Contacts of the helix formed by residues 145 - 167 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR 3.5 0.6 + - - -
144A PRO* 1.3 74.8 - - + +
146A ALA* 1.3 64.9 + - - +
147A GLU 3.3 3.1 - - - -
148A THR* 3.2 11.7 + - - -
149A ARG* 2.9 29.9 + - + +
178C HIS* 2.9 37.3 + - - -
182C ILE* 3.8 22.4 - - + +
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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
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135A SER* 4.5 1.6 - - - +
138A LEU* 3.6 16.2 - - + +
139A ILE* 3.6 42.4 - - + +
143A THR* 3.3 19.7 + - - +
144A PRO 3.1 3.8 + - - -
145A GLU* 1.3 76.0 - - - +
147A GLU* 1.3 58.0 + - - +
149A ARG* 3.3 0.8 + - - -
150A ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 4.9 11.8 + - + +
135A SER* 3.6 24.1 + - - +
139A ILE* 5.3 7.2 - - + +
145A GLU 3.3 1.0 - - - -
146A ALA* 1.3 79.4 - - - +
148A THR* 1.3 63.5 + - - +
150A ALA* 3.4 5.0 + - - +
151A ALA* 3.2 17.5 + - - +
175C TYR* 3.7 12.0 + - + +
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Residues in contact with THR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 3.2 15.1 + - - -
147A GLU* 1.3 76.0 - - - +
149A ARG* 1.3 61.8 + - - +
151A ALA* 3.2 2.9 + - - +
152A LEU* 2.9 28.3 + - + +
175C TYR* 3.6 21.3 + - + +
178C HIS* 3.3 29.0 + - + -
179C ALA* 3.5 35.9 - - + -
182C ILE* 3.9 14.8 - - + -
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Residues in contact with ARG 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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138A LEU* 4.1 5.4 - - + -
143A THR* 3.7 7.6 - - - +
144A PRO* 3.1 35.8 + - - +
145A GLU* 2.9 19.6 + - - +
146A ALA 3.8 4.0 - - - +
148A THR* 1.3 75.0 - - - +
150A ALA* 1.3 58.0 + - - +
152A LEU* 3.3 4.4 + - - -
153A LEU* 2.9 26.7 + - - +
186A MSE 3.6 4.0 + - - -
187A ILE* 2.7 67.3 + - + +
189A GLN* 2.9 25.7 + - - +
182C ILE* 4.1 18.8 - - + +
186C MSE 3.9 28.8 - - + +
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Residues in contact with ALA 150 (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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131A ARG* 4.0 6.2 - - + +
134A LEU* 3.7 24.1 - - + +
135A SER* 3.2 43.1 - - - +
138A LEU* 3.6 8.6 - - + +
146A ALA 2.9 12.2 + - - +
147A GLU 3.4 5.2 - - - +
148A THR 3.2 0.2 - - - -
149A ARG* 1.3 76.5 - - - +
151A ALA* 1.3 62.1 + - - +
153A LEU* 3.3 3.4 + - - +
154A LEU* 3.1 19.6 + - - +
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 3.6 33.0 - - - +
147A GLU 3.2 6.0 + - - +
148A THR* 3.2 5.1 + - + +
150A ALA* 1.3 75.0 - - - +
152A LEU* 1.3 59.0 + - + +
154A LEU* 3.4 3.7 + - - +
155A ALA* 3.0 28.2 + - - +
160C LEU* 4.6 5.1 - - + +
163C ASP* 4.8 1.6 - - - +
171C TYR* 4.7 7.4 + - + -
175C TYR* 3.3 33.7 - - + +
179C ALA* 5.7 0.9 - - + -
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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
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148A THR* 2.9 18.5 + - + +
149A ARG* 3.6 8.5 - - - +
150A ALA 3.3 0.2 - - - -
151A ALA* 1.3 71.3 - - - +
153A LEU* 1.3 60.8 + - - +
155A ALA* 3.1 4.5 + - - +
156A THR* 2.9 31.9 + - - -
183A GLN* 4.0 4.9 - - - +
187A ILE* 4.5 2.2 - - + -
156C THR* 3.7 22.1 - - + +
160C LEU* 3.9 19.5 - - + -
179C ALA* 3.5 34.5 - - + +
182C ILE* 3.7 18.4 - - + -
183C GLN* 3.6 33.7 - - + +
186C MSE 3.8 6.5 - - + -
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Residues in contact with LEU 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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85A LEU* 4.0 27.4 - - + -
89A MSE 3.9 22.4 - - + -
134A LEU* 4.3 7.6 - - + -
138A LEU* 5.6 2.7 - - + -
