Contacts of the helix formed by residues 190 - 196 (chain A) in PDB entry 1U5Q
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A TRP 3.6 0.6 + - - -
189A MET* 1.3 76.5 - - - +
191A PRO* 1.3 76.9 - - + +
192A GLU* 3.3 20.6 - - + +
193A VAL* 3.1 16.2 + - + +
194A ILE* 3.3 11.3 + - - +
206A VAL* 3.9 19.9 + - + +
209A TRP* 3.4 30.0 - - + -
210A SER* 4.7 1.8 + - - -
237A ILE* 4.4 0.7 - - - -
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Residues in contact with PRO 191 (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 MET 3.9 0.2 - - - -
190A ALA* 1.3 87.8 - - + +
192A GLU* 1.3 59.2 + - - +
194A ILE* 2.9 9.3 + - + +
195A LEU* 2.7 45.5 + - + +
209A TRP* 3.8 25.8 - - + -
237A ILE* 4.0 18.6 - - + +
238A ALA* 4.4 7.0 - - - -
264A LYS* 3.4 47.1 - - + +
269A ARG* 4.3 0.4 - - - +
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Residues in contact with GLU 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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190A ALA* 3.9 2.7 - - - -
191A PRO* 1.3 84.8 - - - +
193A VAL* 1.3 61.3 + - - +
195A LEU* 3.6 14.9 - - + +
196A ALA* 3.1 20.1 + - - +
200A GLY* 5.9 0.2 - - - -
201A GLN 4.5 9.0 + - - +
202A TYR* 3.5 18.5 - - + +
203A ASP 5.3 1.1 + - - +
205A LYS* 4.2 2.3 - - - +
206A VAL* 3.4 29.6 + - + +
264A LYS 3.9 2.4 - - - +
266A PRO* 3.5 29.2 - - + +
269A ARG* 2.5 49.7 + - - -
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Residues in contact with VAL 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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150A ARG* 6.0 1.6 - - + -
181A SEP 3.8 15.7 - - - +
182A PHE* 3.7 6.4 - - + -
183A VAL 3.8 25.8 - - - +
189A MET* 3.8 17.0 - - + -
190A ALA* 3.1 18.4 + - + +
192A GLU* 1.3 74.4 - - - +
194A ILE* 1.3 67.5 + - - +
196A ALA* 3.1 16.8 + - - +
197A MET 3.6 2.1 + - - -
202A TYR* 3.9 21.5 - - + -
206A VAL* 3.6 34.1 - - + -
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Residues in contact with ILE 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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182A PHE* 3.7 6.5 - - - -
189A MET* 3.7 22.2 - - + +
190A ALA 3.3 6.7 + - - +
191A PRO* 2.9 8.0 + - + +
193A VAL* 1.3 78.2 - - - +
195A LEU* 1.3 55.3 + - + +
197A MET* 2.7 54.7 + - - +
234A LEU* 3.5 48.2 - - + +
235A TYR* 5.8 0.4 - - - -
237A ILE* 3.7 30.3 - - + -
238A ALA* 4.2 14.1 - - + +
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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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191A PRO* 2.7 34.0 + - + +
192A GLU* 3.6 12.6 - - + +
194A ILE* 1.3 69.7 - - + +
196A ALA* 1.3 57.3 + - - +
197A MET 2.8 5.8 - - - -
198A ASP* 2.8 30.1 + - - +
199A GLU 4.0 1.0 + - - -
200A GLY* 4.6 2.9 + - - -
238A ALA* 3.9 25.8 - - + -
239A GLN* 5.2 4.7 - - - +
264A LYS* 6.0 1.1 - - - +
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Residues in contact with ALA 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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180A ASN 3.6 25.2 - - - +
181A SEP 4.9 2.0 - - - +
182A PHE* 5.6 2.2 - - - +
192A GLU 3.1 13.2 + - - +
193A VAL 3.1 14.8 - - - +
194A ILE 3.1 0.2 - - - -
195A LEU* 1.3 71.6 - - - +
197A MET* 1.3 51.4 + - - +
198A ASP 2.4 31.6 - - - +
199A GLU* 3.5 2.4 + - - -
200A GLY* 3.8 23.3 + - - +
202A TYR* 4.2 12.8 - - + -
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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