Contacts of the helix formed by residues 282 - 296 (chain B) in PDB entry 1ZUM
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 ASP 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ASP 3.8 0.4 + - - -
281B ALA* 1.3 69.3 - - - +
283B MET* 1.3 57.7 + - - +
284B ASP* 3.4 10.7 + - - +
285B TRP* 3.0 35.9 + - + +
286B ALA* 2.9 30.5 + - - +
432B PHE* 5.7 0.4 - - - -
434B LYS* 4.1 27.7 + - + +
454B ASN* 5.8 1.0 + - - -
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Residues in contact with MET 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ALA 3.1 9.4 + - - +
282B ASP* 1.3 71.1 + - - +
284B ASP* 1.3 65.8 + - - +
286B ALA* 3.3 4.0 + - - +
287B VAL* 2.9 45.1 + - - +
314B ILE* 3.8 44.9 - - + +
317B GLU* 3.5 26.2 - - - +
318B PHE* 4.1 18.2 - - - +
321B ARG* 3.7 32.3 - - - +
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASP* 3.4 7.9 + - - +
283B MET* 1.3 77.9 - - - +
285B TRP* 1.3 62.8 + - - +
287B VAL* 3.9 3.1 - - - +
288B GLU* 3.2 24.3 + - - +
321B ARG* 2.5 41.8 + - - +
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Residues in contact with TRP 285 (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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494A LYS* 3.6 34.3 - - + +
282B ASP* 3.0 29.8 + - + +
284B ASP* 1.3 77.0 - - - +
286B ALA* 1.3 58.9 + - - +
287B VAL 3.3 0.2 + - - -
288B GLU* 3.4 8.0 + - + +
289B GLN* 2.9 70.8 + - + +
432B PHE* 3.8 18.2 - + - -
454B ASN* 2.8 30.8 + - + -
455B CYS* 5.1 3.1 - - + -
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 3.9 31.5 - - + +
281B ALA* 4.2 4.9 - - + -
282B ASP 2.9 19.7 + - - +
283B MET* 3.8 3.8 - - - +
285B TRP* 1.3 77.1 - - - +
287B VAL* 1.3 57.9 + - - +
289B GLN* 3.8 0.3 - - - +
290B ALA* 2.8 32.7 + - - +
318B PHE* 3.9 6.0 - - + -
432B PHE* 4.0 23.7 - - + -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 2.9 41.3 + - - +
284B ASP* 3.9 5.4 - - - +
286B ALA* 1.3 76.0 - - - +
288B GLU* 1.3 65.6 + - - +
290B ALA* 3.9 1.9 - - - +
291B HIS* 3.1 22.7 + - + +
318B PHE* 3.8 21.5 - - + +
321B ARG* 3.8 46.7 - - + +
322B SER* 4.1 9.1 + - - +
325B ARG* 4.7 9.4 - - + -
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Residues in contact with GLU 288 (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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284B ASP 3.2 15.1 + - - +
285B TRP* 3.9 9.6 - - + +
287B VAL* 1.3 80.5 - - - +
289B GLN* 1.3 67.7 + - - +
291B HIS* 3.4 6.7 + - - +
292B PHE* 3.0 28.6 + - + +
325B ARG* 3.0 48.0 + - - +
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Residues in contact with GLN 289 (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 ASN* 4.7 1.3 - - - -
285B TRP* 2.9 68.7 + - + +
286B ALA 4.1 0.4 - - - +
288B GLU* 1.3 82.5 + - - +
290B ALA* 1.3 54.5 + - - +
292B PHE* 3.4 20.2 + - - +
293B ALA* 2.7 36.0 + - - +
432B PHE* 3.5 23.1 - - + -
455B CYS* 3.9 3.5 - - - +
456B TYR* 3.7 28.1 + - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASN* 3.5 23.7 + - - +
277B ILE* 4.6 2.5 - - + -
286B ALA 2.8 20.0 + - - +
287B VAL 3.9 1.6 - - - +
289B GLN* 1.3 73.6 - - - +
291B HIS* 1.3 65.0 + - - +
293B ALA* 3.5 2.3 - - - +
294B LEU* 3.2 18.2 + - - +
305B GLY 5.0 0.3 - - - +
