Contacts of the helix formed by residues 188 - 199 (chain A) in PDB entry 4QBT
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 GLN 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A VAL* 3.6 16.4 - - - +
170A GLN* 3.2 12.5 + - - +
184A GLY* 4.5 2.2 - - - -
185A GLY 3.3 22.8 - - - +
186A ILE 3.0 1.0 - - - -
187A ASP* 1.3 113.1 + - - +
189A ARG* 1.3 51.6 + - - +
190A LYS* 2.5 1.1 + - - +
191A ILE* 2.4 41.5 + - + +
192A PHE* 3.2 33.0 + - + -
506A TYR* 2.9 48.6 + - - -
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Residues in contact with ARG 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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20A GLU* 2.8 41.4 + - - -
22A LEU* 4.1 16.2 - - + +
151A GLU* 5.3 2.7 - - - +
185A GLY 4.3 0.2 + - - -
186A ILE* 3.0 27.4 + - - +
187A ASP 2.9 3.6 + - - +
188A GLN* 1.3 75.9 - - - +
190A LYS* 1.3 61.0 + - + +
192A PHE* 3.2 5.7 + - - +
193A THR* 2.8 50.0 + - + +
211A MET* 3.7 22.7 - - + +
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Residues in contact with LYS 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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147A LYS* 3.7 33.4 - - + +
148A ALA* 3.6 22.6 - - - +
150A ALA* 4.9 5.6 - - + -
151A GLU* 3.5 36.3 - - + +
187A ASP 4.2 1.7 + - - +
188A GLN 2.5 5.9 + - - -
189A ARG* 1.3 74.9 - - + +
191A ILE* 1.3 62.8 + - - +
193A THR* 3.1 9.0 + - - +
194A PHE* 3.1 23.9 + - - +
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Residues in contact with ILE 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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148A ALA* 3.2 20.6 - - - +
149A GLY* 4.8 2.2 - - - -
152A VAL* 3.8 32.5 - - + -
166A TYR* 4.0 12.8 - - + -
167A PRO* 4.4 18.6 - - + +
170A GLN* 3.6 50.7 - - + +
171A ALA 5.2 1.3 - - - +
188A GLN* 2.4 28.3 + - - +
190A LYS* 1.3 68.3 - - - +
192A PHE* 1.3 58.4 + - + +
194A PHE* 3.1 9.0 - - + +
195A ALA* 2.9 28.0 + - + +
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Residues in contact with PHE 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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22A LEU* 5.0 3.4 - - + -
170A GLN* 3.8 8.1 - - - -
174A GLU* 4.7 0.2 - - - -
182A GLN* 3.4 44.4 - - + -
184A GLY* 3.9 18.8 - - - -
185A GLY 4.4 0.2 - - - -
188A GLN* 3.2 34.7 + - + -
189A ARG* 3.2 9.1 + - - +
191A ILE* 1.3 78.4 - - + +
193A THR* 1.3 62.3 + - - +
195A ALA* 3.2 3.0 + - + +
196A GLU* 3.0 26.1 + - - +
209A HIS* 3.4 42.6 - + + +
210A LEU 4.0 4.3 - - - -
211A MET* 3.7 36.1 - - + -
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Residues in contact with THR 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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22A LEU* 4.2 16.8 - - + -
189A ARG* 2.8 46.3 + - - +
190A LYS* 3.1 15.4 + - - +
192A PHE* 1.3 70.0 - - - +
194A PHE* 1.3 68.0 + - - +
196A GLU* 3.2 11.8 + - - +
197A LYS* 3.1 22.5 + - - +
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Residues in contact with PHE 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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136A LEU* 5.0 2.5 - - + -
140A VAL* 3.9 33.7 - - + -
144A ASP* 4.2 5.8 - - + -
145A SER* 4.3 15.3 - - - -
148A ALA* 3.7 19.3 - - + -
167A PRO* 3.6 30.1 - - + -
168A GLY* 3.7 20.2 - - - -
171A ALA* 4.4 5.8 - - + -
190A LYS 3.1 21.1 + - - +
191A ILE 3.1 9.4 - - - +
193A THR* 1.3 75.4 + - - +
195A ALA* 1.3 65.3 + - - +
197A LYS* 3.1 4.8 + - - -
198A TYR* 3.0 60.3 + + + +
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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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171A ALA* 3.6 32.1 - - + -
174A GLU* 3.8 29.6 - - - +
191A ILE* 2.9 13.5 + - + +
192A PHE* 3.2 8.3 + - - +
194A PHE* 1.3 77.0 - - - +
196A GLU* 1.3 62.9 + - - +
198A TYR 4.7 0.2 - - - +
199A LEU* 3.2 30.6 + - + +
206A LYS* 4.9 0.5 - - - -
209A HIS* 4.4 0.7 - - + -
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Residues in contact with GLU 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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22A LEU* 3.5 35.5 - - - +
23A GLY* 5.7 0.6 - - - -
192A PHE 3.0 10.1 + - - +
193A THR* 3.2 13.3 + - - +
195A ALA* 1.3 78.3 - - - +
197A LYS* 1.3 56.9 + - - +
200A PRO* 3.2 23.2 - - - +
206A LYS* 3.8 32.1 + - + +
207A ARG 3.4 11.4 - - - +
209A HIS* 2.6 37.8 + - + -
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Residues in contact with LYS 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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144A ASP* 3.4 10.9 + - - +
193A THR 3.1 10.8 + - - +
194A PHE* 3.1 9.5 + - - +
196A GLU* 1.3 78.4 - - - +
198A TYR* 1.3 99.2 + - + +
199A LEU 3.7 0.2 - - - -
200A PRO* 3.6 10.7 - - - +
201A ALA* 4.3 6.8 + - - +
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Residues in contact with TYR 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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136A LEU* 3.9 15.7 - - + -
139A VAL* 3.7 30.9 + - + -
140A VAL* 3.5 26.5 - - + -
141A THR* 4.7 1.9 + - - +
144A ASP* 2.6 30.3 + - + +
171A ALA* 6.0 1.1 - - + -
194A PHE* 3.0 57.4 + + + +
195A ALA* 5.3 0.7 - - - -
197A LYS* 1.3 106.0 + - + +
199A LEU* 1.3 70.3 + - + +
200A PRO 3.2 2.0 - - - -
201A ALA* 3.0 19.4 + - + +
202A LEU* 3.4 12.3 + - - +
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Residues in contact with LEU 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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136A LEU* 5.9 2.0 - - + -
171A ALA* 3.6 35.7 - - + +
172A LEU* 4.2 19.7 - - + +
174A GLU* 3.5 26.9 - - + +
175A GLU* 4.8 2.2 - - + +
195A ALA* 3.2 21.5 + - + +
198A TYR* 1.3 77.6 - - + +
200A PRO* 1.4 62.0 - - + +
202A LEU* 2.9 24.8 + - + +
204A TYR* 3.0 36.5 + - + +
205A SER 3.8 16.4 - - - +
206A LYS* 5.1 1.1 - - - -
207A ARG* 4.0 11.2 - - - +
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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