Contacts of the helix formed by residues 264 - 276 (chain A) in PDB entry 1YY4
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 SER 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A LEU* 1.3 77.6 - - - +
265A PRO* 1.3 71.3 - - - +
266A GLU* 3.4 8.8 + - - +
267A GLN* 2.9 32.2 + - - +
268A LEU* 2.8 25.3 + - - +
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Residues in contact with PRO 265 (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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263A LEU 3.8 1.8 - - - +
264A SER* 1.3 87.8 - - - +
266A GLU* 1.3 56.0 + - - +
268A LEU* 3.2 9.7 + - + +
269A VAL* 2.9 36.4 + - - +
432A ALA 5.8 0.4 - - - +
435A ASP* 3.6 23.8 - - + +
436A ALA* 4.0 12.8 - - + -
439A TRP* 3.7 34.8 - - + +
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Residues in contact with GLU 266 (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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264A SER* 3.1 8.6 + - - +
265A PRO* 1.3 80.6 - - - +
267A GLN* 1.3 61.0 + - + +
269A VAL* 3.5 1.6 + - - +
270A LEU* 3.0 51.1 + - + +
395A LYS* 5.3 4.5 + - - -
439A TRP* 3.3 44.8 - - + +
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Residues in contact with GLN 267 (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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263A LEU* 3.3 28.7 - - + +
264A SER* 2.9 23.8 + - - +
266A GLU* 1.3 79.3 - - + +
268A LEU* 1.3 59.7 + - - +
270A LEU* 3.4 25.8 - - - +
271A THR* 3.1 26.3 + - - +
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Residues in contact with LEU 268 (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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263A LEU* 4.1 18.4 - - + +
264A SER 2.8 11.8 + - - +
265A PRO* 3.5 10.5 - - + +
267A GLN* 1.3 76.7 - - - +
269A VAL* 1.3 61.6 + - - +
271A THR* 2.7 34.1 - - + +
272A LEU* 3.2 20.7 + - + +
316A ILE* 5.8 1.1 - - + -
317A PRO* 4.1 20.9 - - + -
429A LEU* 5.9 3.1 - - + -
432A ALA* 3.6 46.2 - - + +
433A VAL* 3.9 10.5 - - + +
436A ALA* 4.0 11.9 - - + -
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Residues in contact with VAL 269 (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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265A PRO 2.9 23.0 + - - +
266A GLU 3.8 4.9 - - - +
268A LEU* 1.3 73.9 - - - +
270A LEU* 1.3 68.8 + - + +
272A LEU* 3.2 10.7 + - - +
273A LEU* 3.0 20.2 + - + +
395A LYS* 4.0 40.4 - - + +
398A LEU* 4.1 11.1 - - + +
399A CYS* 3.9 23.3 - - - -
436A ALA* 3.9 11.0 - - + -
439A TRP* 4.2 7.6 - - + -
440A VAL* 4.1 11.4 - - + -
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Residues in contact with LEU 270 (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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266A GLU* 3.0 39.0 + - + +
267A GLN* 3.4 32.5 - - - +
268A LEU 3.2 0.2 - - - -
269A VAL* 1.3 82.7 - - + +
271A THR* 1.3 62.9 - - - +
273A LEU* 2.9 28.0 + - + +
274A GLU* 2.9 18.3 + - + +
395A LYS* 5.5 11.2 - - - +
439A TRP* 6.0 0.7 - - + -
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Residues in contact with THR 271 (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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263A LEU* 4.8 2.5 - - + -
267A GLN 3.1 8.6 + - - +
268A LEU* 2.7 37.9 - - + +
270A LEU* 1.3 80.0 - - - +
272A LEU* 1.3 57.2 + - + +
274A GLU* 3.1 12.0 + - - +
275A ALA* 2.9 26.3 + - - +
315A LYS* 3.5 17.2 + - - +
317A PRO* 3.6 28.4 - - + +
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Residues in contact with LEU 272 (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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268A LEU* 3.2 24.6 + - + +
269A VAL* 3.2 14.5 + - + +
270A LEU 3.1 0.6 - - - -
271A THR* 1.3 77.6 - - + +
273A LEU* 1.3 65.9 + - - +
275A ALA* 3.0 16.4 + - + +
276A GLU* 3.1 14.9 + - - +
312A TRP* 4.8 6.3 + - + +
316A ILE* 4.1 35.9 - - + -
317A PRO* 5.0 0.7 - - + -
398A LEU* 3.7 39.9 - - + +
399A CYS* 4.1 11.2 - - - +
402A ALA* 4.0 19.3 - - + -
433A VAL* 4.7 7.2 - - + -
436A ALA* 5.7 0.4 - - + -
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Residues in contact with LEU 273 (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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269A VAL* 3.0 11.1 + - + +
270A LEU* 2.9 23.7 + - + +
272A LEU* 1.3 77.0 - - - +
274A GLU* 1.3 70.2 + - - +
276A GLU* 3.2 27.1 - - + +
394A HIS* 3.5 34.1 - - + +
395A LYS* 6.5 1.1 - - - -
398A LEU* 3.9 13.9 - - + +
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Residues in contact with GLU 274 (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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270A LEU* 2.9 18.3 + - + +
271A THR* 3.4 13.9 - - - +
272A LEU 3.0 0.2 - - - -
273A LEU* 1.3 93.8 - - - +
275A ALA* 1.3 59.3 + - - +
276A GLU 3.2 4.3 + - - +
315A LYS* 3.7 15.3 - - - +
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Residues in contact with ALA 275 (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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271A THR 2.9 12.6 + - - +
272A LEU* 3.0 13.8 + - + +
274A GLU* 1.3 76.2 - - - +
276A GLU* 1.3 67.0 + - - +
277A PRO* 3.2 2.8 - - - +
312A TRP* 3.1 40.2 - - + +
315A LYS* 3.5 38.5 + - + +
316A ILE* 4.8 2.7 - - + +
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Residues in contact with GLU 276 (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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272A LEU 3.1 6.0 + - - +
273A LEU* 3.2 22.4 - - + +
274A GLU 3.2 4.3 - - - +
275A ALA* 1.3 77.1 - - - +
277A PRO* 1.3 79.2 - - - +
278A PRO* 3.9 1.6 - - - +
312A TRP* 4.3 5.0 + - - -
345A TRP* 5.6 0.2 - - - -
394A HIS* 4.3 9.0 + - + +
397A TYR* 3.4 23.6 + - - -
398A LEU* 3.7 27.8 - - + +
401A LYS* 2.5 28.3 + - - -
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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