Contacts of the helix formed by residues 151 - 174 (chain D) in PDB entry 3ENM
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 PRO 151 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D THR* 3.1 17.7 - - + +
150D ILE* 1.4 87.5 - - + +
152D GLU* 1.3 65.6 + - - +
153D ASP* 3.4 9.6 - - + +
154D ILE* 3.1 26.0 + - + +
155D LEU* 3.1 16.5 + - - +
327D PHE* 3.7 20.4 - - + -
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Residues in contact with GLU 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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150D ILE 3.6 0.8 + - - -
151D PRO* 1.3 69.3 - - - +
153D ASP* 1.3 60.8 + - - +
155D LEU* 3.0 9.5 + - + +
156D GLY* 2.7 34.3 + - - -
282D LYS 4.6 1.4 - - - +
283D PHE* 3.6 13.3 - - + -
284D SER* 2.8 51.6 + - - -
286D GLU* 5.0 0.5 - - - +
287D PHE* 3.6 32.2 - - + +
313D PHE* 3.7 9.2 - - + -
317D HIS* 3.9 11.4 + - - +
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Residues in contact with ASP 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D PRO* 3.4 7.0 - - + +
152D GLU* 1.3 77.8 + - - +
154D ILE* 1.3 64.0 + - + +
156D GLY* 3.5 1.0 + - - -
157D LYS* 3.2 27.4 + - - +
317D HIS* 3.6 16.2 + - - +
320D LYS* 3.1 33.5 + - - -
322D THR* 3.7 24.8 + - + +
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Residues in contact with ILE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D PHE* 5.5 1.1 - - + -
150D ILE* 3.5 19.5 - - + -
151D PRO* 3.1 23.6 + - + +
152D GLU 3.1 0.4 - - - -
153D ASP* 1.3 77.8 - - + +
155D LEU* 1.3 64.1 - - - +
156D GLY 3.3 0.3 + - - -
157D LYS* 3.3 6.5 + - - +
158D ILE* 2.9 33.0 + - + +
187D ILE* 5.4 2.5 - - + -
322D THR* 4.1 16.2 - - + -
323D ASP 4.9 1.8 - - - +
324D VAL* 4.2 25.6 - - + -
327D PHE* 3.2 54.5 - - + -
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 3.5 39.5 - - + +
151D PRO 3.1 7.8 + - - +
152D GLU* 3.0 15.6 + - + +
154D ILE* 1.3 73.7 - - - +
156D GLY* 1.3 52.9 + - - +
158D ILE* 3.1 8.4 + - + +
159D ALA* 2.7 36.0 + - - +
247D MSE 4.5 8.5 - - - +
250D LEU* 3.6 37.9 - - + -
251D ALA* 4.1 15.5 - - + +
283D PHE* 4.8 5.2 - - + -
287D PHE* 3.8 34.1 - - + -
313D PHE* 4.3 2.7 - - + -
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Residues in contact with GLY 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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152D GLU 2.7 19.5 + - - -
153D ASP 3.9 0.2 - - - -
154D ILE 3.2 0.2 - - - -
155D LEU* 1.3 72.0 - - - +
157D LYS* 1.3 50.1 + - - +
159D ALA* 3.0 3.6 + - - +
160D VAL* 2.7 38.1 + - - +
313D PHE* 3.6 21.2 - - - -
317D HIS* 3.7 23.6 - - - -
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Residues in contact with LYS 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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153D ASP 3.2 15.1 + - - +
154D ILE 3.7 7.0 - - - +
156D GLY* 1.3 72.2 - - - +
158D ILE* 1.3 68.1 + - + +
160D VAL* 3.9 9.5 - - + +
161D SER* 3.1 25.6 + - - -
193D VAL* 4.8 5.8 - - + +
317D HIS* 2.9 29.7 - - + +
318D GLU* 4.8 4.9 - - - +
320D LYS 2.5 27.3 + - - +
322D THR* 3.2 27.4 + - - +
324D VAL* 4.1 24.8 - - + +
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Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D LEU* 3.4 43.3 - - + -
139D PHE* 5.5 1.3 - - + -
150D ILE* 4.8 8.3 - - + -
154D ILE* 2.9 36.3 + - + +
155D LEU* 3.1 15.9 + - + +
157D LYS* 1.3 78.6 - - + +
159D ALA* 1.3 64.8 + - - +
161D SER* 3.1 2.3 + - - -
162D ILE* 3.1 34.0 + - + +
187D ILE* 4.6 4.3 - - + -
193D VAL* 4.1 25.7 - - + +
247D MSE 4.2 3.8 - - - -
250D LEU* 3.8 19.3 - - + -
324D VAL* 6.1 0.2 - - + -
