Contacts of the helix formed by residues 150 - 172 (chain D) in PDB entry 4HHM
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 150 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C LEU* 5.7 5.0 - - - +
277C SER* 5.7 0.7 + - - -
335C LEU* 4.0 10.1 - - + +
338C LEU* 3.7 11.4 - - + +
147D ALA 4.9 0.2 + - - -
149D LYS* 1.3 71.2 - - - +
151D VAL* 1.3 64.9 + - - +
152D ARG* 3.4 16.2 + - - +
153D ALA* 2.9 38.6 + - + +
154D ALA* 3.0 22.2 + - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PRO 5.4 0.2 - - - -
230C HIS* 3.3 52.9 - - + +
233C ALA* 3.5 20.6 - - + +
234C GLN* 5.3 1.1 - - + -
149D LYS* 3.3 9.8 + - + +
150D ASP* 1.3 72.2 + - - +
152D ARG* 1.3 57.9 + - - +
154D ALA* 3.2 7.0 + - - +
155D LEU* 2.8 49.0 + - + +
192D LEU* 4.3 18.6 - - + -
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ALA* 3.7 25.9 - - + +
236C LEU* 4.3 12.4 + - - +
237C TRP* 3.7 34.2 - - + +
274C LEU* 4.9 9.7 - - + +
277C SER* 4.8 2.4 + - - -
278C ALA* 3.7 29.6 + - - +
150D ASP* 3.3 13.1 + - - +
151D VAL* 1.3 78.8 - - - +
153D ALA* 1.3 62.7 + - - +
155D LEU* 3.2 5.2 + - - +
156D ASP* 3.0 28.9 + - - +
340H GLU* 3.1 38.3 + - - -
341H PRO* 4.9 5.9 - - - +
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Residues in contact with ALA 153 (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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335C LEU 5.8 0.2 - - - +
338C LEU* 3.9 24.7 - - + +
339C ALA* 4.4 14.8 - - + -
150D ASP* 2.9 24.5 + - + +
152D ARG* 1.3 77.3 - - - +
154D ALA* 1.3 57.6 + - - +
156D ASP* 3.2 13.5 + - - +
157D ARG* 3.0 34.4 + - - +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C LEU* 4.1 10.5 - - + +
105D THR* 3.1 23.0 - - - +
149D LYS* 4.0 21.1 - - + -
150D ASP 3.0 17.2 + - - +
151D VAL 3.2 5.8 + - - +
153D ALA* 1.3 76.9 - - - +
155D LEU* 1.3 58.4 + - - +
157D ARG* 3.5 1.0 + - - +
158D MET* 3.0 21.0 + - - +
192D LEU* 3.6 25.1 - - + -
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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
----------------------------------------------------------
234C GLN* 3.8 31.6 - - + +
237C TRP* 3.6 40.2 - - + -
151D VAL* 2.8 40.6 + - + +
152D ARG* 3.6 4.9 - - - +
154D ALA* 1.3 75.1 - - + +
156D ASP* 1.3 60.5 + - - +
158D MET* 3.0 28.8 + - + +
159D LYS* 2.8 31.0 + - - +
192D LEU* 5.0 6.7 - - + -
193D LEU* 4.2 15.0 - - + +
202D PHE* 3.9 8.5 - - + -
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Residues in contact with ASP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C TRP* 2.7 29.3 + - - +
152D ARG* 3.0 20.9 + - - +
153D ALA* 3.2 13.7 + - - +
155D LEU* 1.3 76.6 - - - +
157D ARG* 1.3 77.2 + - - +
159D LYS* 3.2 8.9 + - - +
160D GLU* 2.9 29.1 + - - +
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Residues in contact with ARG 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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338C LEU* 2.9 44.6 + - + +
339C ALA* 3.1 21.8 + - - +
340C GLU 3.5 12.8 + - - -
341C PRO* 4.0 11.1 - - - +
342C THR* 3.5 7.8 + - - +
104D PHE 3.7 18.8 - - - +
105D THR* 4.5 1.6 - - - -
112D ARG* 3.3 27.6 - - - +
153D ALA* 3.0 19.0 + - - +
154D ALA* 3.7 8.5 - - - +
155D LEU 3.2 0.2 - - - -
156D ASP* 1.3 95.3 + - - +
158D MET* 1.3 58.7 + - - +
160D GLU* 3.2 27.4 + - - +
161D ALA* 2.9 29.1 + - - +
