Contacts of the helix formed by residues 272 - 282 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A PRO* 3.6 31.4 - - + -
270B GLY 4.2 0.2 + - - -
271B ARG* 1.3 72.0 - - - +
273B ASP* 1.3 59.6 + - - +
275B MET* 2.9 24.6 + - - +
276B MET* 2.9 13.0 + - - +
296B PRO* 4.8 10.1 - - + +
299B GLN* 3.6 46.6 - - + +
300B ASN 3.6 18.8 - - - +
301B LEU* 3.6 23.6 - - + +
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Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ARG* 3.1 41.1 + - - -
272B LEU* 1.3 77.1 - - - +
274B THR* 1.3 80.0 + - - +
276B MET* 3.3 8.8 + - - +
277B ALA* 2.8 29.2 + - - +
377B NAD 4.5 3.2 + - - -
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B PHE* 3.8 18.9 - - + -
250B ILE* 6.3 0.4 - - + -
267B GLU* 2.8 30.7 + - - +
269B ILE* 3.6 24.5 - - + +
271B ARG* 3.0 19.1 - - - +
273B ASP* 1.3 85.2 + - - +
275B MET* 1.3 57.3 + - - +
277B ALA* 3.9 5.6 - - + +
278B SER* 2.9 30.1 + - - -
377B NAD 3.7 17.5 - - + +
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Residues in contact with MET 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A PRO* 3.6 31.0 - - - -
267B GLU* 3.6 29.2 - - + +
270B GLY* 4.4 6.5 - - - -
271B ARG 3.1 19.4 + - - +
272B LEU* 2.9 12.6 + - - +
274B THR* 1.3 75.2 - - - +
276B MET* 1.3 57.9 + - - +
278B SER* 3.3 5.0 + - - -
279B LEU* 2.9 28.4 + - - +
291B ILE* 3.4 40.3 - - + +
293B GLY 3.9 9.9 - - - +
295B PRO* 4.1 15.3 - - + -
301B LEU* 3.8 14.1 - - + -
314B TRP* 4.7 6.0 + - + -
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Residues in contact with MET 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU 2.9 6.3 + - - +
273B ASP* 3.3 11.7 - - - +
275B MET* 1.3 73.0 - - - +
277B ALA* 1.3 59.9 - - - +
278B SER 3.0 1.1 - - - -
279B LEU* 2.7 43.4 + - + +
280B LEU* 2.9 38.2 + - + +
301B LEU* 3.4 27.8 - - + -
302B SER 4.3 9.6 - - - +
303B ILE* 3.7 31.6 - - + -
307B LEU* 4.7 4.9 - - + -
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PHE* 4.0 12.3 - - + -
250B ILE* 3.7 30.5 - - + -
251B GLN* 3.7 22.3 - - + +
273B ASP 2.8 20.0 + - - +
274B THR* 4.1 3.6 - - + +
276B MET* 1.3 72.4 - - - +
278B SER* 1.3 61.6 + - - +
280B LEU* 4.0 0.6 - - - +
281B CYS* 3.1 27.9 + - - +
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PHE* 4.1 15.7 - - - -
265B SER* 2.6 43.5 + - - -
266B PHE 3.8 2.1 + - - -
267B GLU* 3.7 28.7 + - - +
274B THR 2.9 20.7 + - - -
275B MET 3.4 6.1 - - - -
276B MET 3.0 0.2 - - - -
277B ALA* 1.3 80.4 - - - +
279B LEU* 1.4 60.1 + - - +
281B CYS* 3.6 4.0 - - - -
289B SER* 3.5 7.9 + - - -
290B VAL 4.9 0.2 + - - -
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B MET 2.9 11.9 + - - +
276B MET* 2.7 36.5 + - + +
278B SER* 1.4 70.2 - - - +
280B LEU* 1.3 62.3 + - - +
282B CYS* 3.0 24.8 + - - -
289B SER* 3.4 13.9 + - - +
303B ILE* 4.7 8.1 - - + -
307B LEU* 4.7 14.1 - - + -
308B LEU* 4.7 4.9 - - + -
312B ARG* 3.6 32.1 + - + +
313B THR 4.8 0.9 - - - +
314B TRP* 3.7 59.2 - - + +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B GLN* 3.3 44.4 - - + +
255B LYS* 3.3 29.6 - - - +
276B MET* 2.9 34.5 + - + +
277B ALA* 4.5 0.4 - - - +
279B LEU* 1.3 76.1 - - - +
281B CYS* 1.3 59.9 + - - +
282B CYS 3.4 6.1 + - - +
307B LEU* 4.0 36.6 - - + -
312B ARG* 3.9 8.7 + - - +
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Residues in contact with CYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ALA* 4.4 1.3 - - - -
198B PHE* 4.0 7.4 - - - -
251B GLN* 4.1 10.8 - - - +
254B LEU* 3.8 40.6 - - + +
255B LYS* 4.3 7.0 + - - +
258B THR* 4.8 1.0 + - - -
261B GLY* 3.3 7.3 - - - -
262B VAL* 2.8 27.3 + - - +
265B SER* 3.9 15.3 - - - -
277B ALA 3.1 21.4 + - - +
278B SER 3.6 11.2 - - - -
279B LEU 3.2 0.6 + - - -
280B LEU* 1.3 74.7 - - - +
282B CYS* 1.3 58.8 + - - +
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Residues in contact with CYS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B GLY 4.7 0.8 - - - +
261B GLY* 4.2 0.7 - - - -
262B VAL* 3.1 21.8 - - + +
263B ASP 4.7 0.2 - - - +
265B SER* 3.6 22.0 - - - +
279B LEU 3.0 26.2 + - - -
280B LEU 3.7 1.1 - - - +
281B CYS* 1.3 80.8 - - - +
283B HIS* 1.3 66.6 + - - +
284B GLU 3.2 1.2 + - - -
287B GLY* 3.8 19.7 - - - -
288B THR 4.2 2.9 - - - +
289B SER* 3.9 15.7 - - - -
312B ARG* 2.9 37.8 + - - -
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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