Contacts of the helix formed by residues 193 - 204 (chain A) in PDB entry 3ECP
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 ILE 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A SER* 3.8 40.6 - - - +
165A TRP* 3.9 8.5 - - + -
166A LEU* 5.7 2.9 - - + -
190A GLU 3.5 24.5 - - - +
191A ALA 2.6 12.2 + - - +
192A ASP* 1.3 76.4 - - - +
194A HIS* 1.3 68.3 + - - +
195A ALA* 3.8 17.0 - - + +
196A TYR* 3.2 13.9 + - + +
197A LEU* 3.1 25.1 + - - +
215A ARG* 3.8 2.2 - - - +
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Residues in contact with HIS 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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193A ILE* 1.3 75.6 - - - +
195A ALA* 1.3 66.4 + - - +
196A TYR 3.1 0.3 + - - -
197A LEU* 3.3 6.8 + - - +
198A GLN* 3.0 55.2 + - - +
215A ARG* 3.4 15.8 - - - +
272A LEU* 4.5 3.6 - - + -
274A GLN* 2.8 77.2 + - + +
275A GLY* 3.7 2.1 + - - -
277A ILE* 3.9 15.6 - - + +
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Residues in contact with ALA 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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166A LEU* 4.0 15.1 - - + +
193A ILE* 3.3 11.9 - - + +
194A HIS* 1.3 86.0 + - - +
196A TYR* 1.3 57.1 + - - +
198A GLN* 3.6 12.1 + - - +
199A ASP* 3.1 27.4 + - - +
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Residues in contact with TYR 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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96A GLU* 4.2 5.2 + - - -
165A TRP* 3.3 46.4 - + + -
166A LEU* 3.8 19.7 - - + +
169A ALA* 4.7 4.2 - - + +
185A ALA* 3.8 8.1 - - - +
187A CYS* 3.8 16.6 - - - -
191A ALA* 3.5 26.0 - - + +
193A ILE* 3.2 20.9 + - + +
194A HIS 3.1 0.6 - - - -
195A ALA* 1.3 77.4 - - - +
197A LEU* 1.3 70.8 + - + +
199A ASP* 3.3 4.3 + - - +
200A LYS* 3.1 61.8 + - + +
207A PHE* 5.3 0.9 - + + -
209A VAL* 3.7 25.4 - - + -
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Residues in contact with LEU 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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191A ALA 5.0 0.4 - - - +
192A ASP* 4.5 7.0 - - - +
193A ILE 3.1 18.7 + - - +
194A HIS* 3.7 9.6 - - - +
196A TYR* 1.3 78.5 - - + +
198A GLN* 1.3 62.4 + - - +
200A LYS* 3.2 8.9 + - - +
201A LEU* 3.0 35.0 + - + +
207A PHE* 4.0 26.2 - - + -
209A VAL* 4.3 22.2 - - + -
215A ARG* 4.7 2.0 - - - +
272A LEU* 4.2 22.0 - - + -
277A ILE* 4.3 8.1 - - + -
279A LEU* 4.6 4.7 - - + -
301A LEU* 3.9 30.3 - - + -
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Residues in contact with GLN 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 HIS* 3.0 44.6 + - + +
195A ALA* 3.6 11.4 - - - +
197A LEU* 1.3 76.4 - - - +
199A ASP* 1.3 57.5 + - - +
201A LEU* 3.3 3.5 + - - +
202A ALA* 2.9 33.9 + - + +
275A GLY* 4.1 12.1 - - - +
277A ILE* 3.9 29.3 - - + +
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Residues in contact with ASP 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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166A LEU* 3.5 36.7 - - + +
169A ALA* 3.9 11.4 - - - +
173A ARG* 3.0 23.7 + - - -
195A ALA 3.1 7.6 + - - +
196A TYR* 3.3 5.0 + - - +
198A GLN* 1.3 75.7 - - - +
200A LYS* 1.3 67.8 + - - +
202A ALA* 3.6 5.2 + - - +
203A HIS* 3.1 48.0 + - - +
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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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169A ALA* 4.6 11.4 - - + +
180A MET* 4.1 13.7 - - - +
185A ALA* 3.8 12.9 - - - +
196A TYR* 3.1 57.1 + - + +
197A LEU* 3.2 7.8 + - - +
199A ASP* 1.3 76.6 - - - +
201A LEU* 1.3 58.5 + - - +
203A HIS* 3.1 3.1 + - - -
204A ASN 2.9 8.5 + - - -
205A GLU* 2.8 68.0 + - - +
206A ARG 3.7 21.9 + - - -
207A PHE* 3.6 25.6 - - + -
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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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197A LEU* 3.0 23.3 + - + +
198A GLN* 3.8 3.1 - - - +
200A LYS* 1.3 74.7 - - - +
202A ALA* 1.3 54.8 + - - +
204A ASN* 2.8 33.0 + - - +
205A GLU 4.8 1.1 - - - +
207A PHE* 3.7 26.0 - - + -
277A ILE* 4.2 28.5 - - + -
278A THR 3.9 24.9 - - - +
279A LEU* 4.3 16.2 - - + -
303A SER* 4.8 9.0 - - - -
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Residues in contact with ALA 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 GLN* 2.9 21.2 + - + +
199A ASP* 3.9 6.5 - - - +
201A LEU* 1.3 77.4 - - - +
203A HIS* 1.3 64.0 + - + +
204A ASN* 3.5 5.7 + - - -
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Residues in contact with HIS 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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173A ARG* 3.3 38.7 + - - -
199A ASP* 3.1 41.7 + - - +
200A LYS 3.1 2.6 + - - +
202A ALA* 1.3 78.4 - - + +
204A ASN* 1.3 71.4 + - - +
205A GLU* 3.3 25.5 + - - +
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Residues in contact with ASN 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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181A SER* 5.7 5.9 - - - -
200A LYS 2.9 0.4 + - - -
201A LEU* 2.8 21.5 + - - +
202A ALA 3.1 5.3 + - - -
203A HIS* 1.3 81.9 - - - +
205A GLU* 1.3 63.4 + - - +
206A ARG* 4.6 6.6 - - - +
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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