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Residues in contact with MET 158 (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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104D PHE* 4.8 4.7 - - + -
105D THR* 3.9 16.3 - - + +
141D GLU* 5.0 15.3 - - - +
154D ALA 3.0 16.4 + - - +
155D LEU* 3.0 25.7 + - + +
157D ARG* 1.3 75.6 - - - +
159D LYS* 1.3 64.5 + - - +
161D ALA* 3.3 5.1 + - - +
162D PHE* 3.1 47.9 + - + -
192D LEU* 4.1 14.8 - - + -
193D LEU* 3.3 42.0 - - + -
202D PHE* 3.3 14.6 - - + -
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Residues in contact with LYS 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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237C TRP* 4.1 20.9 - - + -
155D LEU 2.8 19.4 + - - +
156D ASP* 3.5 7.0 - - - +
158D MET* 1.3 72.2 - - - +
160D GLU* 1.3 58.7 + - - +
162D PHE* 3.2 2.6 + - - +
163D ASP* 2.8 58.8 + - - +
202D PHE* 3.6 12.7 - - + -
205D ARG* 2.9 32.5 + - - +
206D LEU* 3.9 10.9 - - + +
207D GLU* 3.5 16.2 - - - +
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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
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341C PRO* 3.8 5.7 - - - +
342C THR* 2.9 30.2 + - - -
343C ALA* 2.8 34.5 + - - +
344C ALA* 4.1 0.3 + - - -
156D ASP 2.9 15.0 + - - +
157D ARG* 3.2 25.6 + - - +
159D LYS* 1.3 78.3 - - - +
161D ALA* 1.3 62.4 + - - +
163D ASP* 3.7 8.4 - - - +
164D LEU* 3.0 42.2 + - + +
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C THR* 5.9 2.0 + - + +
104D PHE* 3.6 39.3 - - + +
116D LEU* 3.7 24.1 - - + +
157D ARG 2.9 17.7 + - - +
158D MET 3.6 4.9 - - - +
159D LYS 3.2 0.2 - - - -
160D GLU* 1.3 77.9 - - - +
162D PHE* 1.3 57.6 + - - +
164D LEU* 3.2 3.7 + - - +
165D LEU* 2.9 31.4 + - - +
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Residues in contact with PHE 162 (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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104D PHE* 4.1 17.0 - + - -
136D ALA* 3.8 31.0 - - + -
158D MET* 3.1 45.1 + - + +
159D LYS 3.9 2.7 - - - +
161D ALA* 1.3 75.9 - - - +
163D ASP* 1.3 57.0 + - - +
165D LEU* 3.2 20.6 + - + +
166D GLY 2.9 14.7 + - - -
178D PHE* 5.2 6.3 - + + -
180D ILE* 4.1 24.5 - - + -
193D LEU* 5.6 0.2 - - + -
202D PHE* 3.7 17.9 - + - -
206D LEU* 4.0 11.7 - - + -
212D TYR* 2.4 52.9 + + + -
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Residues in contact with ASP 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 LYS* 2.8 56.2 + - - +
160D GLU* 3.7 7.3 + - - +
162D PHE* 1.3 69.3 - - - +
164D LEU* 1.3 68.6 + - + +
166D GLY* 3.1 2.1 + - - -
167D GLU* 2.8 25.4 + - - +
206D LEU* 3.8 8.3 - - - +
207D GLU* 2.9 43.3 + - + +
208D ARG* 4.5 4.5 + - - -
212D TYR* 3.9 4.1 + - - -
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Residues in contact with LEU 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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342C THR* 4.9 0.2 - - + -
343C ALA* 3.8 24.2 - - + +
346C GLY* 4.5 4.7 - - - -
347C LEU* 4.0 37.4 - - + +
350C LEU* 4.5 3.8 - - + -
116D LEU* 3.7 30.7 - - + -
120D ILE* 6.0 0.9 - - + -
160D GLU* 3.0 33.5 + - + +
161D ALA 3.5 5.8 - - - +
163D ASP* 1.3 77.8 - - + +
165D LEU* 1.3 64.6 + - + +
167D GLU* 3.1 21.9 + - - +
168D TYR* 2.9 23.4 + - - +
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Residues in contact with LEU 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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104D PHE* 3.8 29.4 - - + -
