Contacts of the helix formed by residues 145 - 167 (chain D) in PDB entry 2NP5
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 145 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B HIS* 3.4 24.8 + - - -
182B ILE* 3.8 32.0 - - + +
143D THR 3.5 0.8 + - - -
144D PRO* 1.3 74.6 - - + +
146D ALA* 1.3 65.0 + - - +
147D GLU 3.2 2.8 + - - -
148D THR* 3.2 12.1 + - - -
149D ARG* 2.9 32.8 + - + +
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D SER* 4.2 2.4 - - - +
138D LEU* 3.6 15.8 - - + +
139D ILE* 3.6 41.3 - - + +
143D THR* 3.5 18.5 + - - +
144D PRO 3.2 3.7 + - - -
145D GLU* 1.3 75.9 - - - +
147D GLU* 1.3 58.2 + - + +
149D ARG 3.5 0.2 + - - -
150D ALA* 2.9 29.9 + - - +
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Residues in contact with GLU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 4.4 1.9 + - - -
139C ILE* 5.1 13.7 - - - +
131D ARG* 5.1 5.7 + - - +
135D SER* 4.1 22.6 + - - +
139D ILE* 4.7 15.0 - - + +
145D GLU 3.4 1.0 - - - -
146D ALA* 1.3 75.1 - - + +
148D THR* 1.3 67.9 + - - +
150D ALA* 3.3 3.3 + - - +
151D ALA* 3.0 22.7 + - - +
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Residues in contact with THR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 4.1 16.1 + - - +
178B HIS* 3.1 40.6 + - + +
179B ALA* 3.9 20.6 - - + -
182B ILE* 3.9 20.6 - - + -
145D GLU* 3.2 16.0 + - - -
147D GLU* 1.3 79.5 - - - +
149D ARG* 1.3 56.1 + - - +
151D ALA* 3.2 3.1 + - - +
152D LEU* 2.9 27.7 + - + +
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Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ILE* 4.2 13.8 - - + +
186B MSE 3.8 34.6 - - - +
189B GLN* 5.9 2.8 - - - +
138D LEU* 4.1 9.2 - - + -
143D THR* 3.9 3.9 - - - +
144D PRO* 3.2 37.9 + - - +
145D GLU* 2.9 23.1 + - - +
146D ALA 3.9 3.1 - - - +
148D THR* 1.3 75.3 - - - +
150D ALA* 1.3 56.6 + - - +
152D LEU* 3.2 5.4 + - - +
153D LEU* 2.8 26.2 + - - +
186D MSE 3.7 3.6 + - - -
187D ILE* 2.7 59.5 + - + +
189D GLN* 2.8 27.9 + - - +
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D ARG* 4.0 8.2 - - + +
134D LEU* 3.8 21.6 - - + +
135D SER* 3.6 33.9 - - - +
138D LEU* 3.8 7.3 - - + +
146D ALA 2.9 18.2 + - - +
147D GLU 3.5 5.8 - - - +
148D THR 3.3 0.2 - - - -
149D ARG* 1.3 76.1 - - - +
151D ALA* 1.3 63.6 + - - +
153D LEU* 3.3 6.4 + - - +
154D LEU* 3.2 18.4 + - - +
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 5.0 3.3 - - + +
163B ASP* 5.1 0.7 - - - +
171B TYR* 5.1 6.1 + - + +
175B TYR* 3.2 32.1 - - + +
179B ALA* 5.9 0.9 - - + -
131D ARG* 3.6 33.6 - - - +
147D GLU 3.0 9.1 + - - +
148D THR* 3.5 5.8 - - + +
150D ALA* 1.3 75.6 - - - +
152D LEU* 1.3 58.7 + - + +
154D LEU* 3.4 2.9 + - - +
155D ALA* 2.9 29.7 + - - +
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B THR* 3.5 31.0 - - + -
160B LEU* 4.2 5.4 - - + -
179B ALA* 3.6 42.2 - - + +
182B ILE* 3.7 13.5 - - + -
183B GLN* 3.5 31.0 - - + +
186B MSE 3.6 13.0 - - + -
148D THR* 2.9 17.2 + - + +
149D ARG* 3.5 8.3 - - - +
151D ALA* 1.3 74.7 - - - +
153D LEU* 1.3 59.0 + - - +
155D ALA* 3.7 1.5 - - - +
