Contacts of the helix formed by residues 149 - 173 (chain A) in PDB entry 3CJD
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 ASP 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLU 3.7 1.6 + - - +
148A SER* 1.3 76.6 - - - +
150A ASP* 1.3 61.9 + - - +
151A ALA* 3.4 11.2 + - - +
152A GLU* 2.8 47.3 + - - +
153A LEU* 2.8 27.7 + - - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 5.8 0.2 - - - +
149A ASP* 1.3 76.7 - - - +
151A ALA* 1.3 52.7 - - - +
153A LEU* 3.3 16.6 + - - +
154A ASP* 2.7 36.5 + - - +
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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
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149A ASP* 3.4 11.2 + - - +
150A ASP* 1.3 75.7 - - - +
152A GLU* 1.3 56.8 + - + +
154A ASP* 3.3 7.5 + - - +
155A LEU* 2.9 41.9 + - + +
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU 4.2 2.8 - - - +
148A SER* 3.4 20.4 - - - +
149A ASP* 2.8 50.0 + - - +
151A ALA* 1.3 77.7 - - + +
153A LEU* 1.3 55.9 + - - +
155A LEU* 3.5 10.1 + - + +
156A MSE 3.0 29.7 + - - +
187B MSE 5.2 1.4 - - - +
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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
----------------------------------------------------------
138A THR* 3.9 18.8 - - + +
141A LEU* 3.7 40.4 - - + +
142A ALA* 3.8 22.0 - - + +
145A PHE* 4.2 4.9 - - + +
148A SER* 3.9 29.8 - - - +
149A ASP 2.8 23.0 + - - +
150A ASP* 3.7 18.6 - - - +
152A GLU* 1.3 68.9 - - - +
154A ASP* 1.3 56.1 + - - +
156A MSE 3.3 5.9 + - + +
157A THR* 2.7 37.6 + - - -
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Residues in contact with ASP 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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134A PHE* 5.3 4.2 - - - -
138A THR* 5.0 3.7 - - - +
150A ASP 2.7 21.5 + - - +
151A ALA* 3.5 8.4 - - - +
153A LEU* 1.3 69.1 - - - +
155A LEU* 1.3 70.5 + - - +
157A THR* 3.3 7.6 + - - -
158A ARG* 3.1 57.9 + - - +
180B PRO* 5.8 1.6 - - - +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA* 2.9 25.7 + - + +
152A GLU* 3.7 9.2 - - + +
154A ASP* 1.3 82.1 - - - +
156A MSE 1.3 51.7 + - - +
158A ARG* 3.4 6.6 + - - +
159A THR* 2.7 36.2 + - - -
179B VAL* 4.3 0.8 - - + +
180B PRO* 3.9 20.0 - - + -
183B GLN* 3.2 54.5 - - + +
186B THR* 5.3 2.9 - - + -
187B MSE 3.6 28.0 - - + +
190B LEU* 5.9 1.1 - - + -
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Residues in contact with MSE 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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141A LEU* 4.0 26.5 - - + -
145A PHE* 4.1 17.3 - - + -
152A GLU 3.0 17.3 + - - +
153A LEU* 3.8 7.2 - - + +
154A ASP 3.3 0.2 - - - -
155A LEU* 1.3 73.4 - - - +
157A THR* 1.3 60.5 + - - +
159A THR* 3.6 7.0 - - - -
160A LEU* 3.0 49.5 + - + +
187B MSE 3.9 24.6 - - + +
190B LEU* 3.9 18.8 - - + +
191B LEU* 5.4 0.9 - - - -
194B GLN* 3.6 31.2 - - - +
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Residues in contact with THR 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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134A PHE* 3.5 36.8 - - + +
137A ILE* 3.7 19.9 - - + +
138A THR* 2.7 29.1 + - - +
141A LEU* 3.5 17.1 - - - +
153A LEU 2.7 18.6 + - - -
154A ASP* 3.5 10.5 - - - -
156A MSE 1.3 75.6 - - - +
158A ARG* 1.3 56.4 + - - +
160A LEU* 3.9 0.7 - - - +
161A PHE* 2.9 30.0 + - - +
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Residues in contact with ARG 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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130A MSE 4.6 7.3 - - - +
134A PHE* 3.8 23.2 - - + -
154A ASP* 3.1 44.7 + - - +
155A LEU* 3.7 6.7 - - - +
157A THR* 1.3 74.8 - - - +
159A THR* 1.3 49.8 + - - +
161A PHE* 3.9 0.7 - - - +
162A SER* 2.7 40.7 + - - -
