Contacts of the helix formed by residues 198 - 209 (chain A) in PDB entry 3MOS
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PRO 4.6 3.6 + - - -
195A LEU* 2.9 33.0 + - + +
196A GLN* 3.3 3.7 - - + +
197A HIS* 1.3 76.4 - - - +
199A MET* 1.3 62.8 + - - +
200A ASP* 3.2 12.1 - - - +
201A ILE* 3.1 45.2 + - + +
202A TYR* 3.4 16.4 + - - -
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Residues in contact with MET 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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184A ILE* 3.8 27.6 - - + -
197A HIS* 2.9 23.2 + - - +
198A GLN* 1.3 72.8 - - - +
200A ASP* 1.3 63.3 + - - +
202A TYR* 3.3 7.6 + - + +
203A GLN* 3.0 21.7 + - - +
215A ILE* 3.7 27.7 - - + +
239A ILE* 3.6 31.9 - - + +
241A LYS* 3.8 51.1 - - + +
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Residues in contact with ASP 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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198A GLN* 3.4 19.4 - - - +
199A MET* 1.3 75.5 + - - +
201A ILE* 1.3 68.9 + - - +
203A GLN* 3.3 10.8 + - - +
204A LYS* 2.9 36.7 + - + +
215A ILE* 4.3 5.9 - - + +
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Residues in contact with ILE 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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195A LEU* 3.7 23.6 - - + -
198A GLN* 3.1 42.4 + - + +
200A ASP* 1.3 85.7 + - - +
202A TYR* 1.3 67.3 + - - +
204A LYS* 3.2 7.7 + - + +
205A ARG* 2.9 50.5 + - + +
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Residues in contact with TYR 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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155A ASP* 3.5 21.7 + - - +
158A LEU* 3.5 31.4 - - + -
164A TRP* 5.4 2.2 - + - -
182A LEU* 4.8 4.9 - - + -
184A ILE* 3.5 37.2 - - + -
193A ALA* 4.4 4.9 - - - +
194A PRO* 5.8 0.2 - - - +
195A LEU* 3.6 44.1 + - + +
196A GLN 3.6 7.7 + - - -
198A GLN 3.4 21.8 + - - -
199A MET* 3.3 9.3 + - - +
201A ILE* 1.3 78.7 - - - +
203A GLN* 1.3 63.0 + - - +
205A ARG* 3.4 5.5 + - + +
206A CYS* 3.0 28.9 + - - -
239A ILE* 3.9 18.2 - - + -
624A EDO 3.9 15.1 + - - -
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Residues in contact with GLN 203 (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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199A MET 3.0 12.7 + - - +
200A ASP* 3.5 10.9 - - - +
201A ILE 3.3 0.2 - - - -
202A TYR* 1.3 75.8 - - - +
204A LYS* 1.3 62.7 + - + +
206A CYS* 3.3 2.1 + - - +
207A GLU* 2.9 54.8 + - - +
213A ALA* 3.1 29.8 + - + -
214A ILE* 4.8 0.2 - - - +
215A ILE* 3.4 27.9 - - + +
239A ILE* 3.5 13.4 - - + +
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Residues in contact with LYS 204 (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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200A ASP* 2.9 24.2 + - + +
201A ILE* 3.7 8.5 - - + +
203A GLN* 1.3 81.9 - - + +
205A ARG* 1.3 58.0 + - + +
207A GLU* 4.0 18.7 + - - +
208A ALA* 2.9 32.1 + - - +
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Residues in contact with ARG 205 (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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164A TRP* 3.6 18.3 - - + -
195A LEU* 3.7 21.5 - - - +
201A ILE* 2.9 38.5 + - + +
202A TYR* 3.8 4.9 - - - +
203A GLN 3.3 0.2 - - - -
204A LYS* 1.3 77.9 - - + +
206A CYS* 1.3 62.0 + - - +
208A ALA* 3.4 4.2 + - - +
209A PHE* 3.2 33.0 + - + -
620A EDO 4.0 4.8 + - - -
624A EDO 2.7 51.6 + - - -
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Residues in contact with CYS 206 (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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164A TRP* 4.5 8.1 - - - -
167A MET* 3.8 27.4 - - + -
182A LEU* 3.9 26.7 - - - -
202A TYR* 3.0 22.1 + - - +
203A GLN 3.8 3.4 - - - +
205A ARG* 1.3 76.2 - - - +
207A GLU* 1.3 63.1 + - - +
209A PHE* 3.2 9.2 + - - +
210A GLY 3.3 0.2 + - - -
211A TRP* 3.1 23.9 + - + +
213A ALA* 3.9 15.7 - - + -
237A ALA* 3.9 14.1 - - + -
239A ILE* 4.1 3.4 - - - -
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Residues in contact with GLU 207 (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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203A GLN* 2.9 49.3 + - - +
204A LYS* 4.0 21.9 + - - +
206A CYS* 1.3 75.8 - - - +
208A ALA* 1.3 60.3 + - - +
210A GLY* 2.8 20.1 + - - -
211A TRP 3.5 17.9 - - - +
213A ALA* 3.9 12.8 + - + +
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Residues in contact with ALA 208 (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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204A LYS 2.9 18.5 + - - +
205A ARG* 3.7 7.4 - - - +
206A CYS 3.2 0.2 - - - -
207A GLU* 1.3 79.5 - - - +
209A PHE* 1.3 67.5 + - + +
210A GLY 3.2 1.1 + - - -
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Residues in contact with PHE 209 (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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164A TRP* 3.7 47.3 - + + -
167A MET* 3.9 10.5 - - + +
168A ALA* 4.1 27.8 - - + -
171A SER* 2.8 23.6 + - - -
205A ARG* 3.2 21.7 + - + +
206A CYS* 3.2 5.8 + - - +
207A GLU 3.0 0.6 - - - -
208A ALA* 1.3 84.2 - - + +
210A GLY* 1.3 57.9 + - - +
211A TRP* 3.4 10.2 - - + -
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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