156D THR* 2.6 38.1 + - - -
183D GLN* 4.3 4.5 - - - +
187D ILE* 4.6 0.7 - - + -
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU* 4.2 32.1 - - + -
89D MSE 3.9 21.8 - - + -
134D LEU* 4.2 9.2 - - + -
138D LEU* 5.9 1.8 - - + -
149D ARG 2.8 19.7 + - - +
150D ALA* 3.3 7.2 + - - +
152D LEU* 1.3 73.9 - - - +
154D LEU* 1.3 63.5 + - - +
156D THR* 3.4 0.9 + - - -
157D VAL* 3.1 31.9 + - + +
180D LEU* 3.9 25.1 - - + -
183D GLN* 3.8 28.3 - - + +
184D ILE* 4.1 9.9 - - + -
187D ILE* 4.1 16.5 - - + +
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ASP* 4.9 2.0 - - - +
171B TYR* 5.5 1.3 - - - +
89D MSE 4.3 8.3 - - - -
92D LEU* 3.7 29.6 - - + -
127D LEU* 3.7 35.2 - - + +
130D ILE* 3.6 34.8 - - + -
131D ARG* 3.8 14.1 - - + -
134D LEU* 4.1 5.3 - - + +
150D ALA 3.2 9.9 + - - +
151D ALA 3.8 7.0 - - - +
153D LEU* 1.3 79.3 - - - +
155D ALA* 1.3 57.7 + - - +
157D VAL* 3.3 1.6 + - - -
158D ASP* 2.9 47.9 + - - +
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B THR* 4.2 3.4 - - + +
159B GLY* 3.1 11.7 - - - -
160B LEU* 3.7 36.3 - - + +
163B ASP* 3.5 21.7 + - - +
171B TYR* 5.7 0.2 - - + -
151D ALA 2.9 18.6 + - - +
152D LEU* 3.7 5.2 - - - +
153D LEU 3.3 0.2 - - - -
154D LEU* 1.3 77.1 - - - +
156D THR* 1.3 57.2 + - - +
158D ASP* 3.3 1.2 + - - -
159D GLY* 2.8 25.8 + - - -
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Residues in contact with THR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 3.6 39.3 - - + +
155B ALA* 3.9 3.3 - - + +
156B THR* 2.7 36.1 + - - +
183B GLN* 4.0 0.3 + - - -
152D LEU 2.6 21.6 + - - -
153D LEU 3.9 2.9 - - - -
155D ALA* 1.3 75.4 - - - +
157D VAL* 1.3 59.3 + - - +
159D GLY* 3.4 0.9 + - - -
160D LEU* 2.8 36.8 + - + +
183D GLN* 3.4 24.5 + - + +
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D MSE 3.7 22.7 - - + +
92D LEU* 3.6 35.2 - - + -
93D LEU* 3.6 21.0 - - + +
153D LEU* 3.1 20.4 + - + +
154D LEU 3.7 3.6 - - - +
156D THR* 1.3 76.5 - - - +
158D ASP* 1.3 64.9 + - - +
160D LEU* 4.4 5.2 - - + -
161D ALA* 3.0 24.3 + - - +
180D LEU* 3.8 29.2 - - + -
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Residues in contact with ASP 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B GLY* 4.3 4.3 - - - -
162B LEU* 4.1 12.5 - - + +
163B ASP* 2.6 36.8 - - - +
92D LEU* 4.3 11.1 - - - +
123D ARG* 3.7 11.4 + - - -
127D LEU* 3.7 11.4 - - - +
154D LEU* 2.9 34.0 + - - +
155D ALA 3.6 4.9 - - - +
157D VAL* 1.3 72.1 - - - +
159D GLY* 1.3 58.4 + - - +
161D ALA* 3.5 5.8 + - - +
162D LEU* 3.0 28.1 + - - +
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Residues in contact with GLY 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ALA* 3.3 27.8 - - - -
158B ASP* 4.3 3.1 - - - -
159B GLY* 3.5 11.2 - - - -
155D ALA 2.8 11.5 + - - -
156D THR 3.7 0.2 - - - -
158D ASP* 1.3 76.1 - - - +
160D LEU* 1.3 58.8 + - - +
162D LEU* 3.2 5.3 + - - +
163D ASP* 2.8 34.7 + - - -
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ALA 4.9 4.3 - - - +
152B LEU* 4.0 21.8 - - + -
155B ALA* 3.7 19.0 - - + +
93D LEU* 3.8 23.6 - - + -
156D THR* 2.8 27.0 + - + +
