Contacts of the helix formed by residues 130 - 154 (chain D) in PDB entry 2Q9Q
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 GLU 130 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LEU* 3.4 23.3 - - + +
93D GLN* 4.8 2.8 - - - +
94D GLU* 4.7 3.6 + - - +
97D ARG* 2.7 29.9 + - - +
128D SER* 3.1 16.1 + - - +
129D PRO* 1.3 80.6 - - + +
131D ASN* 1.3 56.2 + - - -
132D ALA* 3.1 3.4 - - - -
133D ASP* 2.9 26.1 + - + +
134D ILE* 2.8 29.7 + - + +
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Residues in contact with ASN 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.3 14.4 - - + +
123D LEU 4.4 1.4 - - - +
124D LEU* 2.8 52.9 + - + +
127D ASP* 3.9 11.7 - - - +
128D SER* 3.0 33.7 + - - +
129D PRO 3.2 2.0 - - - +
130D GLU* 1.3 77.6 - - - +
132D ALA* 1.3 56.1 + - - +
134D ILE* 3.3 9.5 + - - +
135D SER* 2.8 31.9 + - - -
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.8 18.5 - - + +
129D PRO 4.6 4.1 + - - +
130D GLU* 3.1 1.2 - - - +
131D ASN* 1.3 76.6 - - - +
133D ASP* 1.3 68.9 + - - +
135D SER* 4.0 0.7 - - - -
136D GLN* 3.2 25.5 + - - +
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Residues in contact with ASP 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ARG* 3.1 34.9 + - - +
129D PRO 5.1 0.2 - - - +
130D GLU* 2.9 25.2 + - + +
132D ALA* 1.3 79.1 - - - +
134D ILE* 1.3 65.8 + - - +
136D GLN* 4.0 3.1 - - - +
137D SER* 3.1 25.5 + - - -
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Residues in contact with ILE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LEU* 3.5 40.2 - - + -
92D TYR* 4.1 35.7 - - + +
97D ARG* 4.6 5.2 - - - +
120D GLY 4.3 11.7 - - - +
123D LEU* 4.6 8.3 - - + -
124D LEU* 4.1 13.5 - - + -
128D SER* 4.5 0.9 - - - -
130D GLU 2.8 20.0 + - - +
131D ASN* 3.6 21.8 - - - +
133D ASP* 1.3 76.6 - - - +
135D SER* 1.3 64.4 + - - +
137D SER* 3.2 7.5 + - - -
138D LEU* 3.1 33.5 + - + +
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Residues in contact with SER 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU 4.0 4.9 + - - +
173A ASN* 2.7 30.1 + - - +
174A LEU* 3.6 22.3 - - - +
124D LEU* 4.3 4.2 - - - +
131D ASN 2.8 17.9 + - - -
132D ALA 4.0 1.6 - - - -
134D ILE* 1.3 77.3 - - - +
136D GLN* 1.3 62.3 + - - +
138D LEU* 3.1 23.7 + - - +
139D LEU* 3.3 12.6 + - - +
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Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ALA 3.2 16.6 + - - +
133D ASP* 4.2 3.8 - - - +
135D SER* 1.3 79.1 - - - +
137D SER* 1.3 62.8 + - - +
139D LEU* 3.5 8.3 + - + +
140D GLN* 3.0 49.2 + - + +
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Residues in contact with SER 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ARG* 3.2 34.5 + - - +
100D PHE* 4.4 10.2 - - - +
116D PHE* 5.2 3.4 - - - -
133D ASP 3.1 20.0 + - - -
134D ILE* 3.4 7.4 - - - -
136D GLN* 1.3 77.2 - - - +
138D LEU* 1.3 60.8 + - - +
140D GLN* 4.2 4.2 - - - +
141D THR* 2.6 38.5 + - - -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 4.2 13.9 - - + -
173A ASN* 4.2 15.3 - - - +
92D TYR* 4.1 21.1 - - + -
116D PHE* 3.9 31.6 - - + +
117D TYR* 3.3 23.7 - - + +
120D GLY* 3.7 28.9 - - - +
121D SER* 3.8 13.7 - - - +
124D LEU* 5.0 1.1 - - + -
134D ILE* 3.1 24.6 + - + +
135D SER* 3.1 8.9 + - - +
137D SER* 1.3 79.4 - - - +
139D LEU* 1.3 62.4 + - - +
142D PHE* 3.3 17.2 + - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLN* 3.6 29.2 - - - +
167A MET* 3.9 28.9 - - + +
170A LEU* 3.8 32.5 - - + +
171A ARG* 4.0 23.1 - - + +