116D LEU* 4.2 13.7 - - + +
119D THR* 3.9 27.1 - - + -
120D ILE* 4.1 23.1 - - + -
123D ILE* 4.1 7.4 - - + +
134D TYR* 6.2 0.2 - - + -
161D ALA 2.9 16.7 + - - +
162D PHE* 3.5 24.9 - - + +
163D ASP 3.2 0.4 - - - -
164D LEU* 1.3 77.5 - - - +
166D GLY* 1.3 62.2 + - - +
168D TYR* 3.4 6.1 + - - +
169D VAL* 3.3 26.5 + - - +
178D PHE* 3.8 22.4 - - + -
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Residues in contact with GLY 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 PHE 2.9 11.5 + - - -
163D ASP 3.1 1.1 + - - -
165D LEU* 1.3 74.4 - - - +
167D GLU* 1.3 60.6 + - - +
169D VAL* 3.3 10.6 - - - +
170D THR* 2.6 35.5 + - - -
178D PHE* 4.3 4.3 - - - -
208D ARG* 4.1 7.4 - - - -
211D LEU* 4.3 7.6 - - - +
212D TYR* 3.3 17.7 + - - -
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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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347C LEU* 3.9 23.5 + - + +
348C GLN* 6.0 1.0 - - - +
163D ASP 2.8 12.3 + - - +
164D LEU* 3.4 29.6 - - - +
166D GLY* 1.3 77.8 - - - +
168D TYR* 1.3 57.6 + - - +
170D THR* 3.3 2.3 + - - -
171D SER* 3.0 31.0 + - - +
208D ARG* 3.5 24.8 - - - +
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Residues in contact with TYR 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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347C LEU* 3.5 19.0 - - + +
351C LEU* 4.1 25.8 - - + -
120D ILE* 3.7 40.4 - - + +
123D ILE* 4.3 9.4 - - + -
124D ASP* 2.5 40.4 + - - -
164D LEU 2.9 12.2 + - - +
165D LEU* 3.6 11.0 - - - +
166D GLY 3.2 0.2 - - - -
167D GLU* 1.3 77.6 - - - +
169D VAL* 1.3 72.2 + - + +
171D SER* 2.9 18.1 + - - -
172D GLN* 3.1 42.9 + - + +
174D TYR* 3.9 11.6 + + - -
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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
----------------------------------------------------------
123D ILE* 4.1 15.9 - - + -
165D LEU 3.3 13.4 + - - +
166D GLY* 3.3 16.8 - - - +
168D TYR* 1.3 79.0 - - + +
170D THR* 1.3 63.7 + - - +
173D GLY 3.2 2.1 + - - -
174D TYR* 2.8 51.7 + - + +
176D ILE* 3.9 28.9 - - + +
178D PHE* 3.8 24.2 - - + -
211D LEU* 4.4 11.4 - - + -
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Residues in contact with THR 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 GLY 2.6 22.6 + - - -
167D GLU 3.5 5.2 - - - -
168D TYR 3.1 0.6 - - - -
169D VAL* 1.3 77.0 - - - +
171D SER* 1.3 64.5 + - - +
172D GLN 3.1 0.2 - - - -
173D GLY* 3.1 13.8 + - - +
208D ARG* 3.5 33.9 + - - +
211D LEU* 4.0 7.8 - - - +
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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
----------------------------------------------------------
347C LEU* 4.5 6.0 - - - +
348C GLN* 4.7 10.7 + - - -
167D GLU* 3.0 15.6 + - - -
168D TYR* 2.9 22.0 + - - -
170D THR* 1.3 78.8 - - - +
172D GLN* 1.3 73.7 + - - +
173D GLY 3.3 0.8 + - - -
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Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C GLN* 5.4 3.6 + - - -
351C LEU* 6.2 0.4 - - - +
168D TYR* 3.1 52.1 + - + +
169D VAL 4.1 0.2 - - - +
170D THR 3.1 0.2 - - - -
171D SER* 1.3 91.8 + - - +
173D GLY* 1.3 62.8 - - - +
174D TYR* 3.3 43.7 + - + -
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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