Contacts of the helix formed by residues 282 - 296 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280K ASP 3.8 1.0 + - - -
281K ALA* 1.3 69.0 - - - +
283K MET* 1.3 52.3 + - - +
284K ASP* 3.3 11.8 + - - +
285K TRP* 2.9 43.0 + - + +
286K ALA* 2.8 36.6 + - - +
432K PHE* 5.5 0.7 - - - -
434K LYS* 4.0 27.7 + - + +
454K ASN* 5.8 0.6 + - - -
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Residues in contact with MET 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ILE* 6.1 0.2 - - - -
281K ALA 3.0 9.0 + - - +
282K ASP* 1.3 72.3 + - - +
284K ASP* 1.3 64.8 + - - +
286K ALA* 3.3 3.2 + - - +
287K VAL* 2.9 38.7 + - - +
314K ILE* 3.6 46.2 - - + +
317K GLU* 3.8 24.0 - - + +
318K PHE* 4.0 17.7 - - - -
321K ARG* 3.4 40.8 - - - +
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Residues in contact with ASP 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282K ASP* 3.3 8.9 + - - +
283K MET* 1.3 79.1 - - - +
285K TRP* 1.3 63.0 + - - +
287K VAL* 3.8 3.6 - - - +
288K GLU* 3.2 22.9 + - - +
321K ARG* 2.9 30.5 + - - +
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Residues in contact with TRP 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282K ASP* 2.9 29.0 + - + +
284K ASP* 1.3 72.2 - - - +
286K ALA* 1.3 65.7 + - - +
288K GLU* 3.3 11.2 + - + +
289K GLN* 2.9 63.8 + - + +
432K PHE* 3.7 22.5 - + - -
454K ASN* 2.7 30.0 + - + -
455K CYS* 5.1 2.9 - - + -
494L LYS* 3.6 34.7 - - + +
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Residues in contact with ALA 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ILE* 4.0 34.1 - - + +
281K ALA* 4.4 4.7 - - + -
282K ASP 2.8 24.0 + - - +
283K MET* 3.7 5.4 - - - +
285K TRP* 1.3 74.5 - - - +
287K VAL* 1.3 56.8 + - - +
289K GLN* 3.8 0.7 - - - +
290K ALA* 2.8 33.1 + - - +
318K PHE* 4.0 5.6 - - + -
432K PHE* 3.9 18.8 - - + -
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Residues in contact with VAL 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283K MET* 2.9 22.6 + - - +
284K ASP* 3.8 4.5 - - - +
286K ALA* 1.3 75.7 - - - +
288K GLU* 1.3 64.1 + - - +
290K ALA* 3.3 3.1 + - - +
291K HIS* 3.0 22.6 + - + +
318K PHE* 3.6 31.4 - - + +
321K ARG* 3.8 54.5 - - + +
322K SER* 4.1 9.1 + - - +
325K ARG* 4.7 10.3 - - + -
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Residues in contact with GLU 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284K ASP 3.2 14.8 + - - +
285K TRP* 3.8 10.5 - - + +
287K VAL* 1.3 79.0 - - - +
289K GLN* 1.3 69.4 - - - +
291K HIS* 3.3 7.6 + - - +
292K PHE* 3.0 30.9 + - + +
325K ARG* 2.9 41.3 + - - -
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Residues in contact with GLN 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275K ASN* 4.7 0.4 - - - -
285K TRP* 2.9 69.4 + - + +
286K ALA 3.9 0.4 - - - +
288K GLU* 1.3 81.6 - - - +
290K ALA* 1.3 57.0 + - - +
292K PHE* 3.7 13.6 - - - +
293K ALA* 2.7 36.1 + - - +
432K PHE* 3.4 28.0 - - + -
455K CYS* 4.0 3.4 - - - +
456K TYR* 3.7 28.8 + - + +
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Residues in contact with ALA 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275K ASN* 3.5 22.1 + - - +
277K ILE* 4.8 1.6 - - + -
286K ALA 2.8 19.4 + - - +
287K VAL 3.7 2.7 - - - +
