Contacts of the helix formed by residues 145 - 166 (chain D) in PDB entry 3QNQ
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 GLY 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D ALA* 3.5 15.5 - - - -
111D PHE* 4.6 0.2 - - - -
140D LEU 3.7 15.6 + - - -
142D GLY 2.7 14.2 + - - -
144D GLN* 1.3 80.0 - - - +
146D LEU* 1.3 66.1 + - - +
147D PHE 3.2 2.5 - - - -
148D VAL* 2.8 26.3 + - - +
149D ALA 2.9 8.3 + - - -
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Residues in contact with LEU 146 (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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29D LEU* 4.4 13.2 - - + -
32D THR* 6.1 0.2 - - + -
80D MET* 3.3 21.8 - - + -
81D ALA* 3.8 19.7 - - - +
84D ALA* 3.9 17.5 - - + -
143D SER 3.6 10.7 + - - +
145D GLY* 1.3 73.8 - - - +
147D PHE* 1.3 54.1 + - + +
149D ALA* 2.9 5.3 - - - +
150D MET* 2.7 43.2 + - + +
221D GLN* 5.4 0.2 - - - +
260D SER 4.3 0.4 - - - +
261D PRO* 3.7 34.5 - - + +
264D LEU* 3.2 35.9 - - + -
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Residues in contact with PHE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D GLY 2.8 5.1 + - - -
146D LEU* 1.3 78.0 - - + +
148D VAL* 1.3 59.5 + - + +
150D MET* 3.6 22.8 + - + +
151D ILE* 2.9 31.7 + - + +
216D VAL* 3.6 16.2 - - + -
220D LEU* 3.9 33.9 - - + -
221D GLN* 3.9 37.8 + - + +
224D LEU* 4.1 15.0 - - + -
225D SER* 6.2 0.2 - - - -
261D PRO* 3.6 29.4 - - + -
262D ILE* 3.9 30.5 - - + -
265D SER* 6.4 0.2 - - - -
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D PHE* 3.3 24.7 - - + -
114D ALA* 5.3 2.5 - - + -
115D THR* 4.8 11.0 - - + -
140D LEU 5.3 1.8 - - - +
144D GLN 4.4 5.4 - - - +
145D GLY* 2.8 26.4 + - - +
147D PHE* 1.3 72.3 - - + +
149D ALA* 1.3 59.1 + - - +
151D ILE* 3.7 4.7 - - - +
152D ILE* 2.9 35.2 + - + +
212D ILE* 4.6 17.7 - - + -
213D HIS* 4.5 26.9 - - + +
216D VAL* 4.0 14.6 - - + +
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Residues in contact with ALA 149 (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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81D ALA* 3.9 13.7 - - + +
84D ALA* 4.9 4.5 - - + -
85D VAL* 3.1 35.7 - - + +
88D ILE* 5.4 1.3 - - + -
111D PHE* 3.7 4.4 - - + -
145D GLY 2.9 10.9 + - - +
146D LEU* 2.9 17.0 - - - +
148D VAL* 1.3 74.6 - - - +
150D MET* 1.3 68.8 + - + +
151D ILE 2.9 1.2 + - - -
152D ILE* 4.2 0.2 - - - +
153D ALA* 3.0 26.4 + - - +
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Residues in contact with MET 150 (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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25D ILE* 3.4 37.7 - - + -
29D LEU* 5.8 2.5 - - + -
88D ILE* 4.2 21.0 - - + +
146D LEU* 2.7 23.3 + - + +
147D PHE* 3.8 32.5 - - + +
149D ALA* 1.3 73.0 - - + +
151D ILE* 1.3 64.8 + - + +
153D ALA* 4.0 1.2 - - - +
154D ILE* 3.1 32.8 + - + +
261D PRO* 3.6 32.8 - - + -
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Residues in contact with ILE 151 (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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147D PHE* 2.9 23.7 + - + +
148D VAL* 3.7 6.1 - - - +
149D ALA 2.9 2.4 + - - -
150D MET* 1.3 79.8 - - + +
152D ILE* 1.3 65.9 + - + +
153D ALA 2.9 4.7 + - - -
154D ILE* 3.1 5.4 + - - +
155D ILE* 2.8 54.5 + - + +
212D ILE* 6.5 0.4 - - + -
216D VAL* 4.1 15.5 - - + -
220D LEU* 4.1 25.4 - - + -