135D SER 3.3 8.7 + - - +
136D GLN* 4.0 9.9 - - + +
138D LEU* 1.3 78.4 - - - +
140D GLN* 1.3 65.4 + - + +
142D PHE* 3.2 4.2 + - - +
143D ILE* 2.9 45.9 + - + +
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Residues in contact with GLN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 5.6 2.8 + - - -
139A GLN* 3.9 22.4 - - - +
101D SER* 6.3 3.1 - - - -
104D PRO* 4.3 5.1 - - - +
136D GLN* 3.0 39.9 + - + +
137D SER* 4.2 3.8 - - - +
139D LEU* 1.3 81.4 - - - +
141D THR* 1.3 58.4 + - - +
143D ILE* 3.3 16.4 + - - +
144D GLY* 2.8 27.5 + - - -
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D PHE* 3.6 45.8 + - + +
104D PRO* 3.7 11.2 - - + +
109D LEU* 4.4 1.3 - - + -
116D PHE* 3.8 17.0 - - + -
117D TYR* 3.5 14.6 - - - +
137D SER* 2.6 24.7 + - - -
138D LEU 3.6 4.5 - - - -
139D LEU 3.2 0.2 - - - -
140D GLN* 1.3 78.0 - - - +
142D PHE* 1.3 62.0 + - - +
144D GLY 3.5 0.7 + - - -
145D ARG* 3.1 40.9 + - - +
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Residues in contact with PHE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 3.6 21.8 - - + -
166A HIS* 4.4 6.1 - - + -
167A MET* 3.4 38.8 - - + -
170A LEU* 4.2 12.1 - - + -
117D TYR* 3.5 25.1 + + + -
138D LEU 3.3 4.5 + - - +
139D LEU 3.2 6.8 + - - +
141D THR* 1.3 76.6 - - - +
143D ILE* 1.3 61.6 + - - +
145D ARG* 3.1 1.9 + - - -
146D PHE* 2.8 39.5 + + + +
149D ILE* 4.7 11.0 - - + -
171D MET* 3.4 28.7 - - + -
172D GLU* 4.6 5.4 - - + -
175D LEU* 3.3 33.2 - - + -
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Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 4.9 0.3 - - - +
136A VAL* 4.1 10.2 - - + +
137A ARG* 3.7 51.6 + - - +
139A GLN* 3.7 40.8 - - + +
167A MET* 3.9 19.7 - - + -
139D LEU* 2.9 32.7 + - + +
140D GLN* 3.6 19.7 - - - +
142D PHE* 1.3 79.2 - - - +
144D GLY* 1.3 62.5 + - - +
145D ARG 3.3 0.2 + - - -
146D PHE* 3.5 12.6 + - - +
147D ARG 4.8 1.0 + - - -
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Residues in contact with GLY 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 4.3 16.6 + - - -
104D PRO* 3.9 16.1 - - - +
105D ASN* 3.3 21.3 + - - -
140D GLN 2.8 16.7 + - - -
141D THR 3.9 2.5 - - - -
142D PHE 3.2 0.2 - - - -
143D ILE* 1.3 76.9 - - - +
145D ARG* 1.3 60.3 + - - +
147D ARG* 5.1 3.0 + - - +
148D ARG 5.5 0.7 + - - -
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Residues in contact with ARG 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PRO* 2.8 33.3 + - + +
105D ASN* 3.6 20.0 + - - +
107D VAL* 2.3 37.0 + - - +
109D LEU* 3.4 18.7 - - - +
117D TYR* 3.8 4.7 - - - -
141D THR* 3.1 22.1 + - - +
142D PHE* 3.1 4.9 + - - +
144D GLY* 1.3 75.2 - - - +
146D PHE* 1.3 67.2 + - - +
147D ARG 3.3 2.8 + - - -
148D ARG* 3.3 6.2 + - - +
149D ILE* 3.3 27.5 + - + +
167D ARG* 3.6 13.9 + - - +
168D LEU* 3.8 10.3 - - + +
172D GLU* 2.8 47.1 + - - +
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Residues in contact with PHE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG 5.0 0.4 - - - -
132A ALA* 3.8 26.9 - - + -
133A ASP* 3.9 13.9 - - + -
136A VAL* 3.8 33.2 - - + -
159A PHE* 3.6 22.4 - + - -
160A LEU* 4.0 14.1 - - + -
163A ALA* 3.6 26.5 - - + -
142D PHE* 2.8 27.2 + + + +
143D ILE 3.5 11.1 + - - +
145D ARG* 1.3 75.4 - - - +
147D ARG* 1.3 68.4 + - - +
149D ILE* 3.3 11.0 + - - +
150D MET* 3.1 45.7 + - + +
175D LEU* 5.5 1.1 - - + -
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Residues in contact with ARG 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 5.0 0.2 + - - -
