Contacts of the helix formed by residues 171 - 188 (chain A) in PDB entry 1Q0R
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 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ALA 3.9 2.9 + - - +
170A GLU* 1.3 74.7 + - - +
172A ARG* 1.3 59.5 + - - -
173A ALA 3.4 2.0 - - - -
174A ALA 3.4 1.5 + - - -
175A GLU* 3.0 28.4 + - - +
213A LEU* 3.5 17.3 - - - +
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLY* 1.3 69.4 - - - -
173A ALA* 1.3 67.2 + - - +
175A GLU* 3.2 1.4 + - - +
176A VAL* 2.9 35.8 + - + +
203A GLU* 3.5 37.9 + - - +
206A ILE* 3.4 24.0 - - + +
207A ASP* 2.9 32.5 + - - -
211A GLY* 4.8 5.5 + - - -
213A LEU* 3.5 28.3 - - + +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLY 3.4 0.6 - - - -
172A ARG* 1.3 79.9 - - - +
174A ALA* 1.3 57.8 + - - +
176A VAL* 3.8 5.8 - - - +
177A ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA* 3.7 7.7 - - + +
170A GLU 3.4 35.4 + - - +
171A GLY 3.4 1.7 + - - +
172A ARG 3.3 0.4 - - - -
173A ALA* 1.3 76.1 - - - +
175A GLU* 1.3 61.4 + - - +
177A ALA* 3.8 6.1 - - - +
178A LYS* 3.0 29.6 + - - +
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA* 3.8 22.9 - - + +
171A GLY 3.0 17.7 + - - +
172A ARG 3.2 5.4 + - - +
174A ALA* 1.3 73.5 - - - +
176A VAL* 1.3 64.8 + - - +
178A LYS* 3.3 14.5 + - - +
179A ARG* 2.8 62.9 + - - +
206A ILE* 4.2 5.8 - - + -
213A LEU* 3.2 41.9 - - + +
214A ALA* 5.5 0.7 - - - -
215A GLU* 4.1 9.5 + - - +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ARG* 2.9 27.3 + - + +
173A ALA* 3.8 5.8 - - - +
175A GLU* 1.3 76.6 - - - +
177A ALA* 1.3 63.8 + - - +
179A ARG* 3.2 6.1 + - - +
180A VAL* 2.9 24.7 + - + +
199A ALA* 3.8 39.5 - - + +
202A GLU* 4.5 4.2 - - + +
203A GLU* 3.9 27.6 - - + +
206A ILE* 3.7 22.9 - - + -
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA 3.0 18.3 + - - +
174A ALA* 3.8 7.2 - - - +
176A VAL* 1.3 77.3 - - - +
178A LYS* 1.3 57.7 + - - +
180A VAL* 3.4 6.6 + - - +
181A SER* 2.9 29.9 + - - -
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.2 26.7 - - + +
165A MET* 3.0 28.2 + - - +
166A ASN 4.6 0.2 - - - -
167A GLN* 2.6 26.2 + - + +
168A PRO* 4.8 1.3 - - - +
169A ALA* 3.9 19.3 - - + +
174A ALA 3.0 19.0 + - - +
175A GLU* 3.5 17.4 + - - +
177A ALA* 1.3 76.8 - - - +
179A ARG* 1.3 64.8 + - + +
181A SER* 2.6 25.3 + - - +
182A LYS* 3.1 9.0 + - + +
215A GLU* 5.6 6.7 - - - -
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Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLU* 2.8 40.1 + - - +
176A VAL 3.7 4.0 - - - +
178A LYS* 1.3 76.1 - - + +
180A VAL* 1.3 63.5 + - - +
182A LYS* 3.1 12.5 + - - +
183A TRP* 3.0 28.9 + - - +
202A GLU* 3.0 47.0 + - + +
205A ALA* 4.5 4.6 - - - +
206A ILE* 3.4 29.7 - - - +
212A VAL 4.4 1.8 + - - -
213A LEU 2.9 30.3 + - - -
214A ALA 3.9 3.0 + - - -
215A GLU* 3.8 36.3 - - - +
216A PRO* 5.6 1.2 - - - +
2712A 1PE 4.0 7.3 + - - -
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 2.9 22.8 + - + +
177A ALA* 3.7 7.0 - - - +
179A ARG* 1.3 75.2 - - - +
181A SER* 1.3 58.2 + - - +
183A TRP* 3.2 9.0 + - - +
184A ARG* 2.9 26.3 + - - +
193A PHE* 3.9 6.9 - - + -
195A ASP* 3.7 40.8 - - + +
198A TYR* 3.7 9.0 - - + +
199A ALA* 3.4 39.0 - - + +
202A GLU* 4.8 3.4 - - + -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.0 25.1 - - - +
177A ALA 2.9 15.4 + - - -
178A LYS* 2.6 23.1 + - - +
180A VAL* 1.3 76.2 - - - +
182A LYS* 1.3 59.9 + - - +
184A ARG* 3.4 10.2 + - - +
185A ILE* 3.1 27.2 + - - +
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Residues in contact with LYS 182 (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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34A LEU* 5.5 0.4 - - - +
