0 + + + +
151A VAL* 4.7 0.9 - - - -
153A PHE* 1.3 93.9 - + + +
155A GLY* 1.3 55.6 + - - +
158A SER* 5.9 4.7 - - - -
303A TRD 4.4 17.0 - - + -
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 6.0 1.3 - - - -
151A VAL* 3.0 15.4 + - - -
153A PHE 3.8 0.2 + - - -
154A PHE* 1.3 78.5 - - - +
156A PHE* 1.3 72.6 + - - +
157A THR 3.9 0.2 - - - -
158A SER* 4.9 5.2 - - - -
159A LYS* 3.9 13.2 + - - +
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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