Contacts of the helix formed by residues 162 - 185 (chain D) in PDB entry 4MNE
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 162 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ARG 3.9 5.2 - - - +
161D ILE* 1.3 85.6 - - + +
163D GLU* 1.3 65.5 + - - +
164D GLN* 4.5 4.9 - - + +
165D ILE* 2.8 28.3 + - + +
166D LEU 3.0 8.8 + - - -
374D TRP* 3.4 38.6 - - + +
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Residues in contact with GLU 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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161D ILE 3.3 2.6 + - - -
162D PRO* 1.3 70.2 - - - +
164D GLN* 1.3 57.8 + - - +
166D LEU* 2.9 30.2 + - - +
167D GLY* 2.9 12.3 + - - -
329D VAL 4.8 0.7 - - - +
330D PHE* 3.7 19.9 - - + -
331D SER* 2.8 47.5 + - - -
334D PHE* 3.2 28.7 - - + +
360D PHE* 3.9 8.4 - - + -
363D ARG* 3.0 19.2 + - - +
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D PRO* 3.1 5.7 + - + +
163D GLU* 1.3 79.4 - - - +
165D ILE* 1.3 64.9 + - + +
167D GLY* 3.3 10.8 + - - +
168D LYS* 3.6 14.7 + - - +
363D ARG* 5.3 3.1 - - - +
364D SER* 4.7 1.5 + - - -
367D GLU* 2.8 47.7 + - - +
369D VAL* 4.0 20.6 - - + +
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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
----------------------------------------------------------
151D LEU* 6.2 0.4 - - + -
161D ILE* 3.7 17.7 - - + -
162D PRO* 2.8 27.6 + - + +
164D GLN* 1.3 74.3 - - + +
166D LEU* 1.3 64.8 + - - +
167D GLY 3.1 1.6 - - - -
168D LYS* 3.1 9.4 + - - +
169D VAL* 3.1 24.5 + - + +
369D VAL* 4.8 9.6 - - + -
370D ASP 5.0 0.7 - - - +
371D PHE* 3.6 41.7 - - + -
374D TRP* 3.7 42.6 - - + -
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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
----------------------------------------------------------
161D ILE* 3.4 35.0 - - + +
162D PRO 3.0 10.8 + - - +
163D GLU* 2.9 12.6 + - - +
165D ILE* 1.3 72.3 - - - +
167D GLY* 1.3 58.6 + - - +
169D VAL* 3.7 7.9 - - + +
170D SER* 2.8 35.6 + - - -
253D LEU* 4.0 9.5 - - + +
256D MET* 3.8 35.9 - - + -
257D ALA* 3.5 31.9 - - + +
334D PHE* 3.7 25.4 - - + -
360D PHE* 4.2 1.6 - - - -
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Residues in contact with GLY 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D GLU 2.9 10.3 + - - -
164D GLN 3.3 4.0 + - - -
165D ILE 3.1 1.0 - - - -
166D LEU* 1.3 78.4 - - - +
168D LYS* 1.3 55.2 + - - +
170D SER* 3.4 2.3 + - - -
171D ILE* 3.0 33.0 + - - +
360D PHE* 3.6 15.2 - - - -
361D ILE* 4.4 0.7 - - - +
364D SER* 3.5 30.6 - - - -
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Residues in contact with LYS 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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164D GLN 3.6 8.5 + - - +
165D ILE* 3.1 9.2 + - - +
167D GLY* 1.3 72.1 - - - +
169D VAL* 1.3 66.5 + - - +
171D ILE* 3.5 14.6 + - + +
172D ALA* 3.0 24.3 + - - +
204D ILE* 3.7 16.8 - - + +
364D SER* 2.7 32.2 + - - -
365D ASP* 4.2 8.5 + - - +
367D GLU* 2.9 18.6 + - - -
368D GLU* 5.0 0.2 - - - +
369D VAL* 3.7 40.5 - - + +
371D PHE* 5.1 7.4 - - + -
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 3.6 36.6 - - + -
161D ILE* 5.6 0.9 - - + -
165D ILE* 3.1 25.0 + - + +
166D LEU* 3.7 17.9 - - + +
168D LYS* 1.3 75.8 - - - +
170D SER* 1.3 54.8 + - - +
172D ALA* 3.1 3.2 + - - +
173D VAL* 2.8 47.6 + - + +
196D ILE* 4.1 10.8 - - + -
204D ILE* 3.9 17.0 - - + -
249D MET* 6.5 0.2 - - + -
253D LEU* 5.0 3.6 - - + -
256D MET* 4.4 9.0 - - + -
371D PHE* 5.2 1.3 - - + -
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Residues in contact with SER 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 25.3 + - - -
