Contacts of the helix formed by residues 191 - 199 (chain A) in PDB entry 2C11
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 ALA 191 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 3.2 11.5 + - + +
189A PRO 2.9 1.2 - - - -
190A GLN* 1.3 77.2 - - - +
192A SER* 1.3 61.7 + - - +
194A LEU* 4.4 10.3 - - + -
195A LEU* 3.0 31.0 + - + +
245A LEU* 6.4 0.9 - - + -
274A LEU* 4.2 24.5 - - + +
277A LEU* 5.4 0.9 - - + -
278A GLU* 2.8 30.6 - - + +
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Residues in contact with SER 192 (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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189A PRO 2.7 16.8 + - - -
190A GLN 3.6 0.6 - - - -
191A ALA* 1.3 77.7 - - - +
193A GLY* 1.3 57.6 + - - +
195A LEU* 3.9 0.3 - - - +
196A HIS* 2.8 52.0 + - - +
201A TYR* 3.9 12.7 - - - -
203A HIS* 3.4 22.9 + - - -
278A GLU* 3.4 0.6 + - - +
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Residues in contact with GLY 193 (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 SER* 1.3 82.2 - - - +
194A LEU* 1.3 64.6 + - - +
196A HIS* 3.3 12.0 + - - +
197A HIS* 3.3 8.1 + - - +
278A GLU* 3.0 15.7 + - - -
281A PHE* 3.4 13.5 - - - -
282A GLU* 4.8 3.1 + - - -
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Residues in contact with LEU 194 (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 ALA* 3.7 8.7 - - + +
193A GLY* 1.3 69.8 - - - +
195A LEU* 1.3 63.7 + - + +
197A HIS* 3.2 3.6 + - - +
198A CYS* 3.0 31.5 + - - -
266A TYR* 4.0 18.6 - - + +
277A LEU* 3.4 45.1 - - + -
278A GLU* 2.5 22.5 + - - +
281A PHE* 3.3 29.2 - - + -
286A VAL* 4.8 0.4 - - + -
288A VAL* 3.3 34.1 - - + -
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Residues in contact with LEU 195 (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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188A LEU* 3.4 41.1 - - + +
191A ALA* 3.0 15.6 + - + +
194A LEU* 1.3 76.3 - - + +
196A HIS* 1.3 54.6 + - - +
197A HIS 2.7 15.8 + - - -
198A CYS* 3.6 15.9 - - - -
199A CYS* 2.8 29.0 + - + -
201A TYR* 3.0 53.1 + - + -
208A LEU* 5.1 9.4 - - + -
243A VAL* 6.3 1.3 - - + -
245A LEU* 5.0 16.2 - - + -
266A TYR* 5.7 2.9 - - + -
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Residues in contact with HIS 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 SER* 2.8 40.7 + - - +
193A GLY* 3.6 6.7 - - - +
195A LEU* 1.3 71.6 - - - +
197A HIS* 1.3 59.5 + - - +
200A PHE* 4.5 8.9 + - - -
201A TYR* 3.3 27.9 + + - +
202A LYS* 3.9 18.8 - - + +
203A HIS* 4.6 7.2 - + - -
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Residues in contact with HIS 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 GLY 3.3 3.3 + - - +
194A LEU 3.2 9.6 + - - +
195A LEU 2.7 1.0 + - - -
196A HIS* 1.3 82.1 - - - +
198A CYS* 1.3 67.0 + - + +
199A CYS 3.2 1.5 + - - -
200A PHE* 3.8 8.1 + - - -
281A PHE* 3.8 30.6 - + + -
288A VAL* 5.2 5.6 - - + -
290A LEU* 3.7 23.1 - - + +
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Residues in contact with CYS 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 LEU* 3.0 23.7 + - - +
195A LEU* 3.6 12.6 - - - -
197A HIS* 1.3 80.4 - - - +
199A CYS* 1.3 105.9 + - - +
200A PHE* 3.9 7.1 - - - -
231A TYR* 3.9 2.8 + - - -
266A TYR* 3.4 13.0 - - - +
267A GLN* 4.7 1.1 - - - +
288A VAL* 3.1 27.8 - - + -
289A VAL 4.8 1.1 - - - +
290A LEU* 3.1 30.9 - - - +
291A ILE 3.9 6.8 + - - -
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Residues in contact with CYS 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 LEU* 2.8 21.6 + - + +
198A CYS* 1.3 121.7 - - - +
200A PHE* 1.3 64.2 + - - +
201A TYR* 2.5 24.0 + - + +
207A ASN* 3.8 11.6 + - - -
208A LEU* 4.6 8.3 - - + +
231A TYR* 3.9 16.8 - - + +
243A VAL* 4.4 24.7 - - - -
266A TYR* 4.4 5.4 - - - -
291A ILE* 5.1 3.1 - - - -
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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