308B THR* 4.1 12.3 + - + +
318B PHE* 3.6 24.5 - - + -
322B SER* 5.5 0.2 - - - +
405B MET* 3.4 14.9 - - + +
432B PHE* 5.3 0.2 - - - -
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Residues in contact with HIS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 3.1 18.4 + - + +
288B GLU* 3.5 7.9 - - - +
290B ALA* 1.3 78.9 - - - +
292B PHE* 1.3 60.9 + - - +
295B PHE* 2.9 65.7 + + - +
322B SER* 4.9 3.7 + - - -
325B ARG* 3.5 49.1 + - + +
326B ALA* 3.8 24.9 + - - +
329B ARG* 3.0 36.1 + - - -
405B MET* 3.9 10.8 - - + +
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Residues in contact with PHE 292 (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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288B GLU* 3.0 18.4 + - + +
289B GLN* 3.5 24.5 - - - +
291B HIS* 1.3 80.7 - - - +
293B ALA* 1.3 67.0 + - - +
295B PHE* 5.3 0.4 - - - -
296B PHE* 2.9 73.1 + + + +
329B ARG* 5.9 0.9 - - - +
456B TYR* 3.6 25.4 - - + -
457B ASP* 3.7 19.5 - - + -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASN* 3.8 11.7 - - - +
289B GLN 2.7 22.1 + - - +
290B ALA 3.5 6.5 - - - +
292B PHE* 1.3 74.5 - - - +
294B LEU* 1.3 59.2 + - - +
296B PHE* 4.9 1.2 + - - +
301B CYS* 5.9 0.3 - - - +
304B ALA* 3.6 7.8 - - - -
305B GLY* 2.9 22.5 + - - +
456B TYR* 3.4 47.3 - - + -
457B ASP* 4.3 4.9 - - - +
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Residues in contact with LEU 294 (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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290B ALA 3.2 15.2 + - - +
291B HIS 4.2 0.9 - - - +
292B PHE 3.1 0.2 - - - -
293B ALA* 1.3 80.0 - - - +
295B PHE* 1.3 76.6 + - + +
296B PHE 3.4 2.2 + - - +
299B GLY* 3.2 22.0 - - - -
304B ALA* 4.3 7.0 - - + +
305B GLY 3.6 11.4 - - - +
306B SER* 3.3 36.8 - - - +
402B GLY 4.2 5.2 - - - +
403B PRO 4.1 0.2 - - - -
404B VAL 3.2 47.8 - - - +
405B MET* 3.5 26.2 - - + +
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Residues in contact with PHE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B HIS* 2.9 60.8 + + - +
292B PHE* 5.3 0.2 - - - -
294B LEU* 1.3 82.2 - - + +
296B PHE* 1.3 65.9 + - - +
297B ASN 3.2 0.5 + - - -
298B GLN* 3.1 15.9 + - - -
299B GLY* 3.3 4.2 + - - +
322B SER 5.9 0.2 - - - -
326B ALA* 4.2 11.4 - - + -
329B ARG* 3.3 32.0 + - - +
341B GLN* 4.1 7.4 - - - -
383B PRO* 3.7 22.4 - - + -
384B THR 3.8 15.5 - - - -
385B VAL* 4.4 0.7 - - + -
403B PRO* 3.4 41.3 - - + -
405B MET* 4.1 19.1 - - + -
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Residues in contact with PHE 296 (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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112B LYS* 6.0 0.2 - - - -
116B ILE* 3.9 33.0 - - + -
120B VAL* 4.3 19.5 - - + -
121B ASP* 5.2 0.2 - - - -
124B MET* 5.5 2.2 - - + -
170B PHE* 3.6 35.0 - + - -
292B PHE* 2.9 52.9 + + + +
293B ALA 5.2 1.3 - - - +
294B LEU 3.4 2.2 - - - +
295B PHE* 1.3 75.6 - - - +
297B ASN* 1.3 79.4 + - + +
299B GLY* 3.0 13.7 + - - -
300B GLN 3.8 1.6 + - - -
301B CYS* 4.5 11.1 - - + +
329B ARG* 4.5 4.9 - - - +
457B ASP* 3.9 23.3 - - + +
459B PHE* 6.5 0.4 - + - -
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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