Contacts of the helix formed by residues 326 - 336 (chain B) in PDB entry 1YDY
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 ASP 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LEU* 3.9 6.1 - - - -
324B THR* 3.9 5.1 - - - -
325B PRO* 1.3 80.1 - - - +
327B VAL* 1.3 65.7 + - + +
328B ASN* 2.9 25.5 + - - +
329B GLN* 2.8 50.1 + - - +
330B LEU 3.7 2.1 + - - -
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B VAL* 3.6 28.5 - - + -
317B SER* 3.8 37.9 - - - +
320B LEU* 3.7 13.8 - - + +
326B ASP* 1.3 73.6 - - - +
328B ASN* 1.3 78.5 + - - +
330B LEU* 2.9 14.3 + - + +
331B TYR* 3.0 28.5 + - + +
347B PHE* 6.1 0.2 - - + -
350B LYS* 4.3 14.1 - - + +
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Residues in contact with ASN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASP* 2.9 12.1 + - - +
327B VAL* 1.3 85.6 - - - +
329B GLN* 1.3 58.5 + - + +
331B TYR* 3.8 19.1 - - - -
332B ASP* 2.8 30.5 + - - +
350B LYS* 4.4 3.8 - - - +
354B PHE* 3.4 27.7 - - + +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PRO* 4.8 1.4 - - - +
292B GLY* 4.1 21.6 - - - +
294B ILE* 4.4 4.8 - - + +
323B TYR 4.6 2.0 + - - -
324B THR* 3.9 13.3 - - + +
325B PRO* 3.0 33.9 - - - +
326B ASP* 2.8 37.2 + - - +
328B ASN* 1.3 78.5 - - + +
330B LEU* 1.3 58.1 + - - +
332B ASP* 3.4 7.4 + - - +
333B ALA* 2.8 29.5 + - - +
337B LYS* 5.4 0.7 - - - +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TYR* 3.7 43.1 - - + +
285B ILE* 5.1 1.1 - - + -
315B VAL* 4.0 29.8 - - + -
316B ARG 5.1 0.7 - - - +
320B LEU* 4.5 7.4 - - + -
321B PRO* 3.9 13.5 - - + -
323B TYR* 4.7 4.7 - - + -
324B THR* 3.7 23.5 - - + +
326B ASP 3.7 0.6 + - - -
327B VAL* 2.9 13.7 + - - +
329B GLN* 1.3 77.3 - - - +
331B TYR* 1.3 65.3 + - - +
333B ALA* 3.2 5.7 + - + -
334B LEU* 3.0 46.8 + - + +
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 3.4 29.1 + - + +
327B VAL* 3.0 35.0 + - + +
328B ASN* 3.8 16.4 - - - +
330B LEU* 1.3 76.0 - - - +
332B ASP* 1.3 59.1 + - - +
335B TYR* 2.9 41.0 + + + +
343B LEU* 4.0 23.1 - - + -
345B THR* 2.9 21.0 + - - -
347B PHE* 3.3 17.7 + - - +
350B LYS* 3.6 13.6 - - + +
351B ALA* 3.5 32.3 - - + -
354B PHE* 3.7 31.2 - + + -
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ASN 2.8 19.2 + - - +
329B GLN* 3.6 7.9 - - - +
331B TYR* 1.3 78.9 - - - +
333B ALA* 1.3 56.5 + - - +
336B ASN* 2.9 55.4 + - - +
337B LYS* 3.0 37.4 + - - +
354B PHE* 3.4 16.8 - - + -
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ILE* 4.9 4.7 - - + -
294B ILE* 3.2 37.0 - - + -
296B LEU* 4.7 3.5 - - - +
323B TYR* 5.9 0.2 - - + -
324B THR* 4.8 0.2 - - + -
329B GLN 2.8 15.7 + - - +
330B LEU* 3.2 16.6 + - + +
332B ASP* 1.3 73.4 + - - +
334B LEU* 1.3 60.2 + - + +
337B LYS* 3.3 17.1 - - + +
338B ALA* 2.8 28.4 + - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TYR* 3.8 22.4 - - + -
284B LEU* 4.2 17.7 - - + -
285B ILE* 3.5 29.8 - - + -
312B PRO* 4.4 6.3 - - + -
315B VAL* 3.8 23.8 - - + -
330B LEU* 3.0 34.3 + - + +
333B ALA* 1.3 77.5 - - - +
335B TYR* 1.3 61.5 + - - +
336B ASN 3.4 0.2 - - - -
338B ALA* 3.4 6.2 - - + +
339B GLY 3.0 10.6 + - - -
340B VAL* 2.9 30.2 + - + +
343B LEU* 3.8 17.7 - - + -
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Residues in contact with TYR 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 2.9 46.4 + - + -
32B ILE 2.8 28.8 + - - -
33B VAL* 3.5 16.1 - - - +
331B TYR* 2.9 34.3 + + + +
334B LEU* 1.3 75.1 - - - +
336B ASN* 1.3 68.5 + - - +
339B GLY* 3.2 8.3 - - - -
340B VAL* 3.8 20.0 - - + -
342B GLY* 3.8 9.9 - - - -
343B LEU* 3.4 35.1 - - + +
351B ALA* 4.2 4.2 - - + +
354B PHE* 4.0 14.4 - + + -
355B LEU* 3.6 31.2 - - + -
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Residues in contact with ASN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 4.8 6.5 - - - +
332B ASP* 2.9 33.0 + - - +
335B TYR* 1.3 90.6 + - - +
337B LYS* 1.3 68.0 + - + +
339B GLY* 3.5 7.8 + - - -
354B PHE* 3.5 18.1 - - - -
355B LEU* 6.2 0.8 - - - +
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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