167D GLY 3.5 5.4 - - - -
168D LYS 3.3 0.2 - - - -
169D VAL* 1.3 73.0 - - - +
171D ILE* 1.3 53.2 + - - +
173D VAL* 3.3 5.8 + - - +
174D ILE* 2.8 41.9 + - - +
249D MET* 4.3 5.3 - - - +
253D LEU* 3.3 28.0 - - - +
337D PHE* 3.7 12.6 - - - -
360D PHE* 3.8 9.3 - - - -
361D ILE* 3.9 15.0 - - - -
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Residues in contact with ILE 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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125D TYR* 5.3 3.6 - - + +
167D GLY 3.0 22.9 + - - +
168D LYS* 3.7 22.7 - - + +
169D VAL 3.3 0.2 - - - -
170D SER* 1.3 72.9 - - - +
172D ALA* 1.3 55.6 + - - +
174D ILE* 3.1 6.4 + - - +
175D LYS* 2.6 69.2 + - + +
356D MET* 4.8 5.6 - - + -
361D ILE* 4.0 24.2 - - + +
364D SER* 4.2 2.9 - - - -
365D ASP* 3.9 41.3 - - + +
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Residues in contact with ALA 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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125D TYR* 3.8 22.8 - - + +
168D LYS 3.0 14.5 + - - +
169D VAL 3.4 7.2 - - - +
171D ILE* 1.3 75.4 - - - +
173D VAL* 1.3 53.8 + - - +
175D LYS* 3.6 0.5 - - - +
176D GLY* 2.6 36.0 + - - -
204D ILE* 3.6 41.1 - - + +
206D LEU* 4.8 2.2 - - - +
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Residues in contact with VAL 173 (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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169D VAL* 2.8 30.0 + - + +
170D SER* 3.8 3.4 - - - +
172D ALA* 1.3 72.3 - - + +
174D ILE* 1.3 58.4 + - - +
177D LEU* 2.8 47.0 + - + +
191D VAL* 4.4 7.2 - - + -
196D ILE* 3.8 31.4 - - + -
206D LEU* 3.8 24.4 - - + +
249D MET* 3.5 33.7 - - + -
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Residues in contact with ILE 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 SER 2.8 25.5 + - - +
171D ILE* 3.6 5.2 - - - +
173D VAL* 1.3 68.1 - - - +
175D LYS* 1.3 61.5 + - - +
177D LEU* 3.3 6.0 + - - +
178D THR* 2.5 40.6 + - - +
249D MET* 4.2 14.4 - - + -
337D PHE* 3.8 26.5 - - + -
352D LEU* 4.4 25.2 - - + +
355D LEU* 3.8 21.3 - - + -
356D MET* 3.8 25.1 - - + +
361D ILE* 4.0 18.4 - - + -
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Residues in contact with LYS 175 (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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125D TYR* 3.5 48.3 + - + -
171D ILE* 2.6 42.3 + - + +
172D ALA 3.6 2.7 - - - +
174D ILE* 1.3 73.8 - - - +
176D GLY* 1.3 56.7 + - - +
178D THR* 3.2 7.3 + - - -
179D TYR* 2.9 30.7 + - - +
356D MET* 4.1 25.6 - - - -
365D ASP* 5.0 9.6 + - - -
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Residues in contact with GLY 176 (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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125D TYR* 3.7 17.6 - - - +
126D ILE* 3.9 7.2 - - - +
172D ALA 2.6 21.4 + - - -
173D VAL 3.7 0.9 - - - -
175D LYS* 1.3 74.8 - - - +
177D LEU* 1.3 55.5 + - - +
179D TYR* 3.3 5.0 + - - +
180D LEU* 3.0 31.5 + - - +
206D LEU* 3.9 14.4 - - - -
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Residues in contact with LEU 177 (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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173D VAL* 2.8 41.2 + - + +
174D ILE* 3.9 4.0 - - - +
176D GLY* 1.3 72.9 - - - +
178D THR* 1.3 56.9 + - - +
180D LEU* 3.9 6.3 - - + +
181D ARG* 3.1 28.8 + - - +
186D ILE 5.0 0.3 - - - +
187D MET* 5.8 0.7 - - - -
188D HIS* 3.5 33.9 - - + +
191D VAL* 4.2 4.0 - - + -
206D LEU* 3.8 12.3 - - + +
242D VAL* 4.7 7.3 - - + +
245D ASP* 3.9 35.7 - - + +
