Contacts of the helix formed by residues 196 - 205 (chain A) in PDB entry 6R7Y
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 PRO 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A LEU* 5.3 0.9 - - + -
185A THR* 3.4 36.3 - - - +
186A TRP* 4.4 8.1 - - + +
194A TYR 3.6 5.8 - - - +
195A GLN* 1.3 86.7 - - + +
197A ILE* 1.3 62.9 + - - +
198A ASP 3.2 3.4 - - - +
199A SER* 2.9 30.6 + - - +
200A ILE* 3.1 16.8 + - + +
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Residues in contact with ILE 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 GLN* 3.0 7.3 + - + +
196A PRO* 1.3 71.7 - - - +
198A ASP* 1.3 59.0 + - - +
200A ILE* 3.4 10.7 + - + +
201A ARG* 2.8 27.5 + - - +
209A ALA* 3.7 24.7 - - + +
212A PHE 5.4 0.4 - - - +
213A GLY* 4.2 13.9 - - - +
216A GLU* 3.3 33.0 - - - +
268A MET* 3.7 26.5 - - + -
271A ARG* 5.2 5.6 - - - +
272A TRP* 3.9 18.2 - - + -
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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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196A PRO 3.2 0.8 - - - -
197A ILE* 1.3 78.5 - - - +
199A SER* 1.3 57.3 + - - +
201A ARG* 3.3 6.7 + - - +
202A GLY* 3.1 22.2 + - - -
271A ARG* 2.7 33.9 + - - +
272A TRP* 2.7 36.2 + - - -
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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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182A LEU* 3.6 21.5 - - - +
185A THR* 4.8 2.7 + - - -
196A PRO* 2.9 32.0 + - - +
198A ASP* 1.3 75.7 - - - +
200A ILE* 1.3 63.5 + - - +
202A GLY* 3.4 1.8 + - - +
203A TYR* 3.2 24.4 + - - +
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Residues in contact with ILE 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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182A LEU* 4.3 13.7 - - + -
186A TRP* 3.5 45.3 - - + +
195A GLN* 4.2 9.2 - - + +
196A PRO* 3.1 22.2 + - + +
197A ILE* 3.5 11.4 - - + +
199A SER* 1.3 81.6 + - - +
201A ARG* 1.3 57.5 + - - +
204A PHE* 2.8 46.4 + - + +
205A GLY 4.1 0.2 - - - +
209A ALA* 3.9 25.6 - - + +
212A PHE* 4.5 18.2 - - + -
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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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89A VAL 5.3 1.8 + - - -
90A LYS* 5.5 6.5 - - - +
120A THR* 5.9 5.3 + - - +
122A ALA* 4.7 1.7 - - - +
123A GLU* 3.5 25.2 + - - -
197A ILE 2.8 19.9 + - - +
198A ASP* 3.5 7.9 - - - +
199A SER 3.2 0.4 - - - -
200A ILE* 1.3 74.2 - - - +
202A GLY* 1.3 65.4 + - - +
205A GLY* 3.0 42.9 + - - +
206A GLU* 3.0 29.1 + - + +
209A ALA* 3.7 5.2 - - + -
271A ARG 5.5 0.8 + - - -
272A TRP* 3.4 69.0 + - + +
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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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120A THR* 4.1 22.5 + - - -
121A MET* 4.9 0.9 + - - +
122A ALA* 3.6 18.3 + - - +
198A ASP 3.1 13.6 + - - -
199A SER* 3.4 4.7 + - - -
200A ILE 3.4 0.2 - - - -
201A ARG* 1.3 86.5 - - - +
203A TYR* 1.3 57.5 + - - +
543A ARG* 4.8 0.5 + - - -
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Residues in contact with TYR 203 (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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121A MET* 5.5 2.0 - - + -
122A ALA* 4.0 4.0 - - - +
174A HIS* 2.8 26.1 + - - -
175A ASP* 3.2 25.5 + - + -
178A ALA* 4.8 12.8 - - + -
179A LEU* 3.6 30.0 - - + +
182A LEU* 4.1 16.2 - - + -
199A SER 3.2 15.7 + - - +
200A ILE 4.1 1.6 - - - +
201A ARG 3.1 0.6 - - - -
202A GLY* 1.3 80.1 - - - +
204A PHE* 1.3 90.7 + + - +
205A GLY 3.6 1.1 - - - -
543A ARG* 2.7 65.1 + - - +
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Residues in contact with PHE 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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122A ALA* 5.0 0.4 - - - -
174A HIS* 4.4 6.7 - + - -
179A LEU* 4.5 1.1 - - + -
182A LEU* 3.8 18.4 - - + -
186A TRP* 3.8 17.5 - + - -
200A ILE* 2.8 31.0 + - + +
203A TYR* 1.3 109.1 - + - +
205A GLY* 1.3 63.4 + - - +
208A ILE* 3.4 39.8 - - + +
537A MET* 3.6 35.7 - - + -
538A CYS* 4.5 6.7 - - - -
543A ARG* 4.9 3.6 - - + +
544A PRO* 4.4 28.7 - - + +
546A SER* 4.6 8.6 - - - -
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Residues in contact with GLY 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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122A ALA* 4.2 6.8 - - - +
201A ARG* 3.0 20.5 + - - +
203A TYR 3.6 2.0 + - - -
204A PHE* 1.3 83.1 - - - +
206A GLU* 1.3 66.4 + - - -
207A THR 3.7 0.2 - - - -
209A ALA* 3.4 18.7 + - - +
546A SER* 3.3 26.9 - - - -
547A GLU 4.9 0.4 - - - -
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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