Contacts of the helix formed by residues 270 - 285 (chain A) in PDB entry 2PU1
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLN 5.1 1.6 - - - -
256A GLN* 3.6 33.0 - - + +
257A TYR* 4.2 3.4 - - - -
269A VAL* 1.3 79.5 - - - +
271A ALA* 1.3 59.7 + - - +
272A GLU* 3.4 4.8 + - - +
273A GLN* 2.8 42.5 + - + +
274A LEU* 3.2 25.8 + - - +
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Residues in contact with ALA 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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255A GLN 5.1 5.3 + - - +
257A TYR* 4.0 23.9 - - + -
270A THR* 1.3 75.1 - - - +
272A GLU* 1.3 59.2 + - - +
274A LEU* 3.4 1.5 - - - +
275A ARG* 3.2 16.5 + - - +
294A TYR* 3.3 29.4 + - + -
298A ASP* 4.5 9.4 - - - +
301A GLY* 6.1 1.1 - - - -
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A THR* 3.4 4.9 + - - +
271A ALA* 1.3 75.6 - - - +
273A GLN* 1.3 61.7 + - - +
274A LEU 3.1 1.3 - - - -
275A ARG* 3.8 38.4 + - + -
276A GLU* 3.0 31.5 + - - +
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Residues in contact with GLN 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 TRP 4.2 3.1 + - - +
269A VAL* 3.2 35.0 - - + +
270A THR* 2.8 46.2 + - - +
272A GLU* 1.3 75.8 - - - +
274A LEU* 1.3 57.3 + - - +
276A GLU* 3.6 17.6 - - - +
277A THR* 3.2 25.3 + - - -
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Residues in contact with LEU 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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163A PHE* 4.2 20.2 - - + -
218A ILE* 5.3 2.2 - - + -
257A TYR* 3.5 45.1 - - + -
259A LEU* 4.8 11.0 - - + -
269A VAL* 4.1 15.0 - - + -
270A THR 3.2 11.7 + - - +
271A ALA 3.4 10.3 - - - +
272A GLU 3.1 0.2 - - - -
273A GLN* 1.3 75.4 - - - +
275A ARG* 1.3 59.8 + - - +
276A GLU 3.2 0.2 - - - -
277A THR* 3.0 12.6 + - - +
278A TYR* 2.8 61.7 + - + +
293A PRO 4.0 8.7 - - - +
294A TYR* 4.0 4.3 - - + -
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Residues in contact with ARG 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 ALA 3.2 3.1 + - - +
272A GLU* 3.2 41.8 + - + +
274A LEU* 1.3 77.3 - - - +
276A GLU* 1.3 54.8 + - - +
278A TYR* 3.7 6.6 - - - +
279A CYS* 2.8 40.7 + - - +
294A TYR* 3.1 20.4 - - - +
301A GLY 5.9 0.2 - - - -
304A GLY* 4.4 20.9 + - - -
305A ILE* 4.0 14.1 - - + -
308A ALA* 4.0 27.0 - - - +
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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 GLU* 3.0 15.5 + - - +
273A GLN* 3.6 21.8 - - - +
275A ARG* 1.3 76.1 - - - +
277A THR* 1.3 62.5 + - - +
279A CYS* 3.5 4.9 + - - +
280A LYS* 3.1 24.3 + - + +
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Residues in contact with THR 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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218A ILE* 4.0 16.8 - - + +
219A ASN* 4.0 11.2 + - - +
273A GLN 3.2 12.6 + - - -
274A LEU* 3.0 14.0 + - - +
276A GLU* 1.3 78.1 - - - +
278A TYR* 1.3 62.9 + - + +
280A LYS* 3.3 10.0 + - + +
281A TRP* 2.9 61.7 + - + +
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Residues in contact with TYR 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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163A PHE* 3.5 25.7 - + - -
244A CYS* 3.6 20.1 - - - -
274A LEU* 2.8 45.7 + - + +
275A ARG* 3.2 4.9 + - - +
277A THR* 1.3 72.8 - - + +
279A CYS* 1.3 67.0 + - - +
281A TRP* 3.4 29.3 + + - +
282A ALA* 3.0 25.3 + - - +
290A ILE* 4.2 16.9 - - + +
293A PRO* 2.6 51.6 + - + -
294A TYR* 4.0 13.2 - + - -
305A ILE* 3.9 16.6 - - + -
309A LEU* 4.3 3.1 - - - +
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Residues in contact with CYS 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 ARG* 2.8 29.6 + - - +
276A GLU* 4.0 5.8 - - - +
278A TYR* 1.3 73.3 - - - +
280A LYS* 1.3 56.7 + - - +
282A ALA* 3.5 2.9 + - - +
283A HIS* 3.1 28.5 + - - +
305A ILE* 4.2 16.2 - - - -
308A ALA* 4.2 19.3 - - - -
309A LEU* 4.4 14.7 - - - +
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Residues in contact with LYS 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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219A ASN* 5.4 12.3 - - - +
276A GLU* 3.1 18.7 + - + +
277A THR* 3.5 8.7 - - + +
279A CYS* 1.3 75.1 - - - +
281A TRP* 1.3 56.7 + - + +
283A HIS* 3.2 5.7 + - - +
284A ASP* 2.8 63.6 + - - +
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Residues in contact with TRP 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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163A PHE* 4.0 19.5 - + - -
166A PHE* 4.6 2.0 - + - -
218A ILE* 3.8 28.5 - - + -
219A ASN* 2.6 27.4 + - - +
222A LEU* 3.6 23.6 - - + +
242A MET* 3.7 45.1 - - + -
244A CYS* 4.1 4.9 - - - -
277A THR* 2.9 30.9 + - + +
278A TYR* 3.4 36.1 - + - +
280A LYS* 1.3 79.0 - - + +
282A ALA* 1.3 58.5 + - - +
284A ASP* 4.6 0.9 - - - +
285A TYR* 2.9 37.6 + + - +
287A ILE* 3.5 18.8 - - + +
290A ILE* 4.5 7.9 - - + -
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Residues in contact with ALA 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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278A TYR 3.0 14.1 + - - +
279A CYS 3.7 2.2 - - - +
281A TRP* 1.3 79.9 - - - +
283A HIS* 1.3 59.1 + - - +
285A TYR 3.2 16.3 - - - +
287A ILE* 4.3 11.7 + - + +
290A ILE* 5.3 2.0 - - + -
309A LEU* 3.6 30.1 - - + -
312A LYS* 5.9 5.4 - - + +
313A THR* 3.8 16.2 - - - +
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Residues in contact with HIS 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 CYS 3.1 17.3 + - - +
280A LYS* 3.6 5.8 + - - +
282A ALA* 1.3 80.7 - - - +
284A ASP* 1.3 88.2 + - - +
285A TYR 3.6 1.2 + - - +
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Residues in contact with ASP 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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280A LYS* 2.8 58.8 + - - +
281A TRP* 5.2 0.2 - - - -
283A HIS* 1.3 103.7 + - - +
285A TYR* 1.3 88.9 + - + +
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Residues in contact with TYR 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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219A ASN 5.1 1.0 + - - -
222A LEU* 3.6 45.1 - - + -
223A PRO* 3.4 25.9 - - + +
226A MET* 3.6 32.8 - - + -
240A ILE* 4.1 5.8 - - + -
281A TRP* 2.9 16.3 + + - +
282A ALA 3.2 17.8 - - - +
283A HIS 4.4 1.2 - - - -
284A ASP* 1.3 102.2 - - + +
286A PRO* 1.4 64.1 - - + +
287A ILE* 2.7 28.7 + - + -
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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