246D ILE* 4.9 3.6 - - + +
249D MET* 5.0 4.5 - - - -
352D LEU* 4.0 23.1 - - + +
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Residues in contact with THR 178 (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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174D ILE* 2.5 33.0 + - - +
175D LYS* 3.4 7.2 - - - -
177D LEU* 1.3 75.6 - - - +
179D TYR* 1.3 59.6 + - - +
181D ARG* 3.2 3.2 + - + +
182D GLU* 2.8 61.2 + - + +
352D LEU* 3.9 22.9 - - + +
356D MET* 5.5 1.7 - - - -
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Residues in contact with TYR 179 (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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120D GLU 3.6 1.6 + - - -
121D CYS* 3.4 5.3 - - + -
122D ASN* 2.6 46.3 + - - +
123D SER* 3.6 28.3 - - - +
125D TYR* 5.8 1.6 - - + -
126D ILE* 3.7 17.5 - - + -
175D LYS 2.9 16.1 + - - +
176D GLY 3.3 3.8 + - - +
178D THR* 1.3 76.9 - - - +
180D LEU* 1.3 65.1 + - + +
182D GLU* 5.1 2.5 - - - -
183D LYS* 3.0 51.6 + - + +
184D HIS* 2.7 33.9 + + - -
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Residues in contact with LEU 180 (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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121D CYS* 4.6 11.9 - - - -
126D ILE* 4.1 15.5 - - + -
176D GLY 3.0 19.1 + - - +
177D LEU* 3.9 7.2 - - + +
179D TYR* 1.3 81.2 - - + +
181D ARG* 1.3 62.8 + - - +
184D HIS* 3.2 13.3 + - + +
185D LYS 3.1 17.5 + - - -
186D ILE* 3.3 43.5 + - + +
187D MET* 5.5 0.4 - - - -
188D HIS* 4.4 19.1 - - + +
206D LEU* 5.1 2.7 - - + -
209D PHE* 3.7 47.8 - - + -
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Residues in contact with ARG 181 (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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177D LEU 3.1 19.2 + - - +
178D THR* 3.2 4.9 + - - +
180D LEU* 1.3 75.9 - - - +
182D GLU* 1.3 69.2 + - + +
185D LYS* 2.9 31.4 + - - +
186D ILE 3.7 11.4 + - - +
242D VAL* 3.9 28.6 - - + +
351D ASP* 5.4 5.9 + - - +
352D LEU* 3.9 37.3 - - + +
353D LYS 5.3 1.6 - - - +
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Residues in contact with GLU 182 (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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178D THR* 2.8 42.9 + - + +
179D TYR* 4.6 1.5 - - - +
181D ARG* 1.3 82.2 - - + +
183D LYS* 1.3 76.6 + - + +
185D LYS* 2.8 29.0 + - - +
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Residues in contact with LYS 183 (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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179D TYR* 3.0 39.8 + - + +
182D GLU* 1.3 97.1 + - + +
184D HIS* 1.3 80.4 + - + +
185D LYS* 4.5 6.6 + - - +
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Residues in contact with HIS 184 (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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117D VAL* 5.1 6.9 + - + +
120D GLU* 2.8 44.4 + - + +
121D CYS* 3.8 15.0 - - - -
179D TYR* 2.7 47.6 + + - -
180D LEU* 3.2 12.4 + - + +
183D LYS* 1.3 89.4 + - + +
185D LYS* 1.3 76.5 + - - +
186D ILE* 3.0 25.0 - - + +
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Residues in contact with LYS 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D LEU 3.1 0.4 + - - -
181D ARG* 2.9 19.8 + - - +
182D GLU* 2.8 26.7 + - - +
183D LYS* 4.5 5.4 + - - +
184D HIS* 1.3 84.9 - - - +
186D ILE* 1.3 60.2 + - - +
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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
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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