Contacts of the helix formed by residues 157 - 180 (chain D) in PDB entry 6DWM
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 CYS 157 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A PRO* 4.2 16.5 - - + +
146D SER 3.7 13.2 - - - +
147D ILE 3.5 14.4 - - - +
148D ALA 3.3 17.3 - - - +
149D SER* 4.1 2.2 - - - +
150D ASP* 4.0 6.7 - - - +
156D SER* 1.3 77.2 + - - +
158D TYR* 1.3 66.6 + - - +
159D LEU* 4.3 2.9 - - - -
160D GLU* 3.5 17.5 + - - -
161D GLU* 3.1 22.9 + - - +
359D LEU* 4.1 22.4 - - - -
465D TRP* 4.5 4.9 - - - -
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Residues in contact with TYR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D SER 3.8 23.6 - - - -
145D PHE* 3.4 41.3 - + - +
146D SER 3.6 4.5 + - - +
148D ALA* 3.1 25.3 + - + -
149D SER 3.6 17.5 - - - -
150D ASP* 4.1 20.6 - - - +
151D PRO* 3.2 24.5 - - + +
157D CYS* 1.3 74.3 - - - +
159D LEU* 1.3 66.1 + - - +
161D GLU* 3.0 16.4 + - - +
162D HIS* 3.1 37.2 + + - +
278D ILE 5.7 0.3 + - - -
279D ARG 5.7 2.2 - - - -
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D SER* 3.0 22.5 + - - +
147D ILE* 6.3 0.2 - - + -
157D CYS* 3.4 5.1 - - - -
158D TYR* 1.3 74.9 - - - +
160D GLU* 1.3 64.1 + - - +
162D HIS* 3.2 6.5 + - - +
163D VAL* 2.9 37.1 + - + +
197D VAL* 3.8 28.0 - - + -
201D ILE* 3.9 15.7 - - + -
359D LEU* 5.3 0.9 - - + -
462D ILE* 4.0 33.2 - - + +
465D TRP* 3.6 40.8 - - + -
466D GLU* 4.2 6.5 - - + +
469D LEU* 5.7 1.8 - - + -
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Residues in contact with GLU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PRO* 5.3 2.1 - - - +
155D THR 4.7 0.5 - - - +
156D SER* 3.2 30.3 - - - -
157D CYS* 3.5 18.4 + - - +
158D TYR 3.3 0.4 - - - -
159D LEU* 1.3 78.6 - - - +
161D GLU* 1.3 61.1 + - - +
164D SER* 2.8 39.8 + - - +
357D PRO 5.0 0.2 - - - +
358D ARG* 3.3 31.3 + - - +
359D LEU* 3.2 39.5 + - + +
360D SER 5.0 1.2 + - - -
469D LEU* 3.7 23.3 - - + +
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Residues in contact with GLU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ASP* 3.4 25.9 - - - +
152D ALA* 4.7 6.6 - - - +
153D SER* 3.9 17.4 - - - -
156D SER* 3.0 24.1 + - - -
157D CYS 3.1 11.1 + - - +
158D TYR* 3.0 10.6 + - - +
160D GLU* 1.3 78.5 - - - +
162D HIS* 1.3 68.7 + - + +
164D SER* 3.9 4.3 - - - -
165D LYS* 3.3 21.5 + - - +
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Residues in contact with HIS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D PHE 5.1 0.4 + - - -
150D ASP* 5.4 2.0 - - - -
158D TYR* 3.1 38.7 + + + -
159D LEU* 3.2 4.9 + - - +
161D GLU* 1.3 82.4 - - + +
163D VAL* 1.3 65.1 + - - +
165D LYS* 3.2 10.0 + - - +
166D GLU* 2.9 31.0 + - + +
196D ASN 5.3 0.2 - - - +
197D VAL* 4.2 20.0 - - + -
200D ALA* 3.8 36.2 + - + +
201D ILE* 4.0 22.0 - - + +
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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
----------------------------------------------------------
159D LEU* 2.9 28.7 + - + +
162D HIS* 1.3 75.4 - - - +
164D SER* 1.3 57.8 + - - +
166D GLU* 4.0 1.5 - - - +
167D ALA* 2.8 30.2 + - - +
197D VAL* 3.8 29.8 - - + -
466D GLU* 4.0 17.7 - - + +
469D LEU* 3.6 35.0 - - + -
470D PHE* 3.8 27.4 - - + +
473D ILE* 4.9 2.2 - - + -
