Contacts of the helix formed by residues 189 - 198 (chain A) in PDB entry 1M2V
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 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.8 14.3 - - - +
188A TYR* 1.3 79.4 - - - +
190A LEU* 1.3 69.2 + - - +
191A GLU* 3.2 4.9 - - + +
192A ALA* 2.8 26.2 + - + +
193A LEU* 2.8 9.3 + - - -
271A LEU* 3.8 3.8 - - - -
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Residues in contact with LEU 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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189A GLN* 1.3 69.1 - - - +
191A GLU* 1.3 52.8 + - - +
193A LEU* 3.1 4.7 + - + +
194A THR* 2.6 53.2 + - - +
224A LEU* 5.8 1.1 - - + -
271A LEU* 3.3 55.2 - - + +
272A LEU* 5.5 0.2 - - - -
274A GLN* 3.8 28.7 - - + +
275A GLY* 4.2 11.7 - - - +
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Residues in contact with GLU 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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189A GLN* 3.0 5.7 + - + +
190A LEU* 1.3 77.9 - - - +
192A ALA* 1.3 63.3 + - - +
194A THR* 3.2 6.8 + - - -
195A GLU* 3.0 41.6 + - + +
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Residues in contact with ALA 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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186A ARG* 4.2 21.8 - - - +
188A TYR* 5.1 0.2 - - + -
189A GLN* 2.8 25.4 + - + +
191A GLU* 1.3 77.8 + - - +
193A LEU* 1.3 60.9 + - - +
195A GLU* 3.5 7.1 + - - +
196A MET* 3.1 34.9 + - + +
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Residues in contact with LEU 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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182A PHE* 3.2 43.3 - - + -
188A TYR* 4.6 4.9 - - + -
189A GLN 2.8 16.4 + - - +
190A LEU* 3.6 8.3 - - + +
192A ALA* 1.3 71.3 - - - +
194A THR* 1.3 65.4 + - - +
196A MET* 3.8 7.7 - - + +
197A LEU* 3.1 32.5 + - + +
224A LEU* 5.5 1.1 - - + -
268A ILE* 3.9 33.7 - - + +
271A LEU* 3.4 37.2 - - + -
272A LEU* 4.1 8.5 - - + +
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Residues in contact with THR 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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190A LEU* 2.6 43.5 + - - +
191A GLU* 3.2 7.5 + - - -
193A LEU* 1.3 71.8 - - - +
195A GLU* 1.3 63.5 + - + +
197A LEU 3.7 0.2 - - - -
198A THR* 2.5 48.9 + - + +
224A LEU* 4.7 20.9 - - + +
275A GLY* 5.4 0.9 - - - -
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Residues in contact with GLU 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 GLU* 3.0 30.5 + - + +
192A ALA* 3.8 6.3 - - - +
194A THR* 1.3 77.7 - - + +
196A MET* 1.3 66.1 + - + +
198A THR* 2.9 27.2 + - - +
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Residues in contact with MET 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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180A ASN* 4.7 3.1 - - - +
182A PHE* 4.2 17.9 - - + -
186A ARG* 4.6 3.4 - - - +
188A TYR* 3.2 36.8 - - + -
192A ALA* 3.1 31.7 + - + +
193A LEU* 3.8 8.1 - - - +
195A GLU* 1.3 79.0 - - + +
197A LEU* 1.3 62.4 + - + +
198A THR 3.5 3.5 + - - +
352B ASN* 5.6 1.6 - - - +
379B ALA* 3.7 47.5 - - + +
380B ASP* 3.8 19.7 - - - -
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Residues in contact with LEU 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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168A LEU* 3.4 24.9 - - + -
180A ASN* 3.2 33.7 - - + +
182A PHE* 3.3 30.3 - - + -
193A LEU* 3.1 29.5 + - + +
196A MET* 1.3 77.0 - - - +
198A THR* 1.3 60.1 + - - +
222A PHE 3.3 1.7 - - - +
224A LEU* 3.6 13.7 - - + -
226A ARG* 3.0 28.7 + - - -
227A PHE* 3.5 16.3 - - + -
268A ILE* 5.8 0.4 - - + -
272A LEU* 3.7 15.9 - - + -
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Residues in contact with THR 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 THR* 2.5 33.3 + - + +
195A GLU* 2.9 16.6 + - - +
196A MET 4.1 3.5 - - - +
197A LEU* 1.3 82.6 - - - +
222A PHE* 3.0 36.1 - - - +
223A SER* 4.3 1.6 - - - -
224A LEU* 4.0 27.6 - - + +
352B ASN* 4.6 10.6 - - - +
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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