Contacts of the helix formed by residues 195 - 207 (chain A) in PDB entry 1R6W
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 THR 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ARG* 5.8 2.0 - - - +
193A CYS* 3.8 4.2 - - - +
194A LYS* 1.3 86.1 - - + +
196A ARG* 1.3 59.6 + - - +
197A ASP* 3.7 7.7 + - - +
198A ASP* 3.2 34.1 + - - +
199A SER* 2.9 28.6 + - - -
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Residues in contact with ARG 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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164A ARG* 3.8 12.3 - - - +
191A GLU* 4.8 1.1 - - - +
195A THR* 1.3 74.8 - - - +
197A ASP* 1.3 57.7 + - - +
199A SER* 3.2 2.6 + - - -
200A ARG* 2.9 65.5 + - - +
212A TRP* 3.3 46.2 - - + +
215A SER* 3.1 28.0 + - - +
218A GLU* 3.9 13.0 + - - +
221A PHE* 3.5 40.7 - - - +
222A ALA 4.9 4.6 + - - +
226A GLU* 4.6 2.4 + - - -
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Residues in contact with ASP 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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195A THR* 3.3 8.1 + - - +
196A ARG* 1.3 76.4 - - - +
198A ASP* 1.3 61.4 + - - +
200A ARG* 2.8 30.3 + - - +
201A ALA* 3.0 28.6 + - - +
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Residues in contact with ASP 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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166A TRP 5.7 0.2 - - - +
168A PRO* 3.5 35.0 - - + +
193A CYS* 3.7 20.1 - - + -
194A LYS* 5.7 1.4 + - - +
195A THR* 3.2 29.8 + - - +
197A ASP* 1.3 79.5 - - - +
199A SER* 1.3 60.3 + - - +
201A ALA* 3.3 7.5 + - - +
202A PHE* 2.9 29.6 + - - +
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Residues in contact with SER 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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191A GLU* 4.1 2.3 + - - -
192A PRO* 3.4 22.9 - - - +
193A CYS* 3.0 31.1 + - - +
195A THR 2.9 14.3 + - - -
196A ARG 3.2 8.3 + - - -
198A ASP* 1.3 77.2 - - - +
200A ARG* 1.4 56.2 + - - +
202A PHE* 3.2 4.0 + - - +
203A ALA 3.0 23.6 + - - -
210A ILE* 3.6 12.1 - - - +
212A TRP* 3.8 21.0 - - - -
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Residues in contact with ARG 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 ARG* 2.9 57.1 + - - +
197A ASP* 2.8 43.8 + - - +
199A SER* 1.4 75.1 - - - +
201A ALA* 1.3 62.9 + - - +
203A ALA* 3.3 4.3 + - - +
204A ARG* 3.0 34.2 + - - +
210A ILE* 4.3 5.2 - - - -
212A TRP* 3.8 14.2 - - + -
226A GLU* 2.8 39.4 + - + +
227A GLU 4.8 3.5 - - - +
229A VAL* 4.8 4.0 - - + -
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Residues in contact with ALA 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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168A PRO* 6.6 0.2 - - + -
197A ASP 3.0 16.3 + - - +
198A ASP* 3.6 9.6 - - - +
200A ARG* 1.3 74.7 - - - +
202A PHE* 1.3 60.0 + - - +
204A ARG* 3.2 7.9 + - - +
205A GLU* 2.8 57.2 + - - +
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Residues in contact with PHE 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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166A TRP* 4.5 3.1 - + - -
168A PRO* 5.7 2.0 - - + -
171A GLY* 3.4 40.4 - - - -
172A GLN* 4.8 0.7 - - + -
174A PHE* 4.3 4.7 - + - -
175A ALA* 4.5 1.8 - - + -
189A LEU* 3.7 31.2 - - + -
192A PRO* 3.8 11.2 - - + -
193A CYS* 4.2 8.5 - - - -
198A ASP 2.9 13.7 + - - +
199A SER* 3.4 9.4 - - - +
201A ALA* 1.3 75.9 - - - +
203A ALA* 1.3 63.7 + - - +
205A GLU* 4.5 3.8 + - - -
206A THR* 2.8 60.6 + - + -
208A ILE* 3.9 23.1 - - + -
210A ILE* 3.8 21.1 - - + -
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Residues in contact with ALA 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 SER 3.0 13.7 + - - +
200A ARG* 3.7 8.1 - - - +
201A ALA 3.2 0.2 - - - -
202A PHE* 1.3 77.2 - - - +
204A ARG* 1.3 63.2 + - - +
207A GLY* 3.1 23.9 + - - -
208A ILE 3.4 17.8 + - - +
210A ILE* 3.8 12.1 - - + -
227A GLU 4.5 0.7 - - - +
228A GLY* 3.5 38.6 - - - +
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Residues in contact with ARG 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 ARG* 3.0 27.0 + - - +
201A ALA* 3.9 6.3 - - - +
203A ALA* 1.3 76.9 - - - +
205A GLU* 1.3 64.5 + - + +
207A GLY* 4.3 4.0 + - - -
227A GLU* 3.8 52.4 - - + +
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Residues in contact with GLU 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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172A GLN* 4.1 18.7 + - + +
201A ALA* 2.8 37.5 + - - +
202A PHE* 4.3 3.6 + - - +
204A ARG* 1.3 84.0 - - + +
206A THR* 1.3 63.5 + - + +
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Residues in contact with THR 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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171A GLY 4.8 1.1 - - - +
172A GLN* 5.2 11.7 - - + -
175A ALA* 3.6 31.9 - - + -
183A ARG* 2.9 32.9 + - - +
202A PHE* 2.8 43.0 + - + +
205A GLU* 1.3 81.6 - - + +
207A GLY* 1.3 57.3 + - - +
208A ILE* 3.1 25.0 + - - +
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Residues in contact with GLY 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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183A ARG* 5.0 8.9 - - - +
184A ASP* 5.9 1.0 - - - -
203A ALA 3.1 13.3 + - - -
204A ARG 4.3 3.4 + - - -
205A GLU 3.6 2.0 - - - -
206A THR* 1.3 76.3 - - - +
208A ILE* 1.3 61.3 + - - +
209A ALA* 3.7 2.3 + - - -
228A GLY* 6.5 0.2 - - - -
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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