Contacts of the helix formed by residues 295 - 304 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D SER* 4.7 0.2 - - - -
293D VAL* 4.8 7.9 - - + +
294D LEU* 1.3 75.0 - - - +
296D PRO* 1.3 80.0 - - + +
297D GLN* 4.4 6.1 - - + +
298D GLU* 3.4 29.6 + - + +
299D THR* 2.8 22.8 + - - -
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Residues in contact with PRO 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D GLN* 3.5 22.6 - - + +
179D ARG 3.3 18.9 - - - +
180D GLY* 3.5 16.4 - - - +
181D GLU* 3.7 19.5 - - + +
294D LEU 4.6 0.9 - - - +
295D LEU* 1.3 91.0 - - + +
297D GLN* 1.3 63.2 + - - +
299D THR* 3.0 13.4 + - - +
300D ALA 3.0 9.7 + - - -
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Residues in contact with GLN 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ASN 3.5 6.5 + - - +
179D ARG* 3.5 27.7 + - - +
295D LEU* 3.4 4.5 - - + +
296D PRO* 1.3 76.4 - - - +
298D GLU* 1.3 66.7 + - + +
300D ALA* 3.2 2.8 + - - +
301D GLU* 3.1 40.4 + - - +
305D HIS* 3.4 30.5 - - - -
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Residues in contact with GLU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D VAL 5.1 0.3 - - - +
294D LEU* 3.7 18.2 - - + +
295D LEU* 3.4 44.4 + - + +
296D PRO 3.3 0.6 - - - -
297D GLN* 1.3 76.6 - - + +
299D THR* 1.3 64.4 + - - +
301D GLU* 3.3 14.1 + - - +
302D ILE* 3.1 43.5 + - + +
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Residues in contact with THR 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU* 3.4 30.1 - - + -
146D SER* 2.7 31.1 + - - +
147D PHE* 4.0 11.7 - - + -
180D GLY 4.7 3.6 - - - +
294D LEU* 3.2 21.5 - - + +
295D LEU 2.8 14.6 + - - -
296D PRO* 3.0 13.4 + - - -
298D GLU* 1.3 78.2 - - - +
300D ALA* 1.3 58.8 + - - +
303D HIS* 3.1 24.8 + - + +
304D LEU* 3.6 4.8 + - + +
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Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU 3.9 5.2 - - - +
178D ASN 3.7 3.1 - - - +
179D ARG 3.9 2.7 - - - -
180D GLY* 3.6 26.0 - - - +
296D PRO 3.0 5.6 + - - +
297D GLN* 3.2 8.7 + - - +
299D THR* 1.3 77.3 - - - +
301D GLU* 1.3 54.5 + - - +
304D LEU* 2.8 19.1 + - - +
305D HIS* 2.6 55.5 + - + +
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Residues in contact with GLU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D GLN* 3.1 28.7 + - - +
298D GLU* 3.7 17.2 + - - +
300D ALA* 1.3 79.4 - - - +
302D ILE* 1.3 65.3 + - + +
305D HIS* 3.6 34.9 + - + +
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Residues in contact with ILE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLU* 4.0 6.7 - - - +
294D LEU* 4.2 18.4 - - + -
298D GLU* 3.1 31.2 + - + +
301D GLU* 1.3 82.4 - - + +
303D HIS* 1.3 85.2 + - + +
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Residues in contact with HIS 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ARG* 3.0 33.7 + - - +
140D GLN* 3.7 36.6 + - + -
142D GLU* 2.7 31.5 + - + +
143D LEU* 3.8 49.6 - - + +
294D LEU* 4.4 8.7 - - + -
299D THR 3.1 14.1 + - - +
302D ILE* 1.3 93.9 + - + +
304D LEU* 1.3 63.5 + - + +
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 3.7 28.0 - - + -
136D ARG* 4.7 6.4 + - - +
143D LEU* 4.7 0.4 - - + -
147D PHE* 4.3 14.4 - - + -
175D ILE* 4.0 15.3 - - + -
177D LEU* 3.7 36.1 - - + +
180D GLY* 3.6 31.0 - - - +
299D THR 3.6 3.1 + - - +
300D ALA* 2.8 21.1 + - - +
302D ILE 3.8 0.4 - - - -
303D HIS* 1.3 94.9 - - + +
305D HIS* 1.3 66.0 + - - +
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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