176B ILE 3.0 28.7 + - - -
177B SER* 3.5 10.0 - - - +
178B GLY 3.0 23.2 + - - -
179B VAL* 3.6 19.3 - - + +
180B PRO* 4.2 15.6 - - - +
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Residues in contact with THR 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 LEU 2.7 22.2 + - - -
156A MSE 3.6 11.0 - - - -
157A THR 3.3 0.2 - - - -
158A ARG* 1.3 75.7 - - - +
160A LEU* 1.3 58.6 + - - +
162A SER* 3.4 3.7 + - - -
163A SER* 2.9 32.6 + - - -
167B ILE* 3.8 16.9 - - + +
179B VAL* 3.6 8.1 - - - +
187B MSE 3.1 53.4 - - + +
191B LEU* 4.0 17.3 - - + +
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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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90A LEU* 4.5 8.5 - - + -
137A ILE* 5.3 0.2 - - + -
141A LEU* 3.6 33.7 - - + -
156A MSE 3.0 30.7 + - + +
157A THR* 4.3 1.8 - - - +
159A THR* 1.3 77.1 - - - +
161A PHE* 1.3 66.1 + - - +
163A SER* 3.4 5.7 + - - +
164A VAL* 3.0 28.2 + - - +
191A LEU* 5.8 1.6 - - + -
192A LEU* 4.5 7.2 - - + -
195A VAL* 3.9 33.9 - - + -
203A STE 3.4 18.6 - - + -
191B LEU* 3.9 26.2 - - + -
194B GLN* 5.3 1.1 - - - +
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Residues in contact with PHE 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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97A TYR* 3.5 45.3 - + - -
112A PHE* 3.9 6.1 - + - -
134A PHE* 3.7 24.9 - + + -
137A ILE* 3.9 7.0 - - + -
157A THR 2.9 19.7 + - - +
158A ARG 3.9 1.8 - - - +
160A LEU* 1.3 76.3 - - - +
162A SER* 1.3 64.4 + - - +
164A VAL* 3.2 2.9 + - + -
165A HIS* 3.0 23.8 + - + +
203A STE 3.7 57.2 - - + +
170B LEU* 3.9 13.9 - - + -
177B SER* 3.8 29.2 - - - -
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Residues in contact with SER 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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158A ARG 2.7 29.6 + - - -
159A THR* 3.7 3.8 - - - -
161A PHE* 1.3 73.2 - - - +
163A SER* 1.3 59.7 + - - +
165A HIS* 3.5 2.1 + - - +
166A GLY 3.1 17.7 + - - -
166B GLY* 3.3 19.2 - - - -
167B ILE* 3.6 26.5 + - - -
170B LEU* 3.7 22.3 - - - +
177B SER 4.0 7.4 + - - -
178B GLY* 4.0 8.3 - - - -
179B VAL* 4.2 3.9 + - - +
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Residues in contact with SER 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 THR 2.9 23.2 + - - -
160A LEU* 3.5 8.7 - - - -
162A SER* 1.3 73.3 - - - +
164A VAL* 1.3 64.9 + - - +
166A GLY 3.3 1.6 + - - -
167A ILE* 3.2 26.8 + - - +
191A LEU* 4.2 11.0 - - - -
163B SER* 3.5 31.6 + - - +
167B ILE* 3.8 1.0 - - - +
191B LEU* 3.4 31.3 - - - +
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Residues in contact with VAL 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 SER* 3.6 39.7 - - - +
97A TYR* 4.3 12.8 - - + -
160A LEU 3.0 21.7 + - - +
161A PHE* 3.9 3.6 - - + +
163A SER* 1.3 71.3 - - - +
165A HIS* 1.3 60.1 + - - +
167A ILE* 3.2 9.1 + - - +
168A VAL* 2.9 41.8 + - + +
188A ILE* 4.5 11.4 - - + -
191A LEU* 4.8 5.8 - - + -
192A LEU* 4.2 13.9 - - + -
203A STE 4.1 15.0 - - + -
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Residues in contact with HIS 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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97A TYR* 2.7 32.5 + - - +
108A TRP* 3.6 19.1 - + - -
109A ARG* 6.5 0.2 - - - -
112A PHE* 3.3 41.5 - + - +
161A PHE* 3.0 21.3 + - + +
162A SER 3.6 4.5 - - - +
164A VAL* 1.3 78.0 - - - +
166A GLY* 1.3 52.7 + - - +
168A VAL* 3.4 0.6 + - - +
169A LEU* 2.7 60.9 + - + +
166B GLY* 5.3 1.1 - - - -
169B LEU* 5.2 2.9 - - + +
170B LEU* 3.7 35.0 - - + +
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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 SER 3.1 10.3 + - - -
163A SER 3.3 1.3 + - - -
164A VAL 3.2 0.2 - - - -
