Contacts of the helix formed by residues 271 - 286 (chain A) in PDB entry 1TE6
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 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A GLY 5.1 0.9 - - - -
255A LYS* 4.8 17.9 - - + +
256A TYR* 4.2 1.8 - - - -
270A ILE* 1.3 78.2 - - - +
272A GLY* 1.3 64.2 + - - +
273A ASP* 3.4 10.0 + - - +
274A GLN* 2.7 40.8 + - - +
275A LEU* 3.0 21.3 + - - +
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Residues in contact with GLY 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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254A GLY 4.7 4.0 + - - -
256A TYR* 3.8 25.9 - - - -
271A THR* 1.3 74.6 - - - +
273A ASP* 1.3 62.8 + - - +
275A LEU* 3.1 4.2 + - - +
276A GLY* 2.9 19.9 + - - -
295A PHE* 3.5 16.1 - - - -
299A ASP* 5.2 2.9 - - - -
302A ALA* 5.5 3.6 - - - -
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Residues in contact with ASP 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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271A THR* 3.3 8.4 + - - +
272A GLY* 1.3 77.0 - - - +
274A GLN* 1.3 57.1 + - + +
276A GLY* 3.3 3.0 + - - +
277A ALA* 3.0 27.4 + - - +
305A LYS* 3.6 31.6 + - - +
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Residues in contact with GLN 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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269A TYR 4.7 0.5 - - - +
270A ILE* 3.2 28.0 - - + +
271A THR* 2.7 47.5 + - - +
272A GLY 3.2 0.8 - - - -
273A ASP* 1.3 74.4 - - + +
275A LEU* 1.3 67.1 + - - +
277A ALA* 3.1 10.5 + - - +
278A LEU* 3.0 21.3 + - - +
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Residues in contact with LEU 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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164A MET* 4.2 15.0 - - + -
250A PHE* 4.2 6.1 - - + -
256A TYR* 3.6 37.7 - - + -
258A LEU* 4.4 7.6 - - + -
270A ILE* 3.9 20.1 - - + +
271A THR 3.0 12.6 + - - +
272A GLY* 3.4 8.7 - - - +
274A GLN* 1.3 76.4 - - - +
276A GLY* 1.3 61.0 + - - +
278A LEU* 3.2 11.6 + - + +
279A TYR* 3.1 64.5 + - + +
294A PRO 3.4 11.9 - - - +
295A PHE* 4.2 2.5 - - + -
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Residues in contact with GLY 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 GLY 2.9 13.6 + - - -
273A ASP* 3.3 4.2 + - - -
275A LEU* 1.3 78.2 - - - +
277A ALA* 1.3 60.9 + - - +
279A TYR* 3.2 17.2 + - - +
280A GLN* 3.1 25.9 + - - +
295A PHE* 4.0 10.7 - - - -
306A PHE* 3.9 8.5 - - - -
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Residues in contact with ALA 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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273A ASP 3.0 13.0 + - - +
274A GLN* 3.1 11.4 + - - +
276A GLY* 1.3 76.7 - - - +
278A LEU* 1.3 62.8 + - - +
280A GLN* 3.4 12.3 + - - +
281A ASP* 3.2 27.4 + - - +
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Residues in contact with LEU 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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164A MET* 4.2 11.9 - - + -
219A ASN* 5.4 1.1 - - - +
258A LEU* 3.9 28.3 - - + -
270A ILE* 5.3 1.8 - - + -
274A GLN 3.0 11.0 + - - +
275A LEU* 3.3 15.7 - - + +
276A GLY 3.1 0.2 - - - -
277A ALA* 1.3 74.4 - - - +
279A TYR* 1.3 65.8 + - + +
281A ASP* 2.9 26.8 + - + +
282A PHE* 3.0 45.3 + - + -
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Residues in contact with TYR 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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164A MET* 4.0 11.0 - - + -
243A MET* 5.0 1.1 - - + -
245A VAL* 3.3 31.8 - - + +
275A LEU* 3.1 46.4 + - + +
276A GLY* 3.2 11.9 + - - +
278A LEU* 1.3 78.4 - - + +
280A GLN* 1.3 63.1 + - - +
282A PHE* 3.0 19.9 + + - +
283A VAL* 2.9 27.2 + - - +
291A ILE* 4.2 13.2 - - + -
294A PRO* 2.6 45.7 + - + -
295A PHE* 4.0 7.9 - + - -
306A PHE* 3.5 30.3 - + + -
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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 GLY 3.1 18.3 + - - +
277A ALA* 3.4 13.2 - - - +
278A LEU 3.2 0.2 - - - -
279A TYR* 1.3 76.2 - - - +
281A ASP* 1.3 65.3 + - - +
283A VAL* 3.4 9.3 + - - +
284A ARG* 3.0 24.2 + - - +
306A PHE* 3.6 12.4 - - - -
309A ASN* 3.4 19.9 + - - +
310A VAL* 3.3 30.9 - - - +
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Residues in contact with ASP 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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277A ALA* 3.2 16.6 + - - +
278A LEU* 2.9 19.6 + - + +
280A GLN* 1.3 78.2 - - - +
282A PHE* 1.3 59.1 + - + +
284A ARG* 3.1 35.4 + - - +
285A ASP* 2.7 46.1 + - - +
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Residues in contact with PHE 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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164A MET* 4.0 15.7 - - + -
219A ASN* 4.1 18.2 - - + -
220A SER* 4.0 25.6 - - - -
223A LEU* 3.5 20.4 - - + -
243A MET* 3.8 31.0 - - + -
278A LEU* 3.0 49.9 + - + -
279A TYR* 3.0 18.7 + + - +
281A ASP* 1.3 79.9 - - + +
283A VAL* 1.3 59.4 + - + +
286A TYR* 2.9 45.3 + + - +
288A VAL* 3.9 8.1 - - + +
291A ILE* 5.7 0.9 - - + -
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Residues in contact with VAL 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 TYR 2.9 20.1 + - - +
280A GLN* 3.9 10.1 - - - +
282A PHE* 1.3 74.8 - - - +
284A ARG* 1.3 59.2 + - - +
286A TYR 3.1 15.7 - - - +
288A VAL* 4.0 14.2 + - + +
291A ILE* 3.8 12.8 - - + -
306A PHE* 5.2 3.4 - - + -
310A VAL* 5.6 5.6 - - + -
312A ILE* 3.7 46.9 - - + -
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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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280A GLN 3.0 17.6 + - - +
281A ASP* 3.4 29.9 + - - +
282A PHE 3.1 0.2 - - - -
283A VAL* 1.3 80.7 - - - +
285A ASP* 1.3 92.9 + - - +
286A TYR 3.7 0.9 + - - +
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Residues in contact with ASP 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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227A LYS* 5.8 0.2 - - - +
281A ASP* 2.7 25.7 + - - +
284A ARG* 1.3 113.7 + - - +
286A TYR* 1.3 86.4 + - + +
287A PRO* 4.8 0.2 - - - +
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Residues in contact with TYR 286 (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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220A SER* 3.3 27.2 + - - -
223A LEU* 3.7 36.6 - - + -
224A GLU* 3.0 44.9 + - - -
227A LYS* 4.4 13.7 - - + -
241A ILE* 4.6 4.3 - - + -
282A PHE* 2.9 26.9 + + - +
283A VAL 3.1 18.2 - - - +
284A ARG 3.4 1.4 - - - +
285A ASP* 1.3 100.4 - - + +
287A PRO* 1.3 65.5 - - + +
288A VAL* 2.8 22.4 + - + -
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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