Contacts of the helix formed by residues 271 - 282 (chain D) 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 HIS 271 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267D GLU* 2.9 6.1 + - - +
269D ILE* 3.4 22.1 - - + +
270D GLY* 1.3 86.2 + - - +
272D LEU* 1.3 58.9 + - - +
273D GLU* 4.0 19.1 + - + +
274D THR* 2.8 32.8 + - + +
275D MET* 2.9 19.0 + - - +
296D PRO* 5.1 1.3 - - - -
409D ZN 2.1 37.3 - - - -
512D ACT 3.4 10.0 + - - -
4377D NAD 3.3 14.5 + - - -
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C PRO* 4.2 10.8 - - + -
271D HIS* 1.3 70.1 - - - +
273D GLU* 1.3 74.1 + - - +
275D MET* 2.9 27.5 + - + +
276D ILE* 3.0 17.9 + - + +
295D PRO* 3.8 28.5 - - + -
296D PRO* 4.2 13.2 - - + +
299D LYS* 3.8 23.6 - - + +
300D MET 3.3 27.8 - - - +
301D LEU* 3.4 20.6 - - + +
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Residues in contact with GLU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D HIS* 4.0 19.1 + - + +
272D LEU* 1.3 97.9 + - + +
274D THR* 1.3 58.7 + - + +
276D ILE* 3.3 10.7 + - - +
277D ASP* 3.0 36.1 + - - +
512D ACT 5.0 4.9 - - - +
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Residues in contact with THR 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D PHE* 4.6 13.2 - - + -
243D PRO* 6.5 0.4 - - + -
267D GLU* 2.7 27.4 + - - +
269D ILE* 3.7 26.2 - - + +
271D HIS* 2.8 16.8 + - + +
273D GLU* 1.3 76.1 - - + +
275D MET* 1.3 60.0 + - - +
277D ASP* 3.6 14.7 - - - +
278D ALA* 2.8 31.7 + - - +
4377D NAD 4.0 23.1 - - - +
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Residues in contact with MET 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C PRO* 4.9 8.7 - - - -
267D GLU* 3.6 22.0 - - + +
270D GLY 4.0 1.6 - - - -
271D HIS 2.9 35.4 + - - +
272D LEU* 2.9 23.1 + - - +
274D THR* 1.3 77.2 + - - +
276D ILE* 1.3 57.1 + - - +
278D ALA* 3.4 2.8 + - - +
279D LEU* 2.9 26.9 + - - +
291D VAL* 3.8 28.0 - - + +
293D GLY 3.9 19.7 - - - +
295D PRO* 3.9 24.9 - - + -
301D LEU* 4.8 6.1 - - + -
314D TRP* 4.1 19.9 + - + -
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Residues in contact with ILE 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LEU 3.0 12.1 + - - +
273D GLU* 3.6 9.4 - - - +
275D MET* 1.3 74.8 - - - +
277D ASP* 1.3 62.1 + - - +
279D LEU* 3.2 6.7 + - - +
280D ALA* 2.9 31.2 + - + +
301D LEU* 3.5 25.6 - - + -
302D THR 3.1 28.5 - - - +
303D TYR* 4.0 22.0 - - + -
304D ASP 5.5 0.4 - - - +
307D LEU* 4.4 14.1 - - + -
314D TRP* 5.0 2.0 - - + -
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Residues in contact with ASP 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D PHE* 4.1 8.8 - - + -
250D ILE* 3.9 26.1 - - + +
251D SER* 4.8 0.4 - - - -
273D GLU* 3.0 30.5 + - - +
274D THR* 3.3 19.0 + - - +
276D ILE* 1.3 79.8 - - - +
278D ALA* 1.3 55.0 + - - +
280D ALA* 3.7 5.3 - - - +
281D SER* 2.5 38.3 + - - -
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D PHE* 3.8 26.4 - - + -
265D THR* 2.8 24.6 + - - +
267D GLU* 4.2 19.1 - - + +
274D THR 2.8 17.3 + - - +
275D MET 3.5 4.9 - - - +
277D ASP* 1.3 74.2 - - - +
279D LEU* 1.3 68.5 + - - +
281D SER* 3.1 8.1 + - - -
282D CYS 3.4 2.9 + - - -
289D SER* 3.4 11.2 - - - +
291D VAL* 6.4 0.4 - - + -
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D MET 2.9 14.9 + - - +
276D ILE* 3.5 9.0 - - - +
278D ALA* 1.3 79.8 - - - +
280D ALA* 1.3 60.8 + - - +
282D CYS* 3.1 11.4 + - - -
289D SER* 3.4 12.7 + - - -
303D TYR* 3.7 33.9 - - + -
307D LEU* 4.2 12.8 - - + +
308D LEU* 4.9 4.5 - - + +
312D ARG* 2.9 51.1 + - + -
313D THR 5.2 0.2 - - - +
314D TRP* 3.7 50.7 - - + -
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Residues in contact with ALA 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D SER* 3.6 21.2 - - - +
276D ILE* 2.9 22.1 + - + +
277D ASP* 3.9 5.2 - - - +
279D LEU* 1.3 73.5 - - - +
281D SER* 1.3 58.0 + - - +
307D LEU* 3.9 24.7 - - + -
312D ARG* 2.7 29.8 + - - +
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D PHE* 3.6 12.5 - - - -
250D ILE* 4.0 1.4 - - - +
251D SER* 3.4 26.5 + - - +
254D LEU* 3.5 25.2 - - - +
255D SER* 5.5 0.7 + - - -
262D VAL* 3.2 25.7 - - - +
265D THR* 4.0 7.6 - - - -
277D ASP 2.5 26.8 + - - -
278D ALA 3.1 6.1 + - - -
280D ALA* 1.3 72.2 - - - +
282D CYS* 1.3 58.8 + - - +
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Residues in contact with CYS 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D VAL* 3.6 12.8 - - + +
265D THR* 4.0 11.9 - - + +
278D ALA 3.4 1.8 + - - -
279D LEU 3.1 23.8 + - - -
281D SER* 1.3 78.3 - - - +
283D HIS* 1.3 65.5 + - - +
287D GLY* 3.7 24.9 - - - -
288D THR 3.8 23.3 - - - +
289D SER* 3.9 8.7 - - - -
312D ARG* 2.8 39.2 + - - -
313D THR 5.1 0.2 - - - -
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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