Contacts of the helix formed by residues 282 - 296 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A ASP 3.9 0.6 + - - -
281A ALA* 1.3 68.2 - - - +
283A MET* 1.3 57.7 + - - +
284A ASP* 3.2 13.2 + - - +
285A TRP* 3.0 37.5 + - + -
286A ALA* 2.9 31.2 + - - +
432A PHE* 5.8 0.2 - - - -
434A LYS* 4.0 25.7 + - + +
454A ASN* 6.0 0.4 + - - -
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Residues in contact with MET 283 (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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277A ILE* 6.1 0.2 - - - -
281A ALA* 3.0 10.3 + - - +
282A ASP* 1.3 70.9 + - - +
284A ASP* 1.3 63.6 + - - +
286A ALA* 3.3 3.4 + - - -
287A VAL* 2.9 51.9 + - - +
314A ILE* 3.7 50.9 - - + +
317A GLU* 3.9 20.4 - - - +
318A PHE* 3.8 14.8 - - + +
321A ARG* 3.4 36.6 - - - +
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Residues in contact with ASP 284 (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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282A ASP* 3.2 9.1 + - - +
283A MET* 1.3 76.8 - - - +
285A TRP* 1.3 62.9 + - - +
287A VAL* 3.9 3.3 - - - +
288A GLU* 3.2 24.3 + - - +
321A ARG* 2.9 33.7 + - - +
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Residues in contact with TRP 285 (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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282A ASP* 3.0 29.9 + - + +
284A ASP* 1.3 74.2 - - - +
286A ALA* 1.3 58.6 + - - +
287A VAL 3.3 0.2 + - - -
288A GLU* 3.4 9.4 + - + +
289A GLN* 2.9 72.7 + - + +
432A PHE* 3.8 15.8 - + - -
454A ASN* 2.8 34.9 + - + -
455A CYS* 4.9 4.5 - - + -
150B PHE* 6.5 0.2 - + - -
494B LYS* 3.6 31.4 - - + +
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Residues in contact with ALA 286 (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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277A ILE* 3.8 36.0 - - + +
281A ALA* 4.3 4.7 - - + -
282A ASP 2.9 22.8 + - - +
283A MET* 3.9 4.3 - - - +
285A TRP* 1.3 73.8 - - - +
287A VAL* 1.3 58.4 + - - +
289A GLN* 4.0 0.3 - - - +
290A ALA* 2.9 32.7 + - - +
318A PHE* 3.9 5.3 - - + -
432A PHE* 4.1 18.6 - - + -
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Residues in contact with VAL 287 (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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283A MET* 2.9 43.4 + - - +
284A ASP* 3.9 4.0 - - - +
286A ALA* 1.3 76.4 - - - +
288A GLU* 1.3 65.5 + - - +
290A ALA* 3.8 1.7 - - - +
291A HIS* 3.0 23.4 + - - +
318A PHE* 3.7 18.6 - - + +
321A ARG* 3.8 47.8 - - + +
322A SER* 4.1 10.5 + - - +
325A ARG* 4.7 9.2 - - + -
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Residues in contact with GLU 288 (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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284A ASP 3.2 14.9 + - - +
285A TRP* 3.9 9.0 - - + +
287A VAL* 1.3 80.1 - - - +
289A GLN* 1.3 68.2 + - - +
291A HIS* 3.4 4.4 + - - +
292A PHE* 3.0 27.9 + - + +
325A ARG* 2.8 46.2 + - - -
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Residues in contact with GLN 289 (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 ASN* 4.7 1.1 - - - -
285A TRP* 2.9 72.6 + - + +
286A ALA 4.0 0.9 - - - +
288A GLU* 1.3 82.1 + - - +
290A ALA* 1.3 54.0 + - - +
292A PHE* 3.1 22.2 + - - +
293A ALA* 2.6 37.9 + - - +
432A PHE* 3.6 25.8 - - + -
455A CYS* 4.3 0.9 - - - +
456A TYR* 3.8 22.1 + - + +
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Residues in contact with ALA 290 (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 ASN* 3.6 21.5 + - - +
277A ILE* 4.7 2.2 - - + -
286A ALA 2.9 19.5 + - - +
