Contacts of the helix formed by residues 190 - 202 (chain A) in PDB entry 3MWC
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 ASP 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ILE* 4.2 8.9 - - + +
186A LYS 3.5 6.2 - - - +
187A PRO* 3.5 5.9 - - - +
188A GLY* 2.9 29.4 + - - -
189A TRP* 1.3 76.2 + - - +
191A VAL* 1.3 88.3 + - - +
192A GLU 3.3 1.0 + - - -
193A PRO* 3.4 7.2 - - - +
194A LEU* 3.3 24.9 + - - +
215A PHE* 3.8 9.2 - - + -
222A THR* 3.6 21.9 + - + +
226A MET* 3.8 17.7 - - - +
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Residues in contact with VAL 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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190A ASP* 1.3 91.6 + - - +
192A GLU* 1.3 64.9 + - - +
194A LEU* 3.9 1.9 - - - +
195A GLN* 3.0 43.2 + - + +
222A THR* 4.1 11.2 - - + +
225A ALA* 4.0 32.8 - - + +
226A MET* 3.9 21.9 - - + +
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Residues in contact with GLU 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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163A ILE* 3.7 25.1 - - + +
190A ASP 4.6 0.4 - - - +
191A VAL* 1.3 77.9 - - - +
193A PRO* 1.3 75.2 - - + +
195A GLN* 2.9 19.3 + - - +
196A GLU* 2.9 24.8 + - + +
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Residues in contact with PRO 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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163A ILE* 3.4 16.5 - - + -
166A LEU* 3.7 16.7 - - + +
183A ILE* 4.1 8.1 - - + -
189A TRP* 3.2 55.6 - - + +
190A ASP* 3.4 17.0 - - - +
192A GLU* 1.3 96.1 - - + +
194A LEU* 1.3 55.2 + - - +
196A GLU* 3.4 1.6 + - - +
197A THR* 2.7 34.7 + - - -
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Residues in contact with LEU 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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183A ILE* 3.9 17.2 - - + +
190A ASP 3.3 16.1 + - - +
191A VAL 3.9 2.7 - - - +
192A GLU 3.1 1.0 - - - -
193A PRO* 1.3 80.1 - - - +
195A GLN* 1.3 58.3 + - - +
197A THR* 3.8 1.1 - - - -
198A ARG* 2.9 28.2 + - - +
207A LEU* 3.7 28.5 - - + -
209A THR* 4.0 22.9 - - + -
226A MET* 3.7 38.6 - - + +
229A ALA* 3.4 25.1 - - + -
231A CYS* 4.5 12.3 - - - -
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Residues in contact with GLN 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 VAL* 3.0 33.4 + - + +
192A GLU* 2.9 9.3 + - - +
194A LEU* 1.3 78.7 - - - +
196A GLU* 1.3 72.2 + - - +
197A THR 3.4 0.3 + - - -
198A ARG* 3.4 6.7 + - - +
199A ARG* 3.4 21.8 + - - +
225A ALA 5.3 2.6 + - - -
228A ALA* 5.0 13.2 - - + +
229A ALA* 5.0 11.4 - - + +
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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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163A ILE* 3.4 34.3 - - + -
167A ILE* 3.3 18.1 - - + +
192A GLU* 2.9 31.0 + - + +
193A PRO 4.0 2.2 - - - +
195A GLN* 1.3 86.3 - - - +
197A THR* 1.3 61.0 + - - +
199A ARG* 2.3 41.1 + - - +
200A ALA* 3.2 17.0 + - - +
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Residues in contact with THR 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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166A LEU* 3.6 20.6 - - - +
167A ILE* 3.9 9.0 - - - +
170A VAL* 3.9 23.3 - - + -
181A ILE* 4.7 2.2 - - + -
183A ILE* 4.1 11.8 - - + +
193A PRO 2.7 24.6 + - - -
194A LEU* 3.8 7.0 - - - -
196A GLU* 1.3 75.8 - - - +
198A ARG* 1.3 66.9 + - - +
200A ALA* 3.1 11.2 + - - +
201A VAL* 3.2 17.3 + - + +
207A LEU* 3.8 28.3 - - + -
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Residues in contact with ARG 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 LEU 2.9 19.3 + - - +
195A GLN* 3.4 6.0 + - - +
197A THR* 1.3 76.8 - - - +
199A ARG* 1.3 55.6 + - + +
201A VAL* 3.4 11.3 + - - +
202A GLY* 2.7 55.3 + - - +
203A ASP* 3.4 41.3 + - - +
205A PHE 3.0 22.2 + - - -
207A LEU* 3.8 31.1 + - + +
228A ALA 5.6 0.2 - - - +
229A ALA* 2.7 31.4 + - + +
230A LYS* 3.2 24.2 + - - +
231A CYS* 3.6 11.5 - - - +
232A LEU* 5.1 0.6 - - - +
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Residues in contact with ARG 199 (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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195A GLN 3.4 8.8 + - - +
196A GLU* 2.3 44.8 + - - +
197A THR 3.1 0.8 - - - -
198A ARG* 1.3 78.4 - - + +
200A ALA* 1.3 69.9 + - - +
201A VAL 3.0 2.7 + - - -
202A GLY* 3.6 8.8 + - - +
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Residues in contact with ALA 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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167A ILE* 4.2 20.9 - - + -
170A VAL* 4.1 17.5 - - + -
171A GLU* 5.4 7.7 - - + +
174A LEU* 4.2 10.2 - - - +
196A GLU 3.2 18.6 + - - +
197A THR 3.1 7.0 + - - +
199A ARG* 1.3 80.1 - - + +
201A VAL* 1.3 58.3 + - - +
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Residues in contact with VAL 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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170A VAL* 3.3 32.3 - - + -
174A LEU* 4.1 16.6 - - + +
181A ILE* 5.0 3.1 - - + -
197A THR* 3.4 14.4 - - + +
198A ARG* 3.4 20.4 - - - +
199A ARG 3.0 0.2 - - - -
200A ALA* 1.3 81.1 - - - +
202A GLY* 1.3 61.5 + - - +
204A HIS* 2.7 33.8 + - - -
205A PHE* 3.5 35.1 - - + +
207A LEU* 4.7 5.8 - - + -
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Residues in contact with GLY 202 (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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198A ARG* 2.7 37.7 + - - -
199A ARG* 3.6 9.9 + - - -
201A VAL* 1.3 74.2 - - - +
203A ASP* 1.3 64.3 + - - -
204A HIS* 2.9 14.2 + - - -
205A PHE 3.1 6.4 + - - -
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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