157D VAL* 3.4 4.2 + - + -
159D GLY* 1.3 71.2 - - - +
161D ALA* 1.3 58.4 + - - +
163D ASP* 3.9 3.3 - - - +
164D ALA* 2.9 32.8 + - - +
171D TYR* 4.0 24.5 - - + -
175D TYR* 5.4 1.3 - - + -
176D LEU* 4.1 19.1 - - + +
179D ALA* 4.1 21.5 - - + -
180D LEU* 4.6 9.4 - - + +
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU 3.4 25.6 - - - +
93D LEU* 4.0 0.8 - - + +
94D PRO* 4.0 17.9 - - + +
103D ALA* 4.3 11.2 - - + +
107D ALA* 6.5 0.4 - - + -
157D VAL 3.0 15.9 + - - +
158D ASP* 3.8 6.3 - - - +
160D LEU* 1.3 78.1 - - - +
162D LEU* 1.3 56.3 + - - +
164D ALA* 3.3 1.4 + - - +
165D ILE* 2.8 38.4 + - + +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA* 4.4 9.6 - - + +
110B ALA* 3.7 31.0 - - + +
111B VAL* 3.9 12.3 - - + +
123B ARG* 5.2 1.8 - - - +
158B ASP* 4.6 18.2 - - + +
162B LEU* 4.2 32.3 - - + -
107D ALA* 3.9 24.9 - - + -
158D ASP 3.0 17.9 + - - +
159D GLY* 3.2 4.5 + - - +
161D ALA* 1.3 77.8 - - - +
163D ASP* 1.3 65.2 + - - +
165D ILE* 3.2 10.1 + - + +
166D GLY* 3.0 21.1 + - - -
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Residues in contact with ASP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG* 3.1 19.6 + - - +
127B LEU* 4.0 12.5 - - + +
154B LEU* 4.4 1.2 - - - +
155B ALA* 3.6 20.8 + - - +
158B ASP* 2.6 33.0 - - - +
159D GLY 2.8 23.4 + - - +
160D LEU* 3.9 2.9 - - - +
162D LEU* 1.3 75.8 - - - +
164D ALA* 1.3 58.3 + - - +
166D GLY 3.7 0.9 - - - -
167D SER* 2.8 34.5 + - - +
171D TYR* 3.8 29.2 + - + -
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PRO* 3.9 20.8 - - + +
160D LEU 2.9 19.5 + - - +
161D ALA 3.9 2.5 - - - +
163D ASP* 1.3 76.5 - - - +
165D ILE* 1.3 63.1 + - - +
167D SER 4.2 0.7 - - - -
168D PRO* 3.1 26.3 - - - +
171D TYR* 3.4 33.6 - - + +
176D LEU* 4.2 9.2 - - + -
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA 4.3 8.1 - - - +
111B VAL* 4.7 4.9 - - - -
113B ALA 4.6 0.2 - - - -
114B ALA* 3.4 39.0 - - + +
94D PRO* 4.8 7.4 - - + -
100D SER* 5.0 3.6 - - - +
103D ALA* 3.2 44.9 - - + +
104D HIS* 3.5 18.6 - - + +
107D ALA* 3.9 15.7 - - + -
161D ALA* 2.8 28.7 + - + +
162D LEU* 3.5 6.1 - - + +
164D ALA* 1.3 77.4 - - - +
166D GLY* 1.3 61.2 + - - +
167D SER 3.6 0.5 + - - -
168D PRO* 3.7 12.3 - - - +
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Residues in contact with GLY 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA 3.5 19.5 - - - -
113B ALA* 3.5 11.7 - - - +
114B ALA 4.5 0.2 - - - -
120B ALA* 3.3 26.9 - - - +
123B ARG* 3.8 10.7 - - - +
162D LEU 3.0 13.8 + - - -
163D ASP 3.7 0.9 - - - -
165D ILE* 1.3 77.7 - - - +
167D SER* 1.3 63.9 + - - +
168D PRO* 3.9 2.7 - - - -
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA* 3.7 3.5 + - - -
123B ARG* 3.5 6.1 - - - +
124B ARG* 3.1 39.7 + - - -
127B LEU* 3.8 12.9 - - - +
163D ASP 2.8 13.8 + - - -
164D ALA 3.5 2.9 - - - -
166D GLY* 1.3 80.8 + - - +
168D PRO* 1.4 69.8 - - - +
169D ALA 3.1 4.1 + - - -
170D LEU* 3.3 12.2 + - - -
171D TYR* 3.3 15.0 - - - -
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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