Contacts of the helix formed by residues 181 - 193 (chain A) in PDB entry 3QEO
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 THR 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ALA* 1.3 75.5 - - - +
182A PRO* 1.4 77.8 - - + +
183A GLU* 2.8 14.2 + - - +
184A THR* 2.9 31.5 + - - -
185A CYS* 3.3 10.7 + - - -
209A HIS* 4.8 2.5 - - + +
239A ASN* 3.0 20.6 + - - +
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Residues in contact with PRO 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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29A ASN* 5.0 4.3 - - - +
180A ALA 3.8 0.2 - - - -
181A THR* 1.4 84.4 - - + +
183A GLU* 1.3 65.6 + - - +
185A CYS* 3.4 6.9 + - + +
186A LEU* 3.1 22.2 + - - +
202A LEU* 3.6 17.2 - - + +
205A LEU* 4.1 9.3 - - + +
206A GLU* 3.7 47.1 - - + +
209A HIS* 3.8 30.0 - - + +
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Residues in contact with GLU 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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181A THR* 2.8 12.5 + - - +
182A PRO* 1.3 91.5 - - - +
184A THR* 1.3 62.8 + - - +
186A LEU* 3.9 5.0 - - + +
187A HIS* 3.2 22.9 + - - +
202A LEU* 3.4 37.6 - - + +
206A GLU* 4.7 3.0 - - - +
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Residues in contact with THR 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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31A ALA 5.2 0.2 - - - +
180A ALA* 3.7 17.7 - - + -
181A THR* 2.9 16.7 + - - -
183A GLU* 1.3 74.7 - - - +
185A CYS* 1.3 59.9 + - - +
187A HIS* 3.2 8.4 + - + +
188A ARG* 2.8 64.4 + - - +
239A ASN* 2.5 35.2 + - - +
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Residues in contact with CYS 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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29A ASN* 4.0 19.5 - - - +
30A ILE 2.9 28.0 - - - +
31A ALA* 3.3 8.5 - - - +
32A ALA* 3.9 22.0 - - - -
180A ALA* 4.2 11.2 - - - -
181A THR 3.3 11.7 + - - -
182A PRO* 3.8 7.0 - - + +
184A THR* 1.3 74.6 - - - +
186A LEU* 1.3 57.1 + - - +
189A ILE* 2.7 38.7 + - - +
205A LEU* 4.6 11.4 - - + -
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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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182A PRO 3.1 15.9 + - - +
183A GLU* 3.9 7.4 - - + +
185A CYS* 1.3 74.1 - - - +
187A HIS* 1.3 58.9 + - - +
189A ILE* 3.3 11.5 + - + +
190A TYR* 3.0 27.9 + - - +
198A GLN 6.0 0.7 - - - +
200A ILE* 3.5 25.6 - - + +
201A PRO* 4.8 0.2 - - + -
202A LEU* 3.9 32.1 - - + +
205A LEU* 3.7 21.2 - - + +
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Residues in contact with HIS 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 GLU 3.2 11.7 + - - +
184A THR* 3.5 10.1 - - + +
186A LEU* 1.3 79.3 - - - +
188A ARG* 1.3 52.8 + - + +
190A TYR* 3.1 23.7 + + - +
191A LEU* 2.7 74.6 + - + +
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Residues in contact with ARG 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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31A ALA* 3.2 29.4 - - + +
32A ALA 2.9 24.0 + - - -
184A THR* 2.8 34.7 + - + +
187A HIS* 1.3 77.8 - - + +
189A ILE* 1.3 51.1 + - - +
191A LEU* 3.0 18.8 + - + +
192A ARG* 2.8 35.0 + - - +
238A VAL* 2.7 29.0 + - - +
239A ASN 2.8 20.6 + - - -
240A GLU 3.7 9.3 + - - -
241A ASP* 3.8 4.9 - - - +
242A PHE* 3.9 2.2 - - - -
401A UDP 3.4 55.3 + - - +
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Residues in contact with ILE 189 (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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30A ILE* 3.5 28.5 - - + +
31A ALA* 3.5 12.5 - - + +
185A CYS 2.7 26.1 + - - +
186A LEU* 3.4 10.5 - - + +
188A ARG* 1.3 70.9 - - - +
190A TYR* 1.3 58.6 + - - +
192A ARG* 3.4 5.9 + - - +
193A GLY 3.0 15.9 + - - -
194A ARG 4.4 0.2 + - - -
197A GLU* 3.5 36.6 - - + +
198A GLN* 2.9 34.2 + - - +
200A ILE* 4.5 13.0 - - + +
205A LEU* 3.7 28.3 - - + -
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Residues in contact with TYR 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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186A LEU 3.0 14.0 + - - +
187A HIS* 3.3 32.8 - + - +
189A ILE* 1.3 75.7 - - + +
191A LEU* 1.3 71.7 + - + +
193A GLY* 3.8 8.1 + - - -
198A GLN* 3.5 16.4 - - - +
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Residues in contact with LEU 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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187A HIS* 2.7 58.6 + - + +
188A ARG* 3.0 26.7 + - + +
190A TYR* 1.3 81.5 - - + +
192A ARG* 1.3 62.0 + - - +
193A GLY* 3.5 1.0 + - - -
401A UDP 3.8 28.0 - - + +
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Residues in contact with ARG 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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30A ILE* 4.1 18.4 - - - +
31A ALA* 4.3 9.2 - - - +
35A SER* 5.6 0.4 - - - -
188A ARG 2.8 16.2 + - - +
189A ILE* 3.9 4.0 - - - +
191A LEU* 1.3 73.6 - - - +
193A GLY* 1.3 61.0 + - - +
194A ARG* 3.2 47.8 + - + +
197A GLU* 2.7 44.6 + - - -
401A UDP 2.7 73.6 + - - +
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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 ILE 3.0 10.0 + - - -
190A TYR 4.1 7.6 - - - -
191A LEU 3.4 2.1 - - - -
192A ARG* 1.3 77.2 - - - +
194A ARG* 1.3 64.2 + - - +
195A ASN* 3.4 8.3 + - - -
198A GLN* 3.5 15.3 - - - -
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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