287A VAL 3.8 1.8 - - - +
289A GLN* 1.3 74.7 - - - +
291A HIS* 1.3 62.5 + - - +
293A ALA* 3.4 2.6 + - - +
294A LEU* 3.2 22.7 + - - +
305A GLY 5.1 0.5 - - - +
308A THR* 4.2 15.3 + - + +
318A PHE* 3.6 24.2 - - + -
322A SER* 5.7 0.2 - - - +
405A MET* 4.7 8.2 - - + +
432A PHE* 5.3 0.4 - - - -
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Residues in contact with HIS 291 (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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287A VAL 3.0 16.9 + - - +
288A GLU* 3.5 6.3 - - - +
290A ALA* 1.3 76.9 - - - +
292A PHE* 1.3 61.6 + - + +
294A LEU 3.3 1.0 + - - -
295A PHE* 2.8 67.2 + + + +
322A SER* 4.9 3.2 + - - -
325A ARG* 3.2 65.2 + - + +
326A ALA* 3.9 10.0 + - - +
329A ARG* 3.0 38.0 + - + -
405A MET* 5.0 5.3 - - + +
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Residues in contact with PHE 292 (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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288A GLU* 3.0 16.1 + - + +
289A GLN* 3.5 27.4 - - - +
291A HIS* 1.3 82.2 - - + +
293A ALA* 1.3 67.3 + - - +
295A PHE* 5.2 0.2 - - - -
296A PHE* 2.9 75.8 + + + +
329A ARG* 6.0 0.7 - - - +
456A TYR* 3.7 21.5 - - + -
457A ASP* 3.8 18.8 - - + -
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Residues in contact with ALA 293 (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 ASN* 3.7 15.0 - - - +
289A GLN 2.6 21.0 + - - +
290A ALA 3.4 7.0 - - - +
292A PHE* 1.3 75.9 - - - +
294A LEU* 1.3 59.1 + - - +
296A PHE* 4.9 1.2 + - - +
301A CYS* 5.8 1.4 - - - +
304A ALA* 3.7 7.6 - - - +
305A GLY* 3.0 22.3 + - - +
456A TYR* 3.5 43.3 - - + -
457A ASP* 4.5 4.7 - - - +
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Residues in contact with LEU 294 (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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290A ALA 3.2 11.2 + - - +
291A HIS 4.2 1.3 - - - +
292A PHE 3.1 0.2 - - - -
293A ALA* 1.3 82.6 - - - +
295A PHE* 1.3 79.1 + - + +
296A PHE 3.4 1.5 + - - +
299A GLY* 3.2 24.3 - - - -
301A CYS* 6.0 0.2 - - - -
304A ALA* 4.4 6.9 - - + +
305A GLY 3.4 12.8 - - - +
306A SER* 3.4 33.4 - - - -
308A THR* 5.5 0.2 - - - +
402A GLY 4.3 3.4 - - - +
403A PRO 4.1 0.9 - - - -
404A VAL 3.2 46.2 - - - +
405A MET* 3.5 27.8 - - + +
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Residues in contact with PHE 295 (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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291A HIS* 2.8 59.2 + + + +
292A PHE* 5.2 0.2 - - - -
294A LEU* 1.3 83.8 - - + +
296A PHE* 1.3 66.9 + - - +
297A ASN 3.3 0.2 + - - -
298A GLN* 3.0 8.8 + - - -
299A GLY* 3.0 12.3 + - - +
322A SER 5.9 0.2 - - - -
326A ALA* 4.3 10.5 - - + -
329A ARG* 3.6 39.0 + - - +
341A GLN* 4.2 1.3 - - - +
383A PRO* 3.8 21.5 - - + -
384A THR 3.8 15.9 - - - -
385A VAL* 4.4 0.7 - - + -
403A PRO* 3.3 41.3 - - + -
405A MET* 4.0 19.3 - - + -
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Residues in contact with PHE 296 (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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116A ILE* 3.9 29.6 - - + -
120A VAL* 4.3 23.3 - - + -
121A ASP* 5.1 0.2 - - - -
124A MET* 5.9 1.3 - - + -
170A PHE* 3.6 32.8 - + - -
292A PHE* 2.9 54.6 + + + +
293A ALA 5.1 1.1 - - - +
294A LEU 3.4 1.7 - - - +
295A PHE* 1.3 75.7 - - - +
297A ASN* 1.3 75.9 + - + +
299A GLY* 3.0 9.7 + - - -
301A CYS* 3.4 32.5 - - - -
329A ARG* 4.7 4.9 - - - +
457A ASP* 3.8 17.5 - - + +
459A PHE* 6.5 0.9 - + - -
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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