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Residues in contact with ALA 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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155D LEU 2.7 20.8 + - - +
156D GLY 3.5 4.7 - - - +
158D ILE* 1.3 73.3 - - - +
160D VAL* 1.3 64.0 + - + +
162D ILE* 3.4 1.2 + - - +
163D VAL* 3.1 30.1 + - - +
247D MSE 3.7 28.0 - - + -
290D PHE* 4.4 15.9 - - + -
313D PHE* 3.9 21.3 - - + -
314D PHE* 5.2 1.3 - - + -
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Residues in contact with VAL 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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111D PHE* 5.6 2.2 - - + -
156D GLY 2.7 21.9 + - - +
157D LYS* 3.9 11.4 - - + +
158D ILE 3.3 0.2 - - - -
159D ALA* 1.3 74.4 - - + +
161D SER* 1.3 61.0 + - - +
164D LYS* 3.0 41.5 + - + +
313D PHE* 6.5 0.2 - - + -
314D PHE* 3.6 45.9 - - + +
317D HIS* 4.1 3.4 - - + -
318D GLU* 3.6 35.9 - - + +
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Residues in contact with SER 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D PHE* 4.1 22.0 - - - +
157D LYS 3.1 17.2 + - - -
158D ILE 3.1 4.0 + - - -
160D VAL* 1.3 78.2 - - - +
162D ILE* 1.3 66.5 + - - +
164D LYS* 3.3 2.3 + - - +
165D ALA* 2.9 24.3 + - - +
193D VAL* 3.3 40.9 + - - +
194D LYS* 5.5 0.7 - - - -
195D MSE 5.6 1.3 - - - -
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Residues in contact with ILE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D LEU* 5.1 0.9 - - + -
158D ILE* 3.1 24.6 + - + +
159D ALA 4.0 3.4 - - - +
161D SER* 1.3 74.6 - - - +
163D VAL* 1.3 59.3 - - - +
165D ALA* 3.1 4.5 + - - +
166D LEU* 2.8 52.6 + - + +
180D VAL* 4.1 15.0 - - + -
185D VAL* 4.1 33.9 - - + -
195D MSE 4.0 20.0 - - + -
243D LEU* 4.1 8.7 - - + -
246D THR* 4.4 8.3 - - - +
247D MSE 3.0 31.4 - - + -
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Residues in contact with VAL 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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159D ALA 3.1 21.4 + - - +
160D VAL 4.0 2.7 - - - +
162D ILE* 1.3 73.6 - - - +
164D LYS* 1.3 65.9 + - - +
166D LEU* 3.9 7.3 - - - +
167D GLU* 2.9 22.9 + - - +
243D LEU* 3.4 31.2 - - + -
290D PHE* 4.2 15.9 - - + -
305D TYR* 4.5 10.9 - - + -
308D LEU* 4.3 13.9 - - + -
309D MSE 3.9 19.5 - - + -
314D PHE* 3.9 21.5 - - + -
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Residues in contact with LYS 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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111D PHE* 3.3 45.8 - - + -
160D VAL* 3.0 26.0 + - + +
161D SER 3.8 2.5 - - - +
163D VAL* 1.3 76.8 - - - +
165D ALA* 1.3 64.3 + - - +
167D GLU* 3.0 6.7 + - - +
168D HIS* 2.8 25.9 + - - +
309D MSE 4.6 16.8 - - + -
314D PHE* 4.3 14.4 - - + -
318D GLU* 2.8 40.0 + - - +
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Residues in contact with ALA 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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109D CYS* 4.8 0.2 - - - -
111D PHE* 3.9 25.6 - - + +
112D THR* 4.1 10.0 - - + +
161D SER 2.9 13.7 + - - +
162D ILE 3.3 8.7 - - - +
164D LYS* 1.3 74.9 - - - +
166D LEU* 1.3 65.2 + - - +
168D HIS* 3.3 5.2 + - - +
169D LEU* 3.0 29.0 + - + +
195D MSE 3.9 27.6 - - + -
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Residues in contact with LEU 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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162D ILE* 2.8 38.3 + - + +
163D VAL* 3.9 3.1 - - - +
165D ALA* 1.3 74.6 - - - +
167D GLU* 1.3 58.9 + - - +
169D LEU* 3.4 5.4 + - + +
170D HIS* 2.8 32.2 + - - +
175D VAL 4.8 0.2 - - - +
177D HIS* 3.7 28.7 - - + +
180D VAL* 4.0 17.7 - - + -