161A ALA* 4.2 14.3 - - + +
164A LEU* 4.6 5.2 - - + -
165A MET* 3.7 31.9 - - + -
178A LYS* 3.1 8.3 + - + +
179A ARG* 3.3 11.1 - - - +
181A SER* 1.3 80.6 + - - +
183A TRP* 1.3 90.4 + - - +
185A ILE* 3.3 12.8 + - - +
186A LEU* 3.1 35.2 + - + +
202A GLU* 4.8 3.8 + - - -
215A GLU* 3.0 19.2 + - - +
3482A SO4 2.6 42.0 + - - +
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Residues in contact with TRP 183 (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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34A LEU* 3.9 11.4 - - + -
179A ARG 3.0 25.7 + - - -
180A VAL* 3.2 6.9 + - - +
182A LYS* 1.3 83.8 - - - +
184A ARG* 1.3 57.5 + - - +
186A LEU* 3.9 8.4 - - + +
187A SER* 2.8 34.0 + - - -
193A PHE* 3.7 11.4 - - + -
198A TYR* 3.4 36.1 - + + -
202A GLU* 2.7 26.4 + - + -
276A HIS 3.9 14.8 - - - -
277A ALA* 4.0 7.0 - - + +
2712A 1PE 3.0 73.5 + - - -
3482A SO4 3.6 24.9 - - - -
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Residues in contact with ARG 184 (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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180A VAL 2.9 16.6 + - - +
181A SER* 3.6 9.9 - - - +
182A LYS 3.2 0.2 - - - -
183A TRP* 1.3 76.3 - - - +
185A ILE* 1.3 61.9 + - + +
187A SER* 3.6 1.4 + - - -
188A GLY* 3.2 23.7 + - - +
193A PHE* 3.5 27.8 - - + +
195A ASP* 3.0 37.1 + - - -
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Residues in contact with ILE 185 (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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157A PRO* 3.2 46.4 - - + +
160A ASP* 4.1 18.6 - - + +
161A ALA* 4.1 5.8 - - + +
164A LEU* 3.3 40.4 - - + -
181A SER 3.1 10.4 + - - +
182A LYS* 3.5 8.7 - - - +
184A ARG* 1.3 79.0 - - + +
186A LEU* 1.3 61.8 + - - +
188A GLY* 3.5 9.7 + - - -
249A PRO* 5.1 0.3 - - - +
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Residues in contact with LEU 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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157A PRO 4.0 9.9 - - - +
158A PHE* 4.1 9.9 - - + -
161A ALA* 3.8 22.0 - - + -
165A MET* 6.3 0.4 - - - -
182A LYS* 3.1 34.9 + - + +
183A TRP* 3.9 11.2 - - + +
185A ILE* 1.3 73.9 - - - +
187A SER* 1.3 64.4 + - - +
188A GLY* 4.6 0.3 - - - -
249A PRO* 3.5 23.8 - - + +
250A ILE* 4.1 20.6 - - + -
276A HIS* 2.9 36.8 + - + +
600A AKT 5.6 1.8 - - + -
2712A 1PE 4.0 27.8 - - - +
3482A SO4 5.3 0.4 - - - +
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Residues in contact with SER 187 (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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183A TRP 2.8 21.9 + - - -
184A ARG 4.0 1.8 - - - -
186A LEU* 1.3 73.8 - - - +
188A GLY* 1.3 65.6 + - - +
190A GLY 4.8 0.7 + - - -
191A VAL* 4.4 8.3 + - - +
193A PHE* 3.6 20.9 - - - +
247A HIS* 5.3 1.4 - - - +
273A GLY 4.6 4.2 - - - +
274A MET 4.4 0.3 - - - -
275A GLY* 3.3 22.8 + - - -
276A HIS 4.1 3.6 - - - +
277A ALA* 3.6 13.4 - - - +
279A PRO* 3.6 28.6 - - - +
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Residues in contact with GLY 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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184A ARG* 3.2 17.8 + - - +
185A ILE 3.5 7.1 + - - -
186A LEU 3.3 3.2 - - - -
187A SER* 1.3 86.2 - - - +
189A THR* 1.3 65.1 + - - +
190A GLY 3.6 0.2 - - - -
191A VAL 4.2 6.8 - - - +
193A PHE* 4.6 8.3 - - - +
247A HIS* 6.5 1.3 - - - -
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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