Contacts of the helix formed by residues 326 - 340 (chain A) in PDB entry 1YRT
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 THR 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A GLU 3.5 14.4 - - - +
312A LYS* 4.9 9.0 - - + +
313A ILE* 4.6 0.8 - - - +
325A LEU* 1.3 91.3 - - - +
327A ARG* 1.3 60.2 + - - +
328A GLY* 3.3 3.9 + - - -
329A GLN* 2.9 46.5 + - - +
330A LEU* 3.3 5.9 + - - +
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Residues in contact with ARG 327 (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 PHE* 4.5 19.4 - - - -
309A ALA* 6.0 9.5 - - - +
311A GLU* 4.0 13.9 + - + +
313A ILE* 4.7 6.3 - - + -
326A THR* 1.3 73.6 - - - +
328A GLY* 1.3 60.9 + - - +
329A GLN 3.2 0.4 - - - -
330A LEU* 3.3 16.7 - - + +
331A LYS* 3.1 29.2 + - + +
350A TYR* 4.4 15.7 + - - -
355A LYS* 2.8 49.6 + - - +
357A LEU* 3.8 24.5 - - + +
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Residues in contact with GLY 328 (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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326A THR* 3.3 4.2 + - - -
327A ARG* 1.3 80.4 - - - +
329A GLN* 1.3 64.3 + - - +
330A LEU 3.3 0.2 + - - -
331A LYS* 3.5 17.0 + - - +
332A GLU* 3.6 19.2 + - - +
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Residues in contact with GLN 329 (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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324A MET 3.8 5.9 - - - +
325A LEU* 3.2 21.7 - - + +
326A THR* 2.9 44.6 + - - +
328A GLY* 1.3 80.3 - - - +
330A LEU* 1.3 55.7 + - - +
332A GLU* 3.2 15.0 + - - +
333A TYR* 2.8 29.5 + - - +
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Residues in contact with LEU 330 (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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39A MET* 3.9 20.0 - - + -
192A PHE* 3.5 33.9 - - + -
313A ILE* 3.8 21.1 - - + -
315A VAL* 5.0 2.9 - - + -
325A LEU* 3.6 18.8 - - + +
326A THR 3.3 9.5 + - - +
327A ARG* 3.3 22.2 + - - +
328A GLY 3.1 0.6 - - - -
329A GLN* 1.3 77.7 - - - +
331A LYS* 1.3 57.0 + - - +
333A TYR* 3.5 1.7 - - + +
334A ILE* 2.9 59.8 + - + +
357A LEU* 4.3 10.8 - - + -
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Residues in contact with LYS 331 (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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327A ARG* 3.1 18.9 + - + +
328A GLY* 3.9 9.9 - - - +
329A GLN 3.3 0.4 - - - -
330A LEU* 1.3 76.9 - - - +
332A GLU* 1.3 65.0 + - + +
334A ILE* 3.5 5.8 + - - +
335A GLY* 3.0 20.1 + - - -
356A SER 4.1 14.8 + - - +
357A LEU* 3.6 48.8 - - + +
358A PHE 4.6 2.9 + - - -
359A ASP* 3.3 26.0 + - - -
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Residues in contact with GLU 332 (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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328A GLY 3.6 14.6 + - - +
329A GLN* 3.2 15.9 + - - +
331A LYS* 1.3 77.9 - - + +
333A TYR* 1.3 67.7 + - - +
335A GLY* 3.2 2.2 + - - -
336A GLN* 2.9 43.5 + - + +
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Residues in contact with TYR 333 (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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37A THR* 3.6 25.6 + - + +
39A MET* 4.2 15.0 - - + -
315A VAL* 3.5 21.7 - - + +
317A SER* 2.4 29.4 + - - -
323A GLN* 3.6 27.3 + - - -
325A LEU* 3.3 31.0 - - + -
329A GLN 2.8 8.2 + - - +
330A LEU* 3.5 3.1 - - + +
332A GLU* 1.3 78.4 - - - +
334A ILE* 1.3 60.0 + - + +
336A GLN* 3.1 20.9 + - - +
337A GLN* 2.9 56.1 + - + +
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Residues in contact with ILE 334 (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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39A MET* 4.2 4.9 - - + -
192A PHE* 5.5 0.2 - - + -
195A MET* 4.1 13.4 - - - +
330A LEU* 2.9 44.3 + - + +
331A LYS* 3.8 4.5 - - - +
333A TYR* 1.3 78.6 - - - +
335A GLY* 1.3 59.3 + - - +
337A GLN* 3.4 5.3 + - - +
338A ARG* 2.9 43.6 + - + +
344A PHE* 3.7 48.2 - - + -
357A LEU* 3.6 36.3 - - + +
358A PHE* 5.7 1.1 - - + -
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Residues in contact with GLY 335 (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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331A LYS 3.0 15.3 + - - -
332A GLU* 3.2 4.0 + - - -
334A ILE* 1.3 77.1 - - - +
336A GLN* 1.3 62.8 + - - +
338A ARG* 3.3 13.5 + - - +
339A GLY* 3.1 18.0 + - - -
94B LYS 4.7 2.5 - - - +
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A GLU* 2.9 35.6 + - - +
333A TYR* 3.4 22.8 - - - +
335A GLY* 1.3 77.4 - - - +
337A GLN* 1.3 68.5 + - + +
339A GLY* 3.1 11.5 + - - -
340A GLU* 3.3 20.8 + - - +
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Residues in contact with GLN 337 (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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37A THR* 3.3 16.7 + - - +
195A MET* 3.5 22.0 - - + -
317A SER* 4.5 5.1 + - - -
318A ALA* 5.2 1.4 + - - +
333A TYR* 2.9 59.3 + - + +
334A ILE 3.9 0.4 - - - +
335A GLY 3.3 0.2 - - - -
336A GLN* 1.3 78.9 - - - +
338A ARG* 1.3 57.2 + - - +
340A GLU* 2.9 36.2 + - - +
341A GLY 3.4 0.2 + - - -
342A TYR* 3.2 43.2 + - + -
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Residues in contact with ARG 338 (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 MET* 4.5 3.6 - - + -
334A ILE* 2.9 36.9 + - + +
335A GLY* 3.5 11.5 - - - +
337A GLN* 1.3 76.8 - - - +
339A GLY* 1.3 60.5 + - - +
341A GLY* 3.2 10.9 + - - -
342A TYR 3.4 20.0 + - - +
344A PHE* 4.6 13.2 - - + +
358A PHE* 3.6 40.0 - - - +
359A ASP 5.7 1.6 - - - +
360A ASP* 4.8 3.8 + - - +
90B ARG* 3.1 27.4 + - - +
93B ASP* 3.0 26.1 + - - +
94B LYS* 3.6 33.8 + - - +
96B GLY* 3.9 21.2 - - - -
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Residues in contact with GLY 339 (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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335A GLY 3.1 9.3 + - - -
336A GLN* 3.1 9.3 + - - -
338A ARG* 1.3 77.1 - - - +
340A GLU* 1.3 60.7 + - - +
341A GLY 3.3 0.4 - - - -
94B LYS* 3.3 33.5 + - - -
95B ASP* 6.0 0.7 - - - -
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Residues in contact with GLU 340 (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 HIS* 2.9 23.7 + - - -
336A GLN* 3.3 14.6 + - - +
337A GLN* 2.9 33.8 + - - +
339A GLY* 1.3 80.0 - - - +
341A GLY* 1.3 55.9 + - - +
342A TYR* 3.5 18.8 - - + -
94B LYS* 5.2 0.4 - - - -
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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