Contacts of the helix formed by residues 272 - 285 (chain A) in PDB entry 1Y24
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 ILE 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A VAL* 4.9 6.5 - - + -
270A ILE 3.5 2.4 + - - -
271A SER* 1.3 72.7 - - - +
273A LEU* 1.3 76.6 + - + +
275A GLN* 3.1 17.8 + - - +
276A GLU* 3.2 27.2 + - - +
319A ALA* 3.1 32.5 - - + +
322A VAL* 3.5 23.1 - - + -
323A VAL* 4.4 11.4 - - + +
388A THR* 4.0 22.2 - - - +
407A GLN* 3.4 25.1 - - + +
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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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46A PHE* 6.3 1.3 - - + -
271A SER* 2.9 18.6 + - - +
272A ILE* 1.3 95.0 - - + +
274A GLU* 1.3 58.0 + - - +
276A GLU* 3.1 20.5 + - - +
277A LYS* 2.8 47.3 + - + +
388A THR* 4.9 7.2 - - - +
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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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254A VAL* 3.9 12.1 - - + -
270A ILE* 3.4 24.4 - - + +
271A SER* 2.6 48.0 + - - +
273A LEU* 1.3 81.4 - - - +
275A GLN* 1.3 55.4 + - - +
277A LYS* 3.3 17.2 + - + +
278A VAL* 2.8 29.4 + - - +
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Residues in contact with GLN 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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252A ALA* 3.1 43.1 + - + +
253A GLY 5.4 0.9 - - - +
254A VAL* 3.5 27.8 - - + +
272A ILE 3.1 10.2 + - - +
274A GLU* 1.3 73.7 - - - +
276A GLU* 1.3 59.2 + - - +
278A VAL* 3.1 10.6 - - + +
279A VAL* 3.0 32.6 + - + +
300A ALA* 4.6 7.2 - - - +
301A ASP* 3.3 21.3 + - - +
323A VAL* 3.2 40.4 - - + +
334A LEU* 5.1 9.5 - - + +
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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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46A PHE* 3.3 30.3 - - - -
272A ILE* 3.2 40.7 - - + +
273A LEU* 3.2 21.6 + - - +
275A GLN* 1.3 76.4 - - + +
277A LYS* 1.3 55.8 + - + +
279A VAL* 3.1 13.3 - - - +
280A ALA* 2.9 30.3 + - - +
322A VAL* 4.5 3.0 - - - +
323A VAL* 5.4 3.3 - - + +
326A ILE* 3.4 36.4 - - + +
330A GLN* 4.8 1.2 - - - +
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 2.8 31.2 + - + +
274A GLU* 3.4 21.5 - - + +
276A GLU* 1.3 72.0 - - + +
278A VAL* 1.3 54.2 + - - +
280A ALA* 3.2 8.1 + - + +
281A GLN* 2.7 42.4 + - - +
284A ARG* 5.4 8.1 - - - +
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Residues in contact with VAL 278 (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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225A PHE* 4.2 26.5 - - + -
226A HIS 5.7 0.4 - - - +
251A GLU 5.6 1.1 - - - +
252A ALA* 4.0 24.9 - - + -
253A GLY 5.7 2.2 - - - +
274A GLU 2.8 14.5 + - - +
275A GLN* 3.1 29.1 + - - +
277A LYS* 1.3 73.4 - - - +
279A VAL* 1.3 60.4 - - + +
281A GLN* 3.1 41.7 + - - +
282A GLN* 3.5 10.6 + - - +
297A ASN* 6.2 0.4 - - - -
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Residues in contact with VAL 279 (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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275A GLN* 3.0 17.1 + - + +
276A GLU* 3.1 28.5 - - - +
278A VAL* 1.3 73.1 - - + +
280A ALA* 1.3 65.0 + - - +
282A GLN* 3.2 15.5 + - + +
283A ILE* 3.2 13.7 + - - +
297A ASN* 3.2 29.2 - - - +
326A ILE* 6.0 3.1 - - + -
327A ALA* 4.5 10.1 - - - +
330A GLN* 3.7 21.7 - - + +
331A ASN* 3.5 26.7 - - + +
334A LEU* 4.6 9.9 - - + -
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Residues in contact with ALA 280 (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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276A GLU 2.9 20.4 + - - +
277A LYS* 3.2 8.9 + - - +
279A VAL* 1.3 75.5 - - - +
281A GLN* 1.3 52.3 + - - +
283A ILE* 3.1 4.0 - - - +
284A ARG* 2.7 47.5 + - - +
330A GLN* 3.6 27.9 + - + +
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Residues in contact with GLN 281 (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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226A HIS 6.1 1.0 - - - +
228A PRO* 4.3 28.2 - - + +
277A LYS* 2.7 19.6 + - - +
278A VAL* 3.1 44.6 + - - +
280A ALA* 1.3 72.3 - - - +
282A GLN* 1.3 64.3 + - + +
284A ARG* 3.2 35.7 + - - +
285A GLN* 3.9 6.6 + - - +
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Residues in contact with GLN 282 (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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227A THR 5.6 0.6 + - - -
228A PRO* 4.7 14.6 - - - +
231A SER* 2.7 31.2 + - - -
248A PHE* 3.5 38.9 - - + -
250A GLY* 5.9 1.6 - - - -
278A VAL 3.7 13.2 - - - +
279A VAL* 3.2 5.6 + - - +
281A GLN* 1.3 84.0 - - + +
283A ILE* 1.3 58.5 + - - +
285A GLN* 3.2 43.1 + - - +
295A ILE* 3.7 16.8 - - + +
297A ASN* 5.9 5.6 - - - +
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Residues in contact with ILE 283 (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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279A VAL 3.2 9.9 + - - +
280A ALA 3.1 17.3 - - - +
282A GLN* 1.3 73.4 - - - +
284A ARG* 1.3 52.2 + - - +
285A GLN 2.8 15.2 + - - -
286A LEU* 3.2 49.2 + - + +
291A ALA 5.7 0.4 - - - +
293A THR 5.3 3.6 - - - +
295A ILE* 3.7 26.5 - - + +
330A GLN* 3.2 55.2 - - + +
332A LEU* 6.1 4.0 - - + -
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Residues in contact with ARG 284 (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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277A LYS* 5.4 7.9 + - - +
280A ALA* 2.7 34.6 + - - +
281A GLN* 3.2 25.1 + - - +
283A ILE* 1.3 71.6 - - - +
285A GLN* 1.3 65.3 + - - +
286A LEU* 4.3 5.2 - - - +
287A PHE* 3.3 18.8 - - + -
330A GLN* 5.8 0.9 - - - +
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Residues in contact with GLN 285 (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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231A SER* 4.2 1.4 + - - -
232A PRO* 4.1 18.4 - - - +
235A TRP* 3.6 27.1 - - - +
248A PHE* 5.6 0.4 - - - -
281A GLN 3.9 4.4 + - - +
282A GLN* 3.2 41.4 + - - +
283A ILE 2.8 1.2 + - - +
284A ARG* 1.3 85.5 - - - +
286A LEU* 1.3 67.6 + - - +
287A PHE* 2.8 40.2 + - + +
288A PRO* 3.6 26.7 - - + +
295A ILE* 5.5 4.0 - - + +
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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