Contacts of the helix formed by residues 185 - 201 (chain A) in PDB entry 1QS0
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 ALA 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A LEU* 1.3 74.4 - - - +
186A THR* 1.3 64.1 + - - +
187A GLN* 3.1 21.0 - - - +
188A PHE* 2.8 21.7 + - - +
211A ILE* 3.7 23.6 - - + -
215A ALA* 4.0 4.9 - - + +
218A GLU* 3.4 30.5 - - + -
220A ASP* 3.7 15.9 - - + +
221A PHE 4.5 2.7 - - - +
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 4.4 2.9 - - - -
183A ASN* 3.3 14.5 + - + -
184A LEU 2.9 16.4 + - - +
185A ALA* 1.3 72.1 - - - +
187A GLN* 1.3 63.7 + - - +
188A PHE 3.3 0.3 + - - -
189A VAL 3.6 1.9 + - - -
190A GLN* 2.8 26.8 + - - +
220A ASP* 3.6 14.1 + - - +
94B ASP* 3.1 28.9 - - - +
95B GLN* 3.2 23.1 + - - +
99B GLU* 2.8 37.0 + - + +
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.6 36.1 - - + +
131A PRO 3.9 14.4 - - - +
132A THR* 3.7 16.6 - - - +
178A PHE* 4.9 5.2 - - + -
179A THR 5.9 0.4 - - - +
181A SER* 5.1 8.0 + - - +
183A ASN 3.7 5.7 - - - +
184A LEU* 5.1 1.4 - - - +
185A ALA* 3.5 24.8 + - - +
186A THR* 1.3 85.0 + - - +
188A PHE* 1.3 64.8 + - - +
190A GLN* 3.4 16.6 - - - +
191A ALA* 2.9 25.5 + - - +
210A TRP 3.2 19.8 + - - +
211A ILE* 4.6 2.6 - - - +
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ALA 2.8 15.8 + - - +
187A GLN* 1.3 83.9 - - - +
189A VAL* 1.3 60.7 + - - +
191A ALA* 3.4 10.4 + - - +
192A VAL* 3.5 15.1 - - - +
209A ALA* 3.5 31.2 - - + +
210A TRP 3.5 15.7 - - - +
211A ILE* 3.6 22.0 - - + -
220A ASP 4.3 2.9 - - - +
221A PHE* 3.4 38.1 - + - -
224A ALA* 3.4 24.0 - - + -
225A LEU* 4.4 3.8 - - + -
237A LEU* 3.6 33.4 - - + +
238A ASN 3.5 22.4 - - - -
239A VAL* 4.5 0.7 - - + -
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A THR 3.6 5.2 + - - +
187A GLN 3.4 0.2 - - - -
188A PHE* 1.3 73.9 - - - +
190A GLN* 1.3 67.6 + - - +
192A VAL* 3.0 14.3 + - + +
193A GLY 3.2 8.0 + - - -
220A ASP* 2.8 57.4 - - + +
223A THR* 3.6 22.0 - - + +
224A ALA* 3.7 16.8 - - - +
63B SER 4.6 0.2 - - - +
64B GLY* 4.0 4.3 - - - -
67B GLY* 4.2 2.0 - - - -
68B THR* 3.7 29.9 - - + +
95B GLN* 4.6 4.5 - - - +
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Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 4.0 10.5 - - + -
178A PHE* 3.3 23.8 - - + -
186A THR* 2.8 24.4 + - - +
187A GLN* 3.3 14.2 + - - +
189A VAL* 1.3 77.1 - - - +
191A ALA* 1.3 62.5 + - - +
193A GLY 3.1 1.9 + - - -
194A TRP* 3.0 18.7 + - - +
67B GLY 3.5 21.8 - - - +
70B VAL* 3.5 14.9 - - + +
71B GLY* 3.2 17.5 - - - +
95B GLN* 3.1 22.1 + - - +
99B GLU* 3.2 34.4 + - - +
103B LEU* 5.8 0.2 - - - +
106B ARG* 4.7 0.3 + - - -
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.4 34.2 - - + -
187A GLN 2.9 10.2 + - - +
188A PHE 3.6 1.6 - - - +
189A VAL 3.1 0.2 - - - -
190A GLN* 1.3 77.7 - - - +
192A VAL* 1.3 61.2 + - - +
194A TRP* 3.3 1.0 + - - +
195A ALA* 3.1 18.0 + - - +
207A ALA* 3.2 20.3 - - + +
209A ALA* 3.4 32.8 - - + -
235A VAL* 4.3 1.8 - - + -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PHE 3.5 15.5 - - - +
189A VAL* 3.0 9.1 + - - +
191A ALA* 1.3 73.8 - - - +
193A GLY* 1.3 59.9 + - - +
195A ALA* 3.2 2.8 + - - +
196A MSE 2.8 39.4 + - - +
224A ALA* 3.7 25.6 - - + +
227A PHE* 3.9 15.0 - - + -
228A ALA* 3.8 29.6 - - + +
233A ALA* 4.0 9.6 - - + -
235A VAL* 3.7 9.9 - - + -
237A LEU* 4.2 14.4 - - + -
68B THR* 4.4 2.5 - - + -
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Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL 3.2 6.3 + - - -
