Contacts of the helix formed by residues 272 - 282 (chain A) in PDB entry 1HDZ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A ARG* 1.3 70.1 - - - +
273A ASP* 1.3 67.5 + - - +
275A MET* 3.0 6.9 + - - +
276A MET* 3.0 20.1 + - - +
295A PRO* 5.0 0.2 - - + -
296A PRO* 4.7 9.9 - - + +
299A GLN* 3.4 42.6 - - + +
300A ASN 3.2 24.7 - - - +
301A LEU* 3.4 35.9 - - + +
305B PRO* 3.8 22.7 - - + -
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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 ARG* 3.0 46.1 + - - +
272A LEU* 1.3 77.6 - - - +
274A THR* 1.3 78.0 + - - +
276A MET* 3.5 5.4 + - - +
277A ALA* 2.9 28.8 + - - +
377A NAD 4.9 3.3 + - - -
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Residues in contact with THR 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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198A PHE* 4.2 15.5 - - + -
250A ILE* 6.3 1.6 - - + -
267A GLU* 2.9 26.2 + - - +
269A ILE* 3.8 25.1 - - + +
271A ARG* 3.1 17.9 + - - +
273A ASP* 1.3 83.9 + - - +
275A MET* 1.3 59.8 + - - +
277A ALA* 3.9 6.9 - - + +
278A SER* 3.0 29.3 + - - -
377A NAD 3.9 20.6 - - + +
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Residues in contact with MET 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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267A GLU* 3.5 25.1 - - + +
270A GLY* 4.7 2.2 - - - -
271A ARG 3.1 18.7 + - - +
272A LEU* 3.0 15.4 + - - +
274A THR* 1.3 75.5 - - - +
276A MET* 1.3 65.2 + - - +
278A SER* 3.7 3.4 + - - -
279A LEU* 3.2 20.3 + - - +
289A SER* 4.9 0.3 + - - -
291A ILE* 3.4 39.8 - - + +
293A GLY 3.6 15.3 - - - +
295A PRO* 3.8 20.4 - - + -
301A LEU* 4.0 12.3 - - + -
314A TRP* 4.5 8.4 + - + -
305B PRO* 3.8 26.5 - - + -
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Residues in contact with MET 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 LEU 3.0 15.0 + - - +
273A ASP* 3.6 6.7 - - - +
275A MET* 1.3 74.3 - - - +
277A ALA* 1.3 57.2 + - - +
279A LEU* 2.7 58.0 + - + +
280A LEU* 3.0 30.5 + - + +
301A LEU* 4.1 15.7 - - + +
302A SER 4.4 10.3 - - - +
303A ILE* 4.0 22.9 - - + -
307A LEU* 4.1 14.1 - - + -
314A TRP* 5.0 1.8 - - + -
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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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198A PHE* 4.2 6.7 - - + -
250A ILE* 3.9 17.3 - - + -
251A GLN* 3.3 31.0 - - - +
273A ASP 2.9 18.7 + - - +
274A THR* 4.2 7.2 - - + +
276A MET* 1.3 75.1 - - - +
278A SER* 1.3 56.4 + - - +
280A LEU* 4.3 4.7 - - - -
281A CYS* 2.9 31.7 + - - +
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Residues in contact with SER 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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198A PHE* 3.9 22.8 - - - -
265A SER* 2.6 34.5 + - - -
266A PHE 3.8 5.7 + - - -
267A GLU* 3.7 27.0 + - - +
274A THR 3.0 22.0 + - - -
275A MET 3.9 4.5 - - - -
277A ALA* 1.3 74.3 - - - +
279A LEU* 1.4 65.8 + - - +
281A CYS* 3.6 3.0 - - - -
289A SER* 2.9 10.6 + - - -
290A VAL 4.7 0.5 + - - -
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Residues in contact with LEU 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 MET 3.2 12.8 + - - +
276A MET* 2.7 38.5 + - + +
278A SER* 1.4 69.4 - - - +
280A LEU* 1.3 63.6 + - - +
282A CYS* 2.9 27.4 + - - -
289A SER* 3.3 24.0 - - - +
303A ILE* 4.6 5.8 - - + -
307A LEU* 4.1 18.2 - - + -
308A LEU* 4.9 6.3 - - + -
312A ARG* 3.6 22.5 + - - -
313A THR 4.9 2.0 - - - +
314A TRP* 3.8 47.8 - - + -
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Residues in contact with LEU 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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251A GLN* 3.6 42.0 - - + +
252A GLU* 5.5 0.9 - - - +
255A LYS* 3.8 17.9 + - + +
276A MET* 3.5 34.5 - - + +
277A ALA* 3.8 0.7 - - - +
279A LEU* 1.3 75.6 - - - +
281A CYS* 1.3 60.6 + - - +
282A CYS 3.1 2.9 + - - +
307A LEU* 3.8 35.9 - - + -
312A ARG* 3.2 21.9 + - - +
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Residues in contact with CYS 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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196A ALA* 4.0 6.1 - - - -
198A PHE* 3.8 16.8 - - + -
251A GLN* 3.7 24.4 - - - +
254A LEU* 4.3 16.5 - - + +
255A LYS* 4.4 3.1 + - - +
261A GLY* 3.2 9.3 - - - -
262A VAL* 3.0 28.7 + - - +
265A SER* 3.3 33.7 - - - -
277A ALA 2.9 18.3 + - - +
278A SER 3.6 5.6 - - - -
279A LEU 3.2 0.6 + - - -
280A LEU* 1.3 71.5 - - - +
282A CYS* 1.3 57.6 + - - +
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Residues in contact with CYS 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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255A LYS* 5.5 0.7 - - - +
260A GLY 4.8 0.2 - - - +
261A GLY* 4.1 1.7 - - - -
262A VAL* 3.5 16.4 - - + +
263A ASP 4.8 0.2 - - - +
265A SER* 3.3 21.1 - - - +
279A LEU* 2.9 27.8 + - - -
280A LEU 3.3 2.1 - - - +
281A CYS* 1.3 80.3 - - - +
283A HIS* 1.3 67.3 + - - +
284A GLU 3.2 0.2 + - - -
287A GLY* 4.1 16.6 - - - -
288A THR 4.5 4.0 - - - +
289A SER* 4.2 13.2 - - - -
312A ARG* 3.0 45.0 + - - -
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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