129A ARG* 3.6 21.5 - - - +
130A VAL* 3.3 39.6 - - - +
133A ASP* 3.3 43.8 + - - +
143D ILE 4.8 1.2 + - - -
144D GLY 5.1 3.1 + - - +
145D ARG 3.4 0.8 - - - -
146D PHE* 1.3 84.0 - - - +
148D ARG* 1.3 58.8 + - - +
150D MET* 3.4 2.5 + - - +
151D ASP* 2.8 64.7 + - - +
157D TYR* 4.3 8.9 + - - -
100G ASN* 6.0 4.0 - - - +
101G ALA* 5.7 1.2 - - - +
104G PHE* 6.0 2.8 - - - -
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Residues in contact with ARG 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASP* 5.7 0.8 + - - -
105D ASN* 3.5 52.5 + - - +
144D GLY 5.5 0.6 + - - -
145D ARG 3.3 5.2 + - - +
147D ARG* 1.3 78.3 - - - +
149D ILE* 1.3 60.2 + - + +
151D ASP* 3.9 7.1 - - - +
152D SER* 3.0 27.5 + - - -
164D LEU* 4.2 24.2 - - + -
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.9 19.3 - - + -
142D PHE* 4.7 12.3 - - + -
145D ARG* 3.3 22.0 - - + +
146D PHE* 3.3 6.7 + - - +
147D ARG 3.2 0.4 - - - -
148D ARG* 1.3 76.7 - - + +
150D MET* 1.3 60.2 + - - +
152D SER* 3.4 5.9 + - - -
153D SER* 2.9 32.6 + - - -
164D LEU* 5.0 2.2 - - + -
168D LEU* 4.1 18.8 - - + -
172D GLU* 3.7 57.7 - - + +
175D LEU* 4.4 4.0 - - + -
176D PHE* 4.2 12.5 - - + +
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Residues in contact with MET 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.5 6.3 - - + +
129A ARG* 4.0 34.8 - - + +
132A ALA* 4.1 13.2 - - + -
156A SER* 4.5 22.4 - - - +
159A PHE* 3.4 36.2 - - + -
160A LEU* 5.1 4.9 - - + -
146D PHE* 3.1 39.8 + - + +
147D ARG* 3.9 5.8 - - - +
149D ILE* 1.3 77.0 - - - +
151D ASP* 1.3 63.7 + - - +
153D SER* 2.9 15.9 + - - -
154D GLN* 3.1 32.9 + - - +
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Residues in contact with ASP 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 3.0 24.5 + - - +
147D ARG* 2.8 52.9 + - - +
148D ARG* 3.9 7.9 - - + +
150D MET* 1.3 78.1 - - - +
152D SER* 1.3 57.8 + - - +
154D GLN* 3.4 0.9 + - - -
155D ASN 3.1 6.2 + - - -
156D ALA* 2.9 29.4 + - + +
157D TYR* 3.1 39.6 + - + -
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Residues in contact with SER 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ARG* 3.0 16.8 + - - -
149D ILE 3.4 3.3 + - - -
151D ASP* 1.3 74.4 - - - +
153D SER* 1.3 68.2 + - - +
154D GLN 3.0 2.0 - - - -
155D ASN* 2.9 11.5 + - - +
156D ALA 4.9 0.2 - - - +
157D TYR* 6.5 0.4 - - - -
159D GLU* 3.8 22.2 - - - -
161D THR* 3.5 20.4 - - - +
164D LEU* 3.1 34.5 - - - +
176D PHE* 3.6 7.1 - - - -
180D GLN* 5.2 1.0 - - - +
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Residues in contact with SER 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.6 9.6 - - - -
149D ILE 2.9 16.2 + - - -
150D MET* 2.9 21.0 + - - -
152D SER* 1.3 77.9 + - - +
154D GLN* 1.3 63.6 + - - +
155D ASN* 3.3 0.7 + - - +
176D PHE* 3.4 45.1 - - - -
179D GLY* 3.8 5.0 - - - +
180D GLN* 3.4 30.1 + - - +
183D LEU* 4.5 3.1 - - - +
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Residues in contact with GLN 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.9 13.6 - - + +
129A ARG* 3.0 38.3 + - - +
155A THR* 4.7 6.1 + - - +
156A SER* 2.9 36.0 - - - +
159A PHE* 5.5 2.2 - - - +
150D MET* 3.1 30.6 + - + +
151D ASP 4.1 0.7 - - - +
152D SER 3.0 0.6 - - - -
153D SER* 1.3 84.6 - - - +
155D ASN* 1.3 69.4 + - - +
156D ALA* 3.2 2.6 + - - -
179D GLY* 4.6 13.0 + - - +
183D LEU* 3.1 32.2 - - + +
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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