195D MSE 3.4 24.2 - - - -
239D ASP* 4.7 2.0 - - + +
243D LEU* 4.8 10.8 - - + -
305D TYR* 3.2 42.3 - - + +
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Residues in contact with GLU 167 (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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163D VAL* 2.9 18.8 + - + +
164D LYS* 3.7 2.9 - - - +
166D LEU* 1.3 78.4 - - - +
168D HIS* 1.3 61.4 + - - +
170D HIS* 4.5 1.1 + - + +
171D SER* 2.8 62.0 + - - +
172D LYS* 5.7 1.4 - - - -
305D TYR* 3.5 35.6 - - + -
306D PRO* 4.8 6.7 - - - +
309D MSE 3.9 25.7 - - - +
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Residues in contact with HIS 168 (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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106D THR 5.6 0.2 - - - -
107D VAL* 5.0 1.1 - - + -
108D ASP 3.5 32.3 + - - -
109D CYS* 3.7 26.4 - - + +
111D PHE* 5.9 0.7 - - + -
112D THR* 5.6 0.2 - - - +
164D LYS 2.8 16.1 + - - +
165D ALA 3.6 3.8 - - - +
167D GLU* 1.3 82.4 + - - +
169D LEU* 1.3 73.7 + - - +
171D SER* 4.4 2.0 - - - -
172D LYS* 2.8 62.4 + - + +
173D LEU* 4.5 12.1 - - + -
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Residues in contact with LEU 169 (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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107D VAL* 3.8 39.5 - - + -
112D THR* 4.5 8.5 - - + -
165D ALA* 3.0 22.9 + - + +
166D LEU* 3.7 7.0 - - + +
168D HIS* 1.3 82.5 + - - +
170D HIS* 1.3 62.4 + - - +
173D LEU* 3.1 23.6 + - + +
175D VAL* 2.9 42.2 + - + +
177D HIS* 4.0 24.7 - - + +
195D MSE 5.4 0.4 - - - -
197D ASP* 3.7 28.5 - - + +
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Residues in contact with HIS 170 (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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166D LEU 2.8 21.5 + - - +
167D GLU* 3.9 2.6 + - + +
169D LEU* 1.3 73.6 - - - +
171D SER* 1.3 61.0 + - - +
174D SER* 2.6 41.9 + - - -
175D VAL 3.3 9.6 + - - +
176D ILE* 4.1 16.4 - - + +
236D VAL* 3.6 37.5 - - + +
305D TYR* 4.3 19.6 - - + -
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Residues in contact with SER 171 (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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167D GLU* 2.8 53.1 + - - -
170D HIS* 1.3 78.2 - - - +
172D LYS* 1.3 79.8 + - - +
173D LEU 3.5 0.2 + - - -
174D SER* 4.2 4.0 + - - -
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Residues in contact with LYS 172 (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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167D GLU* 5.7 1.3 - - - -
168D HIS* 2.8 55.5 + - + +
171D SER* 1.3 89.3 + - - +
173D LEU* 1.3 70.1 + - + +
174D SER 3.8 0.2 - - - -
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D THR* 3.7 30.3 - - - +
107D VAL* 3.5 35.0 - - + -
168D HIS* 4.5 7.6 - - + -
169D LEU* 3.1 29.1 + - + +
172D LYS* 1.3 98.9 - - + +
174D SER* 1.3 71.9 + - - +
175D VAL* 3.0 18.0 + - + +
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Residues in contact with SER 174 (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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170D HIS* 2.6 33.4 + - - -
171D SER 4.2 3.0 + - - -
172D LYS 3.8 1.0 - - - -
173D LEU* 1.3 73.5 - - - +
175D VAL* 1.3 59.1 + - - +
176D ILE* 4.0 3.3 + - - +
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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
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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) + - + + + + + -
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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