149A ARG 2.9 16.2 + - - +
150A ALA* 3.3 6.3 + - - +
152A LEU* 1.3 75.1 - - - +
154A LEU* 1.3 63.0 + - - +
156A THR* 3.2 16.3 + - - -
157A VAL* 3.3 12.8 + - - +
180A LEU* 3.8 28.3 - - + -
183A GLN* 3.9 19.0 - - + +
184A ILE* 3.9 19.1 - - + -
187A ILE* 4.5 16.4 - - + +
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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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89A MSE 4.3 4.5 - - - -
92A LEU* 3.8 29.6 - - + -
127A LEU* 3.6 26.7 - - + +
130A ILE* 3.8 32.3 - - + -
131A ARG* 3.9 20.0 - - + -
134A LEU* 4.1 7.1 - - + +
150A ALA 3.1 14.2 + - - +
151A ALA* 3.7 5.6 - - - +
153A LEU* 1.3 81.2 - - - +
155A ALA* 1.3 56.4 + - - +
157A VAL* 3.1 13.5 - - + +
158A ASP* 3.0 40.5 + - - +
163C ASP* 4.2 2.9 - - - +
171C TYR* 5.1 0.7 - - - +
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Residues in contact with ALA 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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151A ALA 3.0 15.2 + - - +
152A LEU 3.1 8.7 + - - +
154A LEU* 1.3 74.8 - - - +
156A THR* 1.3 56.6 + - - +
158A ASP* 3.3 0.4 + - - -
159A GLY* 2.9 26.7 + - - -
155C ALA 3.9 1.2 - - - +
156C THR* 3.6 23.3 - - + +
159C GLY* 3.3 10.5 - - - -
160C LEU* 3.7 26.2 - - + +
163C ASP* 3.5 13.4 + - - +
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Residues in contact with THR 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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152A LEU 2.9 8.0 + - - -
153A LEU* 3.2 10.7 + - + -
155A ALA* 1.3 76.4 - - - +
157A VAL* 1.3 60.7 + - + +
159A GLY* 3.8 0.3 - - - -
160A LEU* 2.9 43.4 + - + +
179A ALA 5.3 0.2 - - - +
180A LEU* 5.3 3.6 - - + -
183A GLN* 2.8 34.9 + - + -
152C LEU* 3.6 30.7 - - + -
155C ALA* 4.5 1.8 - - + +
156C THR* 2.7 27.0 + - - +
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Residues in contact with VAL 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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89A MSE 3.8 36.1 - - + +
92A LEU* 4.2 14.1 - - + +
93A LEU* 3.7 28.4 - - + +
153A LEU 3.3 9.1 + - - +
154A LEU* 3.1 35.7 - - + +
156A THR* 1.3 77.6 - - + +
158A ASP* 1.3 62.4 - - - +
160A LEU* 5.5 0.4 - - + -
161A ALA* 2.9 32.5 + - - +
180A LEU* 3.9 15.3 - - + -
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Residues in contact with ASP 158 (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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92A LEU* 5.1 6.2 - - - +
123A ARG* 3.5 13.5 + - - +
127A LEU* 4.1 9.2 - - - +
154A LEU* 3.0 27.2 + - - +
155A ALA 3.8 3.1 - - - +
157A VAL* 1.3 84.3 - - - +
159A GLY* 1.3 55.8 + - - +
161A ALA* 3.5 6.3 + - - +
162A LEU* 3.0 27.9 + - - +
159C GLY* 4.2 6.3 - - - +
162C LEU* 4.4 10.7 - - + +
163C ASP* 2.5 35.4 - - - +
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Residues in contact with GLY 159 (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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155A ALA 2.9 13.3 + - - -
158A ASP* 1.3 70.0 - - - +
160A LEU* 1.3 65.1 + - - +
162A LEU* 3.3 6.9 + - - +
163A ASP* 3.1 29.7 + - - +
155C ALA* 3.2 28.3 - - - -
158C ASP* 4.3 2.5 - - - -
159C GLY* 3.5 12.2 - - - -
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Residues in contact with LEU 160 (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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93A LEU* 4.0 16.2 - - + -
156A THR* 2.9 38.4 + - + +
157A VAL* 3.9 3.4 - - + +
159A GLY* 1.3 75.4 - - - +
161A ALA* 1.3 63.3 + - - +
163A ASP* 3.5 4.6 + - - +
164A ALA* 3.1 23.7 + - - +
171A TYR* 4.5 8.1 - - + -
175A TYR* 4.5 13.9 - - + +