190A GLN 3.1 6.2 + - - -
192A VAL* 1.3 76.0 - - - +
194A TRP* 1.3 54.3 + - - +
196A MSE 3.1 7.4 + - - +
197A ALA 2.8 30.5 + - - -
68B THR* 3.2 39.0 - - - +
72B MSE 3.4 10.7 - - - +
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Residues in contact with TRP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A THR 3.8 17.9 - - - -
128A MSE 3.4 39.3 - - + +
130A PHE* 3.6 30.7 - + + -
190A GLN 3.0 5.1 + - - -
191A ALA 3.4 9.0 - - - +
193A GLY* 1.3 75.4 - - - +
195A ALA* 1.3 64.0 + - - +
197A ALA* 3.3 6.4 + - - +
198A SER* 3.1 18.2 + - - -
205A LYS* 3.9 25.1 - - + -
206A ILE 3.4 29.2 - - - -
207A ALA* 4.0 8.5 - - + -
71B GLY 3.4 27.0 - - - +
74B ALA* 4.0 8.5 + - + -
75B TYR* 3.4 39.5 - + + +
111B PHE* 6.1 0.2 - + - -
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ALA 3.1 6.3 + - - +
192A VAL 3.5 2.5 - - - +
193A GLY 3.1 0.2 - - - -
194A TRP* 1.3 81.0 - - - +
196A MSE 1.3 65.5 + - - +
198A SER* 3.1 4.2 + - - -
199A ALA 3.0 18.5 + - - -
205A LYS 5.5 0.2 - - - -
207A ALA* 4.0 2.5 - - + +
233A ALA* 4.1 0.9 - - + -
234A PRO* 3.3 38.1 - - + +
235A VAL* 2.9 37.9 - - + -
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Residues in contact with MSE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL* 2.8 25.1 + - - +
193A GLY* 3.1 7.6 + - - +
195A ALA* 1.3 76.8 - - - +
197A ALA* 1.3 57.5 + - - +
199A ALA* 3.2 6.5 + - - +
200A ILE* 2.9 41.7 + - + +
227A PHE* 4.3 5.4 - - + -
231A TYR* 3.6 52.5 - - + -
233A ALA* 4.2 13.9 - - + +
234A PRO* 5.0 1.6 - - - -
29B TYR* 5.3 5.2 - - + -
56B PHE* 3.9 23.6 - - + -
68B THR* 4.1 29.2 - - - +
72B MSE 5.0 4.9 - - + +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLY 2.8 13.1 + - - +
194A TRP 3.4 10.3 - - - +
195A ALA 3.1 0.2 - - - -
196A MSE 1.3 77.3 - - - +
198A SER* 1.3 61.3 + - - +
200A ILE* 3.2 4.0 + - - +
201A LYS* 3.0 27.4 + - - +
72B MSE 3.6 8.7 - - + +
75B TYR* 3.5 27.4 - - + -
77B LEU* 3.4 28.7 - - + +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A TRP* 3.1 14.6 + - - -
195A ALA* 3.1 11.5 + - - -
197A ALA* 1.3 77.6 - - - +
199A ALA* 1.3 58.4 + - - +
201A LYS 3.3 1.2 + - - -
202A GLY 3.3 2.6 + - - -
203A ASP* 2.9 48.1 + - - +
205A LYS 2.8 30.3 + - - -
234A PRO* 4.9 2.3 - - - +
75B TYR* 3.7 22.6 - - - -
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ALA 3.0 13.1 + - - +
196A MSE 3.7 8.3 - - - +
198A SER* 1.3 74.1 - - - +
200A ILE* 1.3 66.1 + - + +
202A GLY* 3.2 12.9 + - - -
203A ASP 5.0 2.2 - - - +
231A TYR 6.1 0.4 - - - +
232A ARG 5.9 1.3 - - - +
233A ALA* 6.1 0.2 - - - -
234A PRO* 4.3 16.5 - - + +
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A MSE 2.9 32.0 + - + +
197A ALA 3.4 4.9 - - - +
199A ALA* 1.3 77.4 - - + +
201A LYS* 1.3 67.5 + - + +
202A GLY 3.3 0.7 + - - -
24B ASP 6.0 1.3 - - - +
27B VAL* 4.3 9.4 - - + -
53B SER* 3.8 40.0 - - - +
54B ARG* 5.5 4.7 - - - -
56B PHE* 4.4 15.5 - - + -
72B MSE 4.0 28.5 - - + -
77B LEU* 4.3 13.5 - - + -
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ALA 3.0 17.0 + - - +
198A SER 3.3 1.5 + - - +
199A ALA 3.1 0.4 - - - -
200A ILE* 1.3 84.4 - - + +
202A GLY* 1.3 62.4 + - - +
203A ASP* 3.1 3.0 + - + +
24B ASP* 3.5 33.0 + - - +
25B ASN* 3.1 26.9 + - - -
75B TYR* 3.8 24.9 - - + +
77B LEU* 3.6 22.7 - - + -
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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
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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