Contacts of the helix formed by residues 197 - 207 (chain A) in PDB entry 2C0O
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A PHE* 3.6 12.3 - - + -
195A PHE* 3.6 9.5 - - - +
196A SER* 1.3 87.7 + - - +
198A LEU* 1.3 66.3 + - - +
199A GLN* 3.8 11.0 + - - +
200A GLU* 3.3 27.6 + - - +
201A LEU* 3.2 16.5 + - - +
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Residues in contact with LEU 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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118A LEU* 3.4 39.3 - - + -
123A TRP* 3.8 21.1 - - + -
124A PHE* 5.1 1.1 - - + -
149A ILE* 4.6 18.2 - - + -
159A TYR* 4.1 19.1 - - + -
179A ILE* 4.3 15.0 - - + -
187A PHE* 3.4 38.9 - - + -
197A THR* 1.3 71.5 - - - +
199A GLN* 1.3 65.6 + - - +
201A LEU* 3.1 19.8 + - + +
202A VAL* 3.0 22.4 + - + +
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Residues in contact with GLN 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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121A GLU* 4.1 14.8 - - - +
123A TRP* 2.8 42.1 + - + -
197A THR* 3.1 10.7 - - - +
198A LEU* 1.3 80.4 - - - +
200A GLU* 1.3 64.8 + - + +
202A VAL* 3.3 5.0 + - - +
203A ASP* 2.9 41.1 + - - +
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Residues in contact with GLU 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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195A PHE* 3.9 16.6 - - + -
196A SER* 3.2 38.6 + - - -
197A THR* 3.3 16.5 + - - +
199A GLN* 1.3 78.0 - - + +
201A LEU* 1.3 66.4 + - - +
203A ASP* 3.1 18.6 + - - +
204A HIS* 3.1 12.5 + - - +
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Residues in contact with LEU 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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149A ILE* 4.5 20.4 - - + -
161A LEU* 4.6 6.1 - - + -
179A ILE* 4.1 24.2 - - + -
187A PHE* 4.2 23.6 - - + -
188A TYR* 4.9 1.1 - - - +
189A ILE* 4.4 18.2 - - + -
195A PHE* 3.7 27.3 - - + -
197A THR 3.2 11.9 + - - +
198A LEU* 3.1 17.1 + - + +
200A GLU* 1.3 78.9 - - - +
202A VAL* 1.3 69.2 + - + +
204A HIS* 3.2 8.8 + - - +
205A TYR* 3.3 36.2 - - + -
216A LEU* 5.4 0.9 - - + -
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Residues in contact with VAL 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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123A TRP* 4.0 34.3 - - + +
147A PHE* 3.8 22.4 - - + -
149A ILE* 4.9 5.8 - - + -
198A LEU 3.0 20.4 - - - +
199A GLN* 3.6 7.4 - - - +
201A LEU* 1.3 80.7 - - + +
203A ASP* 1.3 68.9 + - - +
205A TYR 3.4 1.4 + - - -
206A LYS* 3.0 43.7 + - + +
216A LEU* 3.9 16.7 - - + +
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Residues in contact with ASP 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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199A GLN* 2.9 35.4 + - - +
200A GLU* 3.1 13.1 + - - +
202A VAL* 1.3 79.4 - - - +
204A HIS* 1.3 62.5 + - - +
206A LYS* 3.7 20.5 + - - +
207A LYS* 3.7 20.3 + - - +
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Residues in contact with HIS 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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193A SER* 4.9 4.7 - - - -
195A PHE* 3.6 30.8 - + + -
200A GLU 3.1 5.5 + - - +
201A LEU 3.5 9.2 - - - +
202A VAL 3.1 0.4 - - - -
203A ASP* 1.3 74.2 - - - +
205A TYR* 1.3 86.4 + + - +
206A LYS 2.9 10.3 + - - -
207A LYS* 3.0 28.4 + - - +
208A GLY 3.3 3.4 + - - +
210A ASP* 3.1 37.5 + - + +
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Residues in contact with TYR 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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161A LEU* 5.3 1.1 - - + -
189A ILE* 4.3 25.7 + - + +
190A SER* 3.9 18.2 + - - -
193A SER* 4.3 8.1 - - - -
195A PHE* 3.9 21.6 - + - -
201A LEU* 3.3 31.7 + - + +
202A VAL 3.8 0.7 - - - -
204A HIS* 1.3 93.2 - + - +
206A LYS* 1.3 59.0 + - - +
208A GLY 3.5 6.0 - - - +
209A ASN* 4.5 0.2 - - - -
210A ASP* 3.2 37.7 + - - -
212A LEU* 3.4 41.0 - - + +
215A LYS* 3.6 11.1 - - - +
216A LEU* 2.8 41.4 + - + -
504A ILE* 5.8 1.1 - - + +
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Residues in contact with LYS 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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123A TRP* 6.5 0.2 - - - -
147A PHE* 4.5 10.1 - - + -
202A VAL* 3.0 33.2 + - + +
203A ASP* 3.7 19.6 + - - +
204A HIS 2.9 0.4 + - - -
205A TYR* 1.3 79.3 - - - +
207A LYS* 1.3 60.1 - - + +
208A GLY 3.5 3.8 + - - -
215A LYS* 3.8 14.2 + - - +
216A LEU* 3.1 26.2 - - + +
217A SER* 3.1 21.8 - - - +
218A VAL* 5.0 2.9 - - - +
219A PRO* 5.2 3.8 - - - -
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Residues in contact with LYS 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 ASP 3.9 10.3 - - - +
204A HIS* 3.0 14.7 + - - +
206A LYS* 1.3 75.7 - - - +
208A GLY* 1.3 62.6 + - - +
215A LYS* 5.7 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