Contacts of the helix formed by residues 270 - 282 (chain A) in PDB entry 1YI8
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A ASP* 2.9 22.9 - - - +
269A PRO* 1.3 77.5 - - + +
271A PRO* 1.3 71.3 - - + +
272A ALA* 3.2 10.0 + - + +
273A ARG* 3.4 35.1 + - - +
274A VAL* 3.3 3.8 - - - +
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Residues in contact with PRO 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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265A ASP* 6.0 3.6 - - + +
268A ASP* 5.1 0.2 - - - +
269A PRO 3.7 7.4 - - - +
270A ASP* 1.3 83.7 - - + +
272A ALA* 1.3 61.5 + - + +
273A ARG 3.4 0.2 - - - -
274A VAL* 3.1 13.0 + - + +
275A GLN* 2.8 31.2 + - - +
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Residues in contact with ALA 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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270A ASP* 3.1 10.0 - - + +
271A PRO* 1.3 82.6 - - + +
273A ARG* 1.3 58.8 + - - +
275A GLN* 3.3 6.8 + - - +
276A ALA* 2.9 27.1 + - - +
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Residues in contact with ARG 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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268A ASP* 3.2 16.9 + - - +
269A PRO* 3.0 41.2 - - - +
270A ASP* 3.4 25.1 + - - +
271A PRO 3.4 0.2 - - - -
272A ALA* 1.3 79.5 - - - +
274A VAL* 1.3 57.0 + - - +
276A ALA* 2.9 13.0 - - + +
277A LEU* 2.8 42.9 - - + +
294A HIS* 3.8 31.8 + - + -
298A VAL* 5.4 1.4 - - - +
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Residues in contact with VAL 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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261A PHE* 5.1 1.3 - - + +
264A LEU* 4.1 17.2 - - + +
265A ASP* 3.6 35.9 - - + +
268A ASP* 2.8 39.9 - - - +
270A ASP 3.3 8.5 - - - +
271A PRO* 3.2 13.2 - - + +
272A ALA 3.0 0.4 - - - -
273A ARG* 1.3 73.7 - - - +
275A GLN* 1.3 58.9 + - - +
276A ALA 2.8 9.6 + - - -
277A LEU* 3.1 16.3 + - - +
278A LYS* 3.1 31.2 + - + +
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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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271A PRO 2.8 19.5 + - - +
272A ALA* 3.5 6.1 - - - +
274A VAL* 1.3 70.5 - - - +
276A ALA* 1.3 54.5 + - - +
278A LYS* 3.6 37.9 + - + +
279A ASP* 2.8 61.1 + - - +
282A ARG* 3.7 13.7 - - - +
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Residues in contact with ALA 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 ALA 2.9 13.2 + - - +
273A ARG* 2.9 24.0 - - + +
274A VAL 2.8 0.2 - - - -
275A GLN* 1.3 77.4 - - - +
277A LEU* 1.3 66.1 + - + +
279A ASP* 3.2 12.4 + - - +
280A GLN* 2.9 34.0 + - - +
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Residues in contact with LEU 277 (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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261A PHE* 4.4 4.0 - - + -
264A LEU* 4.6 20.0 - - + -
273A ARG* 2.8 39.3 - - + +
274A VAL* 3.1 5.8 + - - +
276A ALA* 1.3 87.6 - - + +
278A LYS* 1.3 51.4 + - - +
280A GLN* 3.1 24.9 - - - +
281A TYR* 2.5 40.7 + - - +
286A LEU* 3.5 30.0 - - + +
290A LYS 5.9 0.4 - - - +
291A VAL* 5.1 8.7 - - + -
294A HIS* 4.9 12.8 - - + +
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Residues in contact with LYS 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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255A VAL* 3.2 44.7 - - + +
261A PHE* 3.3 23.8 - - + -
265A ASP* 4.7 14.4 + - - +
274A VAL* 3.1 35.3 + - - +
275A GLN* 3.6 38.9 + - - +
276A ALA 3.2 0.2 - - - -
277A LEU* 1.3 76.4 - - - +
279A ASP* 1.3 58.5 + - - +
281A TYR* 3.8 1.5 - - - +
282A ARG* 3.2 35.5 + - - +
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Residues in contact with ASP 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* 2.8 43.6 + - - +
276A ALA* 3.2 8.7 + - - +
278A LYS* 1.3 76.6 - - - +
280A GLN* 1.3 62.6 + - + +
281A TYR 3.4 0.2 - - - -
282A ARG* 4.1 9.4 + - - +
283A ALA* 3.1 24.1 + - - +
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Residues in contact with GLN 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 ALA* 2.9 24.2 - - - +
277A LEU* 3.1 40.7 + - - +
279A ASP* 1.3 81.1 - - + +
281A TYR* 1.3 61.1 + - - +
283A ALA* 3.7 4.7 - - - -
284A GLY* 3.2 19.9 + - - -
286A LEU* 3.4 32.8 + - + +
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Residues in contact with TYR 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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242A THR* 3.8 0.7 - - - -
243A ASP* 3.0 15.3 + - - -
246A HIS* 3.7 12.1 + + - -
251A ASP 3.7 5.2 - - - +
252A PRO* 3.4 3.1 - - - +
253A GLY* 2.4 64.2 + - - -
254A ARG 3.5 13.0 - - - -
255A VAL* 4.4 0.9 - - + -
258A ASN* 2.8 23.7 + - - -
261A PHE* 3.2 37.7 - + + -
277A LEU 2.5 22.1 + - - +
278A LYS 4.1 2.0 - - - +
280A GLN* 1.3 72.5 - - - +
282A ARG* 1.3 50.9 + - - +
283A ALA 3.0 7.8 + - - -
284A GLY 4.3 0.3 + - - -
286A LEU* 3.5 23.1 - - + +
288A ASP* 3.0 27.0 + - - -
291A VAL* 4.4 15.7 - - + -
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Residues in contact with ARG 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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252A PRO* 2.8 22.3 - - + +
253A GLY 2.7 23.2 + - - +
254A ARG* 4.0 14.6 - - + +
255A VAL* 4.1 11.0 - - - +
256A GLU* 3.1 28.1 + - - -
275A GLN* 3.7 24.4 - - - +
278A LYS* 3.2 22.4 + - - +
279A ASP* 4.2 8.8 + - - +
280A GLN 3.5 0.2 - - - -
281A TYR* 1.3 76.0 - - - +
283A ALA* 1.3 57.4 + - - +
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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