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Residues in contact with ILE 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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85D VAL* 4.2 6.5 - - + -
107D SER* 3.6 6.2 + - - +
110D THR* 3.3 19.5 - - + +
111D PHE* 3.3 49.6 - - + +
114D ALA* 4.5 13.9 - - + -
148D VAL* 2.9 32.7 + - + +
149D ALA 4.4 0.2 - - - +
151D ILE* 1.3 81.2 - - + +
153D ALA* 1.3 59.0 + - - +
155D ILE* 4.2 10.7 - - + +
156D SER* 3.0 30.5 + - - -
197D VAL* 4.5 13.9 - - + -
200D ILE* 6.1 2.9 - - + -
212D ILE* 4.9 13.2 - - + -
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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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85D VAL* 3.9 23.1 - - + +
88D ILE* 4.2 18.4 - - + -
89D ALA* 4.4 4.3 - - - +
92D LEU* 5.6 0.2 - - - -
107D SER* 3.2 16.9 + - - +
149D ALA 3.0 19.4 + - - +
150D MET 4.0 2.7 - - - +
151D ILE 2.9 0.2 + - - -
152D ILE* 1.3 75.8 - - - +
154D ILE* 1.3 67.1 + - - +
157D THR* 2.9 31.7 + - - -
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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
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21D HIS* 3.9 48.7 - - + +
24D ALA* 5.8 1.1 - - + -
25D ILE* 4.2 26.2 - - + -
88D ILE* 4.8 8.5 - - + +
92D LEU* 4.4 11.1 - - + +
150D MET 3.1 18.5 + - - +
151D ILE* 3.1 4.3 + - - +
153D ALA* 1.3 77.1 - - - +
155D ILE* 1.3 62.7 + - + +
158D GLU* 2.8 39.8 + - + +
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Residues in contact with ILE 155 (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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151D ILE* 2.8 45.3 + - + +
152D ILE* 4.2 8.5 - - + -
154D ILE* 1.3 78.6 - - + +
156D SER* 1.3 65.3 + - - +
158D GLU* 4.1 3.7 - - - +
159D ILE* 3.2 40.5 + - + +
193D VAL* 5.9 0.4 - - + -
196D VAL* 5.0 6.5 - - + -
197D VAL* 4.8 16.4 - - + -
200D ILE* 4.7 19.1 - - + -
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Residues in contact with SER 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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103D SER 5.5 0.2 - - - -
106D LEU* 4.1 7.9 - - - +
107D SER* 3.5 16.2 - - - -
110D THR* 3.1 28.6 + - - +
152D ILE 3.0 21.2 + - - -
153D ALA 3.3 0.2 + - - -
155D ILE* 1.3 82.3 - - - +
157D THR* 1.3 59.4 + - - +
159D ILE 3.3 0.2 + - - -
160D TYR* 2.8 29.6 + - - +
193D VAL* 3.3 24.6 - - - +
197D VAL* 4.3 2.3 - - - +
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Residues in contact with THR 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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89D ALA* 3.4 32.4 - - - +
92D LEU* 3.9 19.3 - - + +
93D GLY* 3.8 14.1 - - - +
96D TYR* 5.2 0.2 - - + -
98D VAL* 4.9 2.7 - - + -
103D SER* 3.5 31.8 + - - +
106D LEU* 5.9 0.2 - - - -
107D SER* 3.8 0.2 + - - -
153D ALA 2.9 16.9 + - - -
156D SER* 1.3 75.2 - - - +
158D GLU* 1.3 56.1 + - - +
160D TYR* 4.0 8.1 - - + -
161D ARG* 2.7 35.1 + - + +
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Residues in contact with GLU 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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21D HIS* 2.7 33.9 + - + +
92D LEU* 4.0 2.8 - - - +
96D TYR* 2.5 36.7 + - - -
154D ILE* 2.8 25.8 + - + +
155D ILE* 4.1 4.0 - - - +
157D THR* 1.3 77.1 - - - +
159D ILE* 1.3 61.2 + - + +
161D ARG* 2.9 39.7 + - - +
162D PHE* 3.4 11.6 - - - +
