Contacts of the helix formed by residues 195 - 205 (chain A) in PDB entry 1RQG
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 PHE 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A HIS* 3.2 47.3 - + + -
190A ILE* 4.3 18.6 - - + -
191A LYS 3.8 7.0 - - - -
192A MET* 2.9 15.5 + - - +
194A ASP* 1.3 88.5 - - + +
196A ALA* 1.3 55.3 + - - +
197A GLU 3.3 2.9 - - - -
198A ARG* 3.3 10.3 + - - -
199A LEU* 2.7 55.9 + - + +
309A ALA* 4.0 16.8 - - + -
312A MET* 3.6 26.9 - - + -
313A ALA* 3.6 31.2 - - + -
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Residues in contact with ALA 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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192A MET 3.4 4.4 + - - -
193A GLN* 3.3 33.8 + - - +
195A PHE* 1.3 75.9 - - - +
197A GLU* 1.3 60.4 + - - +
199A LEU* 3.3 3.6 + - - +
200A LYS* 2.9 31.2 + - - +
220A ILE* 4.0 17.1 - - + +
223A GLY* 5.8 0.2 - - - -
224A LEU* 3.7 25.8 - - + -
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Residues in contact with GLU 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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193A GLN 4.9 1.2 + - - -
194A ASP 5.5 0.4 - - - +
195A PHE 3.3 0.8 - - - -
196A ALA* 1.3 77.2 - - - +
198A ARG* 1.3 62.9 + - - +
199A LEU 3.0 0.5 + - - -
200A LYS* 3.1 5.8 + - - +
201A ARG* 2.6 68.8 + - + +
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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 ASP 5.3 2.7 + - - +
195A PHE* 3.3 15.3 + - - +
197A GLU* 1.3 80.0 - - - +
199A LEU* 1.3 62.2 + - - +
201A ARG* 3.6 9.0 + - - +
202A TRP* 3.1 24.9 + - - +
312A MET* 3.7 46.8 - - + +
325A GLU* 4.4 20.2 + - - -
328A LEU* 5.4 4.2 - - - +
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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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195A PHE* 2.7 41.6 + - + +
196A ALA* 3.4 4.0 - - - +
198A ARG* 1.3 70.7 - - - +
200A LYS* 1.3 59.7 - - - +
202A TRP* 2.7 35.2 + - + +
203A ILE* 2.8 20.5 + - + +
220A ILE* 4.7 11.9 - - + -
224A LEU* 4.1 19.1 - - + -
304A ALA 4.9 1.1 - - - +
305A ILE* 3.8 37.9 - - + +
308A PRO* 4.0 15.0 - - + -
309A ALA* 4.3 4.9 - - + +
312A MET* 3.9 24.7 - - + -
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Residues in contact with LYS 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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196A ALA 2.9 13.0 + - - +
197A GLU* 3.6 6.7 - - - +
199A LEU* 1.3 78.6 - - - +
201A ARG* 1.3 80.0 + - - +
203A ILE* 3.5 10.3 + - - +
204A GLU* 2.8 62.8 + - - +
217A LEU* 3.5 28.3 - - + +
220A ILE* 4.6 10.7 - - + +
221A GLU* 3.4 33.7 + - - +
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Residues in contact with ARG 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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197A GLU* 2.6 64.5 + - + +
198A ARG* 3.7 8.7 - - - +
200A LYS* 1.3 115.1 - - - +
202A TRP* 1.3 61.5 + - - +
204A GLU* 3.1 33.4 + - - +
205A LYS* 3.7 7.4 + - - +
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Residues in contact with TRP 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* 3.1 15.4 + - - +
199A LEU* 2.7 28.0 + - + +
201A ARG* 1.3 68.9 - - - +
203A ILE* 1.3 85.5 + - + +
204A GLU 3.2 0.7 + - - -
205A LYS* 3.4 21.6 + - - +
206A GLN* 3.1 30.9 + - - +
208A TRP* 3.3 18.6 - + - -
304A ALA 3.6 20.6 - - - -
308A PRO* 3.9 26.5 - - + -
312A MET* 4.8 6.1 - - + -
328A LEU* 3.8 29.3 - - + +
329A PRO* 3.6 28.3 - - + -
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Residues in contact with ILE 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 LEU* 2.8 19.1 + - + +
200A LYS 3.7 4.0 - - - +
202A TRP* 1.3 93.1 - - + +
204A GLU* 1.3 70.7 + - - +
206A GLN* 3.5 16.5 + - - +
208A TRP* 4.5 12.1 - - + -
213A LYS* 3.3 32.4 - - + +
216A VAL* 3.4 28.7 - - + -
217A LEU* 3.5 21.5 - - + -
220A ILE* 3.6 20.6 - - + -
304A ALA 3.8 11.0 - - - +
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Residues in contact with GLU 204 (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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200A LYS* 2.8 59.0 + - + +
201A ARG* 3.1 30.8 + - - +
203A ILE* 1.3 77.1 - - - +
205A LYS* 1.3 58.8 - - + +
206A GLN 2.7 16.1 + - - -
213A LYS* 2.8 30.2 + - - +
217A LEU* 4.0 8.0 - - - +
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Residues in contact with LYS 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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201A ARG 3.7 5.5 + - - +
202A TRP* 3.4 12.0 + - - +
204A GLU* 1.3 82.3 - - + +
206A GLN* 1.3 64.8 + - - +
207A PRO* 4.6 0.7 - - - +
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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