Contacts of the helix formed by residues 272 - 282 (chain C) in PDB entry 1D1T
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 LEU 272 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C GLY 4.2 0.2 + - - -
271C HIS* 1.3 70.1 - - - +
273C GLU* 1.3 77.6 + - - +
274C THR 3.2 0.4 - - - -
275C MET* 2.9 23.2 + - - +
276C ILE* 3.2 17.6 + - - +
295C PRO* 3.8 24.0 - - + -
296C PRO* 4.2 12.1 - - + +
299C LYS* 3.8 22.2 - - + +
300C MET 3.6 28.0 - - - +
301C LEU* 4.3 14.2 - - + +
305D PRO* 3.7 24.9 - - + -
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Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C HIS* 3.2 26.0 + - + +
272C LEU* 1.3 90.3 + - + +
274C THR* 1.3 57.9 + - + +
276C ILE* 3.5 10.8 + - - +
277C ASP* 2.9 31.6 + - - +
510C ACT 5.4 0.3 - - - +
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Residues in contact with THR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 4.7 9.8 - - + -
243C PRO* 6.4 0.9 - - + -
267C GLU* 2.6 37.1 + - - +
269C ILE* 3.6 25.0 - - + +
271C HIS* 3.1 18.1 + - + +
273C GLU* 1.3 76.8 - - + +
275C MET* 1.3 59.1 + - - +
276C ILE 3.4 0.2 - - - -
277C ASP* 3.6 19.1 - - - +
278C ALA* 3.1 19.9 + - - +
3377C NAD 4.3 18.4 - - - +
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Residues in contact with MET 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C GLU* 3.5 24.9 - - + +
270C GLY 3.9 10.1 - - - -
271C HIS 3.2 23.5 + - - +
272C LEU* 2.9 26.1 + - - +
274C THR* 1.3 76.0 - - - +
276C ILE* 1.3 66.7 + - - +
278C ALA* 3.5 2.3 + - - +
279C LEU* 3.1 23.0 + - - +
291C VAL* 3.9 20.4 - - + -
293C GLY 3.4 26.0 - - - +
295C PRO* 3.9 19.7 - - + -
301C LEU* 4.5 14.4 - - + -
314C TRP* 3.7 15.2 + - + -
305D PRO* 5.1 3.6 - - - -
308D LEU* 6.4 0.7 - - - -
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Residues in contact with ILE 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU 3.2 4.9 + - - +
273C GLU* 3.7 12.1 - - - +
275C MET* 1.3 77.6 - - - +
277C ASP* 1.3 59.5 + - - +
279C LEU* 3.2 7.3 + - - +
280C ALA* 2.9 31.3 + - + +
301C LEU* 3.4 27.4 - - + -
302C THR 3.2 27.6 - - - +
303C TYR* 3.8 20.6 - - + -
304C ASP 5.8 0.2 - - - +
307C LEU* 4.6 11.6 - - + +
314C TRP* 4.8 2.9 - - + -
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Residues in contact with ASP 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 4.1 9.0 - - + -
243C PRO* 6.0 3.1 - - - +
250C ILE* 3.6 28.2 - - + +
251C SER* 6.0 0.2 - - - -
273C GLU* 2.9 21.7 + - - +
274C THR* 3.6 20.2 - - - +
276C ILE* 1.3 80.9 - - - +
278C ALA* 1.3 61.7 + - - +
280C ALA* 3.3 6.2 + - - +
281C SER* 2.9 29.5 + - - -
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 3.7 30.0 - - + -
265C THR* 2.6 34.9 + - - +
267C GLU* 4.3 17.7 - - + +
274C THR 3.1 15.3 + - - +
275C MET 4.1 3.1 - - - +
276C ILE 3.4 0.2 - - - -
277C ASP* 1.3 79.8 - - - +
279C LEU* 1.3 62.2 + - - +
281C SER* 3.4 2.2 + - - -
282C CYS 3.5 0.5 + - - -
289C SER* 3.1 11.2 - - - +
291C VAL* 6.5 0.2 - - + -
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C MET 3.1 15.3 + - - +
276C ILE* 3.5 8.1 - - - +
277C ASP 3.2 0.2 - - - -
278C ALA* 1.3 77.0 - - - +
280C ALA* 1.3 64.2 + - - +
281C SER 3.0 1.4 + - - -
282C CYS* 3.1 11.6 - - - -
289C SER* 3.3 13.2 + - - -
303C TYR* 3.9 10.1 - - + -
307C LEU* 3.9 29.4 - - + +
308C LEU* 4.9 4.3 - - + +
312C ARG* 3.0 43.8 + - + -
313C THR 4.7 0.7 - - - +
314C TRP* 3.8 60.6 - - + -
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C SER* 3.7 23.5 - - - +
276C ILE* 2.9 19.6 + - + +
277C ASP* 3.7 6.7 - - - +
279C LEU* 1.3 75.9 - - - +
281C SER* 1.3 57.7 + - - +
282C CYS 3.6 0.4 - - - +
307C LEU* 4.4 21.1 - - + +
312C ARG* 3.0 25.8 + - - +
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Residues in contact with SER 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 3.9 3.4 - - - -
250C ILE* 4.2 0.5 - - - +
251C SER* 3.3 27.9 + - - +
254C LEU* 3.4 24.8 - - - +
255C SER* 5.6 0.9 + - - -
262C VAL* 3.2 22.9 - - - +
265C THR* 3.6 19.7 - - - -
277C ASP 2.9 20.6 + - - -
278C ALA* 4.2 1.3 - - - -
279C LEU 3.0 1.4 + - - -
280C ALA* 1.3 76.4 - - - +
282C CYS* 1.3 64.8 + - - +
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Residues in contact with CYS 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C VAL* 3.5 11.9 - - + +
264C TYR 4.7 0.4 - - - -
265C THR* 3.5 17.4 - - + +
278C ALA 3.5 2.2 + - - -
279C LEU 3.1 21.0 + - - -
280C ALA 3.7 0.2 - - - +
281C SER* 1.3 81.2 - - - +
283C HIS* 1.3 66.9 + - - +
284C MET 3.3 0.2 + - - -
287C GLY* 3.6 24.0 - - - -
288C THR 3.9 6.7 - - - +
289C SER* 4.1 15.7 - - - -
312C ARG* 3.2 42.1 + - - -
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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