176A LEU* 3.9 31.7 - - + +
179A ALA* 3.9 29.2 - - + -
180A LEU* 4.5 4.3 - - + +
151C ALA* 5.5 2.0 - - + +
152C LEU* 4.6 2.5 - - + -
155C ALA* 3.9 20.7 - - + +
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Residues in contact with ALA 161 (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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92A LEU 4.3 9.0 - - - +
93A LEU* 4.5 0.4 - - - +
94A PRO* 3.9 26.9 - - + +
103A ALA* 4.2 17.5 - - + +
157A VAL 2.9 18.3 + - - +
158A ASP* 3.6 7.4 - - - +
160A LEU* 1.3 76.9 - - - +
162A LEU* 1.3 62.0 + - - +
164A ALA* 3.3 4.0 + - - +
165A ILE* 3.2 25.4 + - - +
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Residues in contact with LEU 162 (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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107A ALA* 4.1 14.1 - - + +
158A ASP 3.0 18.1 + - - +
159A GLY* 3.3 5.6 + - - +
161A ALA* 1.3 75.0 - - - +
163A ASP* 1.3 62.7 + - - +
165A ILE* 3.2 27.9 - - + +
166A GLY 4.2 0.9 + - - -
107C ALA* 4.6 9.0 - - + +
110C ALA* 3.9 28.6 - - + +
111C VAL* 4.0 22.7 - - + -
123C ARG* 4.1 19.5 + - - +
158C ASP* 4.5 19.1 - - + +
162C LEU* 4.2 24.7 - - + -
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Residues in contact with ASP 163 (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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159A GLY 3.1 18.8 + - - +
160A LEU* 4.0 3.9 - - - +
162A LEU* 1.3 77.4 - - - +
164A ALA* 1.3 60.2 + - - +
165A ILE 3.3 0.7 + - - -
166A GLY* 3.5 10.2 + - - -
167A SER* 3.6 9.7 + - - -
171A TYR* 3.5 33.3 + - + +
123C ARG* 2.6 39.2 + - - +
127C LEU* 3.7 20.3 - - + +
154C LEU* 5.6 0.7 - - - +
155C ALA* 4.4 11.6 - - - +
158C ASP* 3.5 10.4 - - - +
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Residues in contact with ALA 164 (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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94A PRO* 3.7 24.0 - - + -
160A LEU 3.1 18.2 + - - +
161A ALA 3.3 5.1 + - - +
163A ASP* 1.3 72.7 - - - +
165A ILE* 1.3 63.6 + - - +
168A PRO* 3.0 30.3 - - + +
171A TYR* 3.7 34.0 - - + +
176A LEU* 4.7 1.6 - - + -
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Residues in contact with ILE 165 (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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100A SER 5.8 0.4 - - - +
103A ALA* 4.0 4.5 - - + +
104A HIS* 3.9 27.1 - - + +
107A ALA* 3.5 31.4 - - + -
161A ALA 3.2 10.8 + - - +
162A LEU* 3.2 25.8 - - + +
163A ASP 3.2 0.2 - - - -
164A ALA* 1.3 78.5 - - - +
166A GLY* 1.3 62.0 + - - +
168A PRO* 3.5 9.2 - - - +
601A NDS 3.9 3.3 - - - -
110C ALA 3.8 8.3 - - - +
111C VAL* 3.9 9.2 - - - +
114C ALA* 3.1 46.0 - - + +
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Residues in contact with GLY 166 (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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162A LEU 4.2 0.8 + - - -
163A ASP 3.5 6.1 + - - -
164A ALA 3.4 0.2 - - - -
165A ILE* 1.3 80.6 - - - +
167A SER* 1.3 61.6 + - - +
168A PRO* 3.4 0.9 - - - -
601A NDS 3.1 29.8 - - - +
110C ALA 4.7 0.4 + - - -
113C ALA* 3.9 32.5 - - - +
120C ALA* 3.3 8.8 - - - +
123C ARG* 6.2 2.0 - - - -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP 3.6 4.9 + - - -
164A ALA 3.4 4.1 + - - -
165A ILE 3.3 0.2 - - - -
166A GLY* 1.3 79.5 + - - +
168A PRO* 1.3 66.4 - - - +
169A ALA 3.2 0.2 - - - -
170A LEU* 3.0 24.4 + - - +
171A TYR* 3.4 28.4 - - - -
601A NDS 3.2 18.5 + - - +
120C ALA* 4.4 5.7 + - - +
124C ARG* 4.2 23.4 - - - +
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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