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Residues in contact with SER 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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160D GLU* 2.8 32.1 + - - +
161D GLU* 3.9 5.6 - - - -
163D VAL* 1.3 78.1 - - - +
165D LYS* 1.3 62.5 + - - +
167D ALA* 3.4 1.4 + - - +
168D GLU* 3.3 29.5 + - - +
356D ARG* 4.0 28.0 + - - -
469D LEU* 4.9 2.3 - - - +
473D ILE* 4.1 15.6 - - - +
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Residues in contact with LYS 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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161D GLU 3.3 11.3 + - - +
162D HIS* 3.2 13.3 + - - +
164D SER* 1.3 81.0 - - - +
166D GLU* 1.3 66.2 + - + +
168D GLU* 3.3 5.9 + - - +
169D VAL* 3.3 29.7 + - + +
206D ARG* 3.7 35.9 - - - +
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Residues in contact with GLU 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 HIS* 2.9 20.8 + - + +
163D VAL 4.0 2.5 - - - +
165D LYS* 1.3 78.3 - - - +
167D ALA* 1.3 59.6 + - - +
169D VAL* 3.5 4.1 + - - +
170D LEU* 3.0 29.8 + - - +
193D SER* 3.8 22.3 + - - +
196D ASN* 3.2 28.6 + - + +
197D VAL* 3.7 17.7 - - + +
206D ARG* 2.6 50.9 + - - +
209D HIS* 5.3 0.7 - - - -
470D PHE* 4.0 12.8 - - + -
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Residues in contact with ALA 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* 2.8 23.0 + - + +
164D SER 3.8 3.8 - - - +
166D GLU* 1.3 73.5 - - - +
168D GLU* 1.3 62.2 + - - +
170D LEU* 3.4 4.8 + - - +
171D ILE* 3.1 29.7 + - - +
470D PHE* 3.9 17.2 - - + -
473D ILE* 3.7 33.4 - - + -
474D LEU* 4.0 10.4 - - + +
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Residues in contact with GLU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D SER 3.3 15.9 + - - +
165D LYS* 3.7 8.1 - - - +
166D GLU 3.3 0.4 - - - -
167D ALA* 1.3 75.4 - - - +
169D VAL* 1.3 66.7 + - + +
171D ILE* 3.1 6.4 + - - +
172D SER* 3.0 26.0 + - - -
356D ARG* 3.3 23.9 + - - +
473D ILE* 4.3 5.4 - - - +
477D ARG* 2.9 39.4 + - - -
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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
----------------------------------------------------------
165D LYS* 3.3 20.7 + - + +
166D GLU* 3.9 5.8 - - - +
168D GLU* 1.3 76.1 - - + +
170D LEU* 1.3 57.5 + - - +
172D SER* 3.3 6.7 + - - -
173D THR* 2.8 36.8 + - - +
206D ARG* 3.9 28.0 - - - +
208D ASP* 6.1 0.7 - - - +
209D HIS* 3.6 26.0 - - + +
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLU 3.0 18.1 + - - +
167D ALA 3.6 5.4 - - - +
169D VAL* 1.3 77.4 - - - +
171D ILE* 1.3 62.7 + - - +
173D THR* 3.3 4.1 + - - -
174D LEU* 3.0 44.6 + - + +
189D TYR* 3.7 31.6 - - + +
190D VAL* 4.2 21.3 - - + +
193D SER* 3.6 26.2 - - - +
209D HIS* 4.0 3.8 - - - +
326D ILE* 6.5 0.2 - - + -
470D PHE* 4.6 12.6 - - + -
474D LEU* 3.9 26.0 - - + -
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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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167D ALA 3.1 16.8 + - - +
168D GLU* 3.1 8.7 + - - +
170D LEU* 1.3 76.8 - - - +
172D SER* 1.3 63.0 + - - +
174D LEU* 3.2 9.5 + - + +
175D GLN* 2.9 40.2 + - + +
473D ILE* 4.3 10.5 - - + +
474D LEU* 3.9 28.9 - - + -
477D ARG* 3.5 48.0 - - + +
478D VAL* 4.2 20.9 - - + -
508D MET* 5.1 1.8 - - - -
510D LEU* 5.2 1.3 - - + -