165A HIS* 1.3 74.6 - - - +
167A ILE* 1.3 65.1 + - - +
169A LEU* 4.5 4.3 - - - -
170A LEU* 3.1 33.1 + - - +
162B SER* 3.3 24.1 - - - -
165B HIS* 5.3 2.7 - - - -
166B GLY* 3.8 13.9 - - - -
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Residues in contact with ILE 167 (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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163A SER 3.2 10.8 + - - +
164A VAL* 3.2 11.4 + - - +
166A GLY* 1.3 77.4 - - - +
168A VAL* 1.3 56.8 + - - +
170A LEU* 4.4 0.5 - - - +
171A GLY 3.1 22.3 + - - -
179A VAL* 4.5 12.3 + - + -
184A LEU* 3.4 27.7 - - + +
187A MSE 5.2 1.3 - - + -
188A ILE* 4.0 29.8 - - + +
191A LEU* 3.4 33.9 - - + -
159B THR* 3.7 30.7 - - + +
162B SER* 3.7 10.4 + - - -
163B SER* 3.5 5.8 - - - +
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Residues in contact with VAL 168 (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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97A TYR* 4.1 15.0 - - + -
98A LEU* 4.0 27.8 - - + -
101A ALA* 3.7 17.0 - - + -
108A TRP* 4.0 9.4 - - + -
164A VAL* 2.9 34.1 + - + +
165A HIS 3.8 3.6 - - - +
167A ILE* 1.3 75.2 - - + +
169A LEU* 1.3 58.9 + - - +
172A LEU* 2.9 55.4 + - + +
184A LEU* 4.9 2.0 - - - -
188A ILE* 4.3 7.9 - - + -
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Residues in contact with LEU 169 (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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108A TRP* 4.0 23.1 - - + -
109A ARG* 4.4 15.7 - - - +
165A HIS* 2.7 39.0 + - + +
166A GLY* 4.0 3.6 - - - +
167A ILE 3.4 0.2 - - - -
168A VAL* 1.3 72.2 - - - +
170A LEU* 1.3 61.4 + - + +
172A LEU* 4.0 0.7 - - - +
173A GLU* 3.0 67.1 + - + +
165B HIS* 5.1 6.3 - - + +
169B LEU* 3.4 33.9 - - + -
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Residues in contact with LEU 170 (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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166A GLY 3.1 13.2 + - - +
169A LEU* 1.3 79.0 - - + +
171A GLY* 1.3 61.6 + - - +
173A GLU* 4.2 7.2 - - - +
174A ASN* 3.4 2.3 + - - -
175A ARG* 3.2 47.6 + - + +
177A SER* 3.7 15.3 - - - +
178A GLY* 3.7 19.5 - - - +
112B PHE* 3.8 21.5 - - + -
161B PHE* 3.9 16.6 - - + -
162B SER* 3.7 24.2 - - - +
165B HIS* 3.8 27.1 - - + +
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Residues in contact with GLY 171 (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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167A ILE 3.1 18.4 + - - -
170A LEU* 1.3 77.0 - - - +
172A LEU* 1.3 57.4 + - - +
174A ASN* 3.1 28.6 + - - -
178A GLY* 4.3 0.6 - - - -
179A VAL 3.4 26.5 - - - +
181A GLY* 4.9 2.8 + - - -
184A LEU* 3.8 14.4 - - - +
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Residues in contact with LEU 172 (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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98A LEU* 4.0 4.3 - - + -
101A ALA* 3.4 43.5 - - + +
102A ARG* 3.5 47.8 - - + +
108A TRP* 4.3 11.2 - - + -
168A VAL* 2.9 30.0 + - + +
169A LEU 4.4 1.1 - - - +
171A GLY* 1.3 74.9 - - - +
173A GLU* 1.3 60.8 + - + +
174A ASN* 3.2 5.6 + - - +
184A LEU* 3.7 11.7 - - + -
117B ARG* 3.6 12.8 + - - -
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Residues in contact with GLU 173 (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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108A TRP* 6.2 1.3 - - + -
109A ARG* 3.0 36.2 + - - +
169A LEU* 3.0 43.8 + - + +
170A LEU* 4.2 4.7 - - - +
171A GLY 3.4 0.2 - - - -
172A LEU* 1.3 75.4 - - + +
174A ASN* 1.3 64.2 + - - +
175A ARG* 3.4 35.7 + - + +
112B PHE* 5.0 5.1 - - - +
117B ARG* 3.1 28.5 + - - +
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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