Contacts of the helix formed by residues 180 - 192 (chain A) in PDB entry 3KTC
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 SER 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A TYR* 3.5 10.9 - - - -
178A TRP 3.6 1.2 - - - -
179A ASP* 1.3 86.4 + - - +
181A ALA* 1.3 62.5 + - - +
182A ALA* 3.6 5.7 + - - +
183A ARG* 3.0 26.2 + - - +
184A THR* 2.8 27.2 + - - -
210A GLU* 3.4 15.0 - - - -
182B ALA* 4.6 3.1 - - - +
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Residues in contact with ALA 181 (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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167A TYR* 3.5 33.8 - - + +
180A SER* 1.3 71.5 - - - +
182A ALA* 1.3 63.5 + - - +
184A THR* 3.2 3.4 + - - -
185A LEU* 2.9 29.2 + - - +
198A VAL* 5.7 0.3 - - - +
210A GLU* 3.0 11.0 + - - +
215A SER* 3.7 23.8 - - - +
218A LEU* 4.9 6.3 - - + -
219A ILE* 3.9 15.0 - - + +
342A EDO 4.9 1.3 - - - +
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Residues in contact with ALA 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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180A SER* 3.3 4.9 + - - +
181A ALA* 1.3 80.2 - - - +
183A ARG* 1.3 63.8 + - - +
185A LEU* 3.2 3.1 + - - +
186A LEU* 3.0 24.3 + - - +
210A GLU* 4.9 0.4 + - - -
218A LEU* 4.5 7.1 - - + +
180B SER* 4.6 2.9 - - - +
182B ALA* 3.6 5.2 - - + -
183B ARG* 3.5 35.7 - - + +
186B LEU* 3.8 21.3 - - + +
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Residues in contact with ARG 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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144A TRP* 3.5 53.9 - - + +
177A THR 3.2 21.4 + - - -
178A TRP* 4.8 0.4 - - - +
179A ASP* 3.3 14.3 + - - +
180A SER* 3.0 21.6 + - - +
182A ALA* 1.3 76.6 - - - +
184A THR* 1.3 58.3 + - - +
186A LEU* 3.2 6.3 + - + +
187A GLY* 2.9 26.0 + - - -
339A EDO 3.0 22.0 + - - -
182B ALA* 3.5 15.9 - - + +
214B ASP* 2.8 40.2 + - - -
218B LEU* 3.7 25.3 - - + +
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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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165A ILE* 4.1 15.3 - - + +
167A TYR* 3.3 19.3 - - - +
178A TRP* 3.6 32.4 - - + +
180A SER 2.8 22.3 + - - -
181A ALA* 3.6 5.8 - - - -
183A ARG* 1.3 77.1 - - - +
185A LEU* 1.3 57.9 + - - +
187A GLY 3.2 0.9 + - - -
188A ILE* 2.9 35.7 + - + +
198A VAL* 3.8 28.7 - - + -
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Residues in contact with LEU 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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181A ALA 2.9 17.2 + - - +
182A ALA 3.2 4.5 + - - +
184A THR* 1.3 74.4 - - - +
186A LEU* 1.3 62.3 + - - +
188A ILE* 3.3 6.9 + - + +
189A GLU* 3.0 26.5 + - - +
198A VAL* 4.3 8.3 - - + -
218A LEU* 3.7 38.4 - - + +
219A ILE* 4.0 20.0 - - + -
222A ARG* 3.6 36.0 + - + -
224A ARG* 4.1 30.1 - - + -
186B LEU* 4.0 10.3 - - + -
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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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144A TRP* 5.0 2.9 - - + +
182A ALA 3.0 13.7 + - - +
183A ARG* 3.2 9.6 + - + +
185A LEU* 1.3 77.2 - - - +
187A GLY* 1.3 61.9 + - - +
189A GLU* 3.2 10.9 + - - +
190A ASP* 3.0 27.7 + - - +
182B ALA* 3.7 34.1 - - + +
185B LEU* 4.0 10.5 - - + -
186B LEU* 3.6 32.0 - - + +
218B LEU* 4.0 23.3 - - + -
222B ARG* 3.4 35.3 + - - +
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Residues in contact with GLY 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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144A TRP* 3.7 23.5 - - - -
148A VAL* 4.4 2.0 - - - +
178A TRP* 3.7 8.7 - - - -
183A ARG 2.9 11.3 + - - -
184A THR 3.7 2.7 - - - -
186A LEU* 1.3 75.1 - - - +
188A ILE* 1.3 57.6 + - - +
190A ASP* 3.1 8.9 + - - +
191A ILE* 2.8 39.5 + - - +
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Residues in contact with ILE 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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165A ILE* 4.3 6.5 - - + -
184A THR* 2.9 23.3 + - + +
185A LEU* 3.6 11.7 - - + +
187A GLY* 1.3 72.4 - - - +
189A GLU* 1.3 65.2 + - - +
191A ILE* 3.3 7.9 + - - +
192A GLY* 3.1 19.2 + - - -
193A LEU 4.4 4.0 + - - +
196A VAL* 3.8 20.2 - - + +
197A GLY* 3.8 21.5 - - - +
198A VAL* 3.6 31.0 - - + -
224A ARG* 3.6 44.5 + - + +
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Residues in contact with GLU 189 (chain A).
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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185A LEU 3.0 13.5 + - - +
186A LEU* 3.3 6.7 - - - +
188A ILE* 1.3 76.7 - - - +
190A ASP* 1.3 65.9 + - - +
192A GLY* 3.2 15.1 + - - -
222A ARG* 2.7 44.3 + - - +
224A ARG* 6.1 0.9 - - - +
186B LEU* 3.5 11.5 - - - +
189B GLU* 3.8 19.2 - - - +
222B ARG* 3.0 31.5 + - - -
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Residues in contact with ASP 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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144A TRP* 4.5 15.4 + - - -
148A VAL* 4.0 15.6 - - + +
152A ARG* 3.0 16.7 + - - +
186A LEU* 3.0 12.3 + - - +
187A GLY* 3.1 8.9 + - - +
189A GLU* 1.3 83.8 - - - +
191A ILE* 1.3 63.6 + - - +
192A GLY* 3.4 1.0 + - - -
222B ARG* 3.2 25.4 + - - -
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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 VAL* 3.7 22.2 - - + +
151A MSE 3.5 32.1 - - + -
152A ARG* 3.0 51.0 + - + +
178A TRP* 3.8 16.4 - - + -
187A GLY 2.8 26.1 + - - +
188A ILE* 3.3 9.6 + - - +
190A ASP* 1.3 71.0 - - - +
192A GLY* 1.3 61.3 + - - +
193A LEU* 3.9 24.1 - - + +
196A VAL* 4.2 17.0 - - + -
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Residues in contact with GLY 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 ILE 3.1 10.3 + - - -
189A GLU* 3.2 14.0 + - - -
190A ASP 4.2 0.9 - - - -
191A ILE* 1.3 78.1 - - - +
193A LEU* 1.3 65.5 + - - +
194A ASP* 5.4 1.3 - - - +
224A ARG* 5.9 2.0 - - - -
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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