289K GLN* 1.3 74.2 - - - +
291K HIS* 1.3 65.3 + - - +
293K ALA* 3.6 2.4 - - - +
294K LEU* 3.3 22.3 + - - +
305K GLY 5.1 1.2 - - - +
308K THR* 4.1 11.2 + - + +
318K PHE* 3.5 25.8 - - + -
322K SER* 5.5 0.4 - - - +
405K MET* 4.7 8.6 - - - +
432K PHE* 5.3 0.2 - - - -
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Residues in contact with HIS 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287K VAL* 3.0 13.3 + - + +
288K GLU* 3.5 9.9 - - - +
290K ALA* 1.3 74.2 - - - +
292K PHE* 1.3 63.7 + - + +
294K LEU 3.3 1.0 + - - -
295K PHE* 2.9 69.9 + + - +
322K SER* 5.0 2.8 + - - -
325K ARG* 3.2 63.1 + - + +
326K ALA* 3.9 8.7 + - - +
329K ARG* 3.2 41.7 + - - -
405K MET* 5.2 4.6 - - + +
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Residues in contact with PHE 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288K GLU* 3.0 20.4 + - + +
289K GLN* 3.7 18.4 - - - +
291K HIS* 1.3 81.4 - - + +
293K ALA* 1.3 66.5 + - - +
295K PHE* 5.3 0.2 - - - -
296K PHE* 3.0 75.0 + + + +
329K ARG* 6.0 0.7 - - - +
456K TYR* 3.8 12.1 - - + -
457K ASP* 3.6 32.8 - - + -
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Residues in contact with ALA 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275K ASN* 4.0 6.3 - - - +
289K GLN 2.7 22.9 + - - +
290K ALA* 3.6 11.0 - - - +
292K PHE* 1.3 75.4 - - - +
294K LEU* 1.3 57.7 + - - +
296K PHE* 5.3 0.7 - - - +
301K CYS* 5.8 0.5 - - - +
304K ALA* 3.5 8.3 - - - +
305K GLY* 2.9 22.9 + - - +
456K TYR* 3.3 45.7 - - + -
457K ASP* 4.3 4.8 - - - +
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Residues in contact with LEU 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290K ALA 3.3 11.1 + - - +
291K HIS 4.2 0.7 - - - +
292K PHE 3.1 0.4 - - - -
293K ALA* 1.3 82.2 - - - +
295K PHE* 1.3 82.0 + - + +
296K PHE 3.4 2.3 + - - +
299K GLY* 3.2 22.5 - - - -
304K ALA* 4.3 8.2 - - + +
305K GLY 3.5 13.0 - - - +
306K SER* 3.4 34.3 - - - +
308K THR* 5.5 0.2 - - - +
402K GLY 4.6 4.0 - - - +
403K PRO 4.3 0.4 - - - -
404K VAL 3.2 26.0 - - - +
405K MET* 3.5 41.3 - - + +
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Residues in contact with PHE 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291K HIS* 2.9 53.7 + + - +
292K PHE* 5.3 0.2 - - - -
294K LEU* 1.3 86.3 - - + +
296K PHE* 1.3 65.6 + - - +
298K GLN* 3.0 16.5 + - - -
299K GLY* 3.1 5.0 + - - +
326K ALA* 4.2 18.8 - - + -
329K ARG* 3.1 35.5 + - - +
341K GLN* 4.0 8.2 - - - +
383K PRO* 3.7 16.6 - - + -
384K THR 3.8 14.4 - - - -
385K VAL* 4.5 0.4 - - + -
403K PRO* 3.4 40.8 - - + -
405K MET* 4.1 17.0 - - + -
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Residues in contact with PHE 296 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K ILE* 4.0 31.0 - - + -
120K VAL* 4.4 22.0 - - + -
121K ASP* 5.4 0.4 - - - -
124K MET* 5.6 2.9 - - + -
170K PHE* 3.8 35.0 - + - -
292K PHE* 3.0 59.1 + + + +
293K ALA 5.2 0.9 - - - +
294K LEU 3.4 2.8 - - - +
295K PHE* 1.3 74.5 - - - +
297K ASN* 1.3 78.9 + - + +
299K GLY* 3.1 13.3 + - - -
300K GLN 3.9 1.6 + - - -
301K CYS* 4.4 12.8 - - + +
329K ARG* 4.2 4.0 - - - +
457K ASP* 3.8 21.3 - - + +
459K PHE* 6.5 0.7 - + - -
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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