Contacts of the helix formed by residues 295 - 304 (chain C) in PDB entry 1YXU
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 LEU 295 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293C VAL 3.7 2.4 + - - +
294C LEU* 1.3 72.4 - - - +
296C PRO* 1.3 69.3 - - + +
297C GLN* 3.4 4.9 - - + +
298C GLU* 2.9 32.7 + - + +
299C THR* 2.8 28.1 + - - -
241D PRO 5.6 2.9 - - - +
247D GLU* 5.8 4.0 - - - +
254D PHE* 3.4 31.2 - - + +
256D ARG* 3.9 49.6 - - + +
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Residues in contact with PRO 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLN* 3.5 21.3 - - - +
179C ARG 3.3 21.3 - - - +
180C GLY* 3.4 17.6 - - - +
181C GLU* 3.8 16.8 - - + +
295C LEU* 1.3 86.5 - - + +
297C GLN* 1.3 57.4 + - - +
299C THR* 3.0 7.3 + - - -
300C ALA 2.9 24.1 + - - -
254D PHE* 3.6 38.6 - - + -
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Residues in contact with GLN 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ASN 2.7 29.5 + - - +
179C ARG* 3.6 23.4 + - - +
295C LEU* 3.4 2.9 - - + +
296C PRO* 1.3 75.9 - - - +
298C GLU* 1.3 65.8 + - - +
300C ALA* 3.4 1.5 + - - +
301C GLU* 3.1 41.0 + - - +
305C HIS* 4.0 12.9 - - - -
247D GLU* 5.9 2.5 - - - +
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Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C VAL 4.8 0.5 - - - +
294C LEU* 3.6 22.9 - - + +
295C LEU* 2.9 47.7 + - + +
297C GLN* 1.3 77.0 - - - +
299C THR* 1.3 63.1 + - - +
301C GLU* 3.3 12.6 + - - +
302C ILE* 3.1 36.8 + - + +
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Residues in contact with THR 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LEU* 3.9 22.4 - - + -
146C SER* 2.7 41.2 + - - +
147C PHE* 3.9 11.7 - - + -
180C GLY 4.8 3.6 - - - +
294C LEU* 3.2 18.9 - - + +
295C LEU 2.8 14.3 + - - -
296C PRO* 3.2 13.9 - - - -
298C GLU* 1.3 77.3 - - - +
300C ALA* 1.3 55.3 + - - +
303C HIS* 3.0 31.4 + - + +
304C LEU* 4.4 2.8 - - + +
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Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LEU 3.8 15.3 - - - +
178C ASN 4.0 2.9 - - - +
180C GLY* 3.7 29.6 - - - +
296C PRO 2.9 8.9 + - - +
297C GLN* 4.0 5.4 - - - +
298C GLU 3.2 0.2 - - - -
299C THR* 1.3 76.1 - - - +
301C GLU* 1.3 63.4 + - - +
302C ILE 3.2 0.2 - - - -
304C LEU* 2.8 32.1 + - + -
305C HIS* 3.0 23.8 + - - +
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Residues in contact with GLU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C GLN* 3.1 37.5 + - + +
298C GLU* 3.7 11.9 - - - +
300C ALA* 1.3 77.6 - - - +
302C ILE* 1.3 63.5 + - + +
305C HIS* 3.7 31.1 + - + +
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Residues in contact with ILE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C GLU* 4.0 8.5 - - - +
294C LEU* 4.3 24.5 - - + -
298C GLU* 3.1 22.1 + - + +
301C GLU* 1.3 82.3 - - + +
303C HIS* 1.3 84.9 + - + +
304C LEU 3.8 0.2 - - - -
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Residues in contact with HIS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ARG* 2.9 29.8 + - - +
140C GLN* 4.0 32.4 + - - -
142C GLU* 2.9 32.4 + - + +
143C LEU* 3.8 47.9 - - + +
294C LEU* 4.3 10.3 - - + -
299C THR* 3.0 18.4 + - + +
302C ILE* 1.3 94.2 + - + +
304C LEU* 1.3 63.9 + - + +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C PHE* 4.0 23.6 - - + -
136C ARG* 4.6 7.0 + - - +
143C LEU* 4.4 0.4 - - + -
147C PHE* 4.2 15.3 - - + -
175C ILE* 3.8 20.4 - - + -
177C LEU* 3.7 42.3 - - + +
180C GLY* 3.8 24.0 - - - -
299C THR 4.4 2.7 - - - +
300C ALA* 2.8 25.4 + - + +
303C HIS* 1.3 97.6 - - + +
305C HIS* 1.3 62.8 + - - +
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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