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Residues in contact with ILE 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 ILE* 3.2 35.1 + - + +
156D SER 3.7 0.9 - - - +
158D GLU* 1.3 76.0 - - + +
160D TYR* 1.3 70.1 + - - +
162D PHE* 3.2 9.1 + - + +
163D LEU* 3.0 35.4 + - + +
192D ILE* 5.1 5.8 - - + +
193D VAL* 4.1 27.4 - - + +
196D VAL* 4.3 26.7 - - + -
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Residues in contact with TYR 160 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600C ZDM 6.0 0.7 - - + -
98D VAL* 4.2 17.7 - - + -
99D ASP* 3.5 18.4 - - - +
102D ALA* 3.4 23.9 - - + +
103D SER* 3.6 28.7 - - - -
106D LEU* 4.4 22.0 - - + -
156D SER 2.8 18.4 + - - +
157D THR* 3.6 7.2 - - - +
159D ILE* 1.3 80.6 - - - +
161D ARG* 1.3 66.9 + - - +
163D LEU* 3.2 6.9 + - - +
164D VAL* 3.1 36.9 + - + +
186D ALA* 3.9 21.7 - - + +
189D PRO* 3.8 25.4 - - + -
190D GLY* 4.5 5.8 - - - -
193D VAL* 4.6 2.7 - - + -
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Residues in contact with ARG 161 (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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20D ARG* 5.4 4.6 - - - +
96D TYR* 3.2 61.1 + - + -
98D VAL* 3.8 21.3 - - + -
157D THR* 2.7 23.0 + - + +
158D GLU* 2.9 33.5 + - - +
160D TYR* 1.3 73.8 - - - +
162D PHE* 1.3 87.8 + - - +
163D LEU 3.0 0.9 + - - -
164D VAL* 3.2 2.8 + - - +
165D GLN* 2.7 58.2 + - - +
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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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158D GLU 3.4 13.0 - - - +
159D ILE* 3.2 12.7 + - + +
161D ARG* 1.3 100.7 - - - +
163D LEU* 1.3 82.3 + - + +
165D GLN* 3.6 6.0 + - - +
166D LYS* 3.3 49.8 + - + +
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Residues in contact with LEU 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 ILE* 3.0 24.3 + - + +
160D TYR 3.7 4.7 - - - +
161D ARG 3.1 0.4 - - - -
162D PHE* 1.3 96.3 - - + +
164D VAL* 1.3 62.3 + - - +
165D GLN 2.9 6.3 + - - -
166D LYS* 3.2 2.8 + - + +
167D LYS 3.1 15.6 + - - -
168D MET* 3.2 39.2 + - + +
188D ILE* 5.2 0.4 - - + -
189D PRO* 3.7 36.3 - - + +
192D ILE* 3.9 36.3 - - + -
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Residues in contact with VAL 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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98D VAL* 4.1 17.0 - - + -
99D ASP 6.0 0.9 - - - +
160D TYR* 3.1 46.4 + - + +
161D ARG 3.2 3.8 + - - +
163D LEU* 1.3 74.0 - - - +
165D GLN* 1.3 57.6 + - + +
167D LYS* 3.4 21.2 + - - +
169D ILE* 3.8 31.4 - - + +
186D ALA* 6.0 0.4 - - - -
189D PRO* 4.2 6.5 - - + -
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Residues in contact with GLN 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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96D TYR* 3.8 25.5 + - - -
98D VAL* 4.9 6.0 - - + +
161D ARG* 2.7 57.5 + - - +
162D PHE* 3.8 3.5 - - - +
163D LEU 2.9 0.8 - - - -
164D VAL* 1.3 79.0 - - + +
166D LYS* 1.3 83.3 + - - +
167D LYS* 3.0 16.1 + - - +
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Residues in contact with LYS 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* 3.3 48.3 + - + +
163D LEU 3.2 5.5 + - - +
165D GLN* 1.3 100.0 + - - +
167D LYS* 1.3 69.2 + - - +
168D MET* 3.1 18.5 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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