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Residues in contact with SER 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D GLU 3.0 15.4 + - - -
169D VAL* 3.8 7.4 - - - -
171D ILE* 1.3 76.8 - - - +
173D THR* 1.3 63.7 + - - +
175D GLN* 3.3 16.3 + - - +
176D GLU* 3.2 32.8 + - - +
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Residues in contact with THR 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 29.3 + - - +
170D LEU* 3.6 8.5 - - - -
172D SER* 1.3 73.0 - - - +
174D LEU* 1.3 61.0 + - + +
176D GLU* 3.5 16.2 + - - +
177D LEU* 3.5 21.6 + - + +
189D TYR* 3.7 37.9 - - + -
209D HIS* 3.4 28.0 + - + +
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Residues in contact with LEU 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 LEU* 3.0 42.1 + - + +
171D ILE* 3.7 2.2 - - - +
173D THR* 1.3 77.0 - - - +
175D GLN* 1.3 65.2 + - - +
176D GLU 3.2 0.4 - - - -
177D LEU* 3.2 16.8 + - + +
178D MET* 3.1 25.8 + - - +
184D PHE* 3.6 34.3 - - + -
186D PRO* 5.5 1.1 - - + -
189D TYR* 4.6 11.4 - - + -
474D LEU* 5.3 2.2 - - + -
480D PHE* 3.8 25.1 - - + -
508D MET* 3.3 31.2 - - + -
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Residues in contact with GLN 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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171D ILE* 2.9 36.5 + - + +
172D SER* 3.3 16.4 + - - +
174D LEU* 1.3 76.0 - - - +
176D GLU* 1.3 63.3 + - - +
178D MET* 3.2 6.2 + - - +
179D ALA* 3.2 21.3 + - - +
508D MET* 3.6 17.7 - - + -
510D LEU* 3.6 33.4 - - + +
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Residues in contact with GLU 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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172D SER* 3.2 22.7 + - - +
173D THR* 3.6 15.4 + - - +
174D LEU 3.2 0.4 - - - -
175D GLN* 1.3 76.4 - - + +
177D LEU* 1.3 62.5 + - + +
179D ALA* 3.2 15.6 + - - +
180D GLY* 3.3 10.0 + - - -
181D PRO* 5.0 0.2 - - - +
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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 THR* 3.5 17.4 + - + +
174D LEU* 3.2 16.0 + - + +
176D GLU* 1.3 79.1 - - + +
178D MET* 1.3 60.3 + - - +
180D GLY 3.4 0.2 + - - -
181D PRO* 3.3 24.6 - - + +
182D GLY* 3.0 22.5 + - - -
183D HIS 4.1 6.3 + - - +
184D PHE* 3.7 26.9 - - + -
189D TYR* 3.4 51.6 - - + +
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Residues in contact with MET 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 LEU 3.1 17.5 + - - +
175D GLN* 3.2 10.3 + - - +
177D LEU* 1.3 76.3 - - - +
179D ALA* 1.3 60.3 + - - +
180D GLY 4.6 0.2 - - - +
182D GLY* 3.4 41.1 - - - +
184D PHE* 4.2 10.3 - - + -
507D GLN* 4.0 12.6 - - + +
508D MET* 3.2 55.0 - - + +
509D GLN* 3.8 17.9 - - - +
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D GLN 3.2 11.2 + - - +
176D GLU* 3.6 10.3 - - - +
177D LEU 3.2 0.4 - - - -
178D MET* 1.3 78.7 - - - +
180D GLY* 1.3 61.1 + - - +
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Residues in contact with GLY 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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176D GLU 3.3 9.9 + - - -
177D LEU 3.4 0.6 + - - -
178D MET 4.6 0.2 - - - +
179D ALA* 1.3 81.8 - - - +
181D PRO* 1.3 75.3 - - - +
182D GLY* 3.1 2.1 + - - -
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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