Contacts of the helix formed by residues 292 - 303 (chain A) in PDB entry 1MZC
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 TYR 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ARG* 5.5 8.1 + - - -
256A LEU* 3.8 25.2 - - + +
283A ILE 4.9 1.0 + - - -
284A LEU* 3.6 48.7 + - + +
287A ARG* 3.4 27.4 - - + +
288A GLY 3.4 22.2 - - - -
289A LEU* 3.4 14.7 + - - +
290A SER 3.1 2.3 - - - -
291A LYS* 1.3 90.0 - - + +
293A PRO* 1.3 65.1 - - - +
294A ASN 3.3 2.2 - - - -
295A LEU* 3.0 31.4 + - + +
296A LEU* 3.8 3.3 + - - +
318A ILE* 6.0 1.0 - - - +
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Residues in contact with PRO 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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290A SER 4.2 8.4 - - - +
291A LYS 3.2 13.0 - - - +
292A TYR* 1.3 85.3 - - - +
294A ASN* 1.3 71.2 + - - +
295A LEU 3.3 0.5 + - - -
296A LEU* 3.4 17.8 + - + +
297A ASN* 3.5 15.2 + - - +
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Residues in contact with ASN 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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292A TYR 3.3 1.0 - - - -
293A PRO* 1.3 85.2 - - - +
295A LEU* 1.3 65.8 + - - +
297A ASN* 3.3 13.4 + - - +
298A GLN* 3.1 37.1 + - + +
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Residues in contact with LEU 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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260A VAL* 5.1 5.2 - - + -
264A LEU* 4.4 23.8 - - + -
280A LEU* 4.6 7.4 - - + -
284A LEU* 3.4 33.0 - - + -
289A LEU* 5.5 4.0 - - + +
292A TYR* 3.0 23.4 + - + +
294A ASN* 1.3 78.8 - - - +
296A LEU* 1.3 62.8 + - - +
298A GLN* 3.4 7.7 + - + +
299A LEU* 3.0 54.0 + - + +
314A PHE* 3.8 22.2 - - + -
318A ILE* 4.7 4.5 - - + -
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Residues in contact with LEU 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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292A TYR 3.8 3.1 + - - +
293A PRO* 3.4 12.9 + - + +
294A ASN 3.3 0.4 - - - -
295A LEU* 1.3 80.8 - - - +
297A ASN* 1.3 59.3 + - - +
299A LEU* 3.8 1.8 - - - +
300A LEU* 2.8 47.2 + - + +
315A LEU* 3.6 26.2 - - + -
318A ILE* 4.1 24.1 - - + +
319A TYR* 4.1 20.0 - - + +
322A MET* 4.1 29.6 - - + -
333A ILE* 5.9 1.1 - - + -
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 3.5 18.7 + - - +
294A ASN* 3.3 15.5 + - - +
295A LEU 3.3 0.4 - - - -
296A LEU* 1.3 78.9 - - - +
298A GLN* 1.3 62.4 + - + +
300A LEU* 3.1 16.0 + - - +
301A ASP* 2.9 38.5 + - - +
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Residues in contact with GLN 298 (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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261A GLN* 5.3 8.1 + - - +
264A LEU* 3.7 28.4 - - + +
268A LYS* 5.8 5.1 - - - +
294A ASN* 3.1 27.7 + - + +
295A LEU* 3.9 9.4 - - + +
297A ASN* 1.3 75.9 - - + +
299A LEU* 1.3 64.8 + - + +
301A ASP* 3.2 19.0 + - - +
302A LEU* 3.2 21.0 + - + +
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Residues in contact with LEU 299 (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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264A LEU* 4.4 15.3 - - + -
267A ILE* 6.3 0.2 - - + -
277A TRP* 4.0 17.0 - - + -
280A LEU* 5.0 1.1 - - + -
295A LEU* 3.0 38.0 + - + +
296A LEU 3.8 2.9 - - - +
298A GLN* 1.3 75.7 - - + +
300A LEU* 1.3 63.4 + - - +
302A LEU* 3.2 15.2 + - + +
303A GLN* 3.0 19.6 + - - +
311A LEU* 3.6 31.9 - - + +
314A PHE* 3.4 41.5 - - + -
315A LEU* 4.3 7.9 - - + -
318A ILE* 3.9 10.3 - - + -
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Residues in contact with LEU 300 (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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296A LEU* 2.8 34.6 + - + +
297A ASN* 3.1 15.9 + - - +
299A LEU* 1.3 79.1 - - - +
301A ASP* 1.3 59.6 + - - +
303A GLN* 3.0 26.2 - - + +
304A PRO* 3.6 4.3 - - - +
315A LEU* 3.4 38.6 - - + -
319A TYR* 4.1 13.0 - - - +
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Residues in contact with ASP 301 (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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297A ASN* 2.9 25.4 + - - +
298A GLN* 3.5 11.3 - - - +
299A LEU 3.1 0.4 - - - -
300A LEU* 1.3 78.6 - - - +
302A LEU* 1.3 64.1 + - + +
303A GLN 3.1 0.4 - - - -
304A PRO* 3.3 12.7 - - - +
305A SER* 4.6 3.3 + - - -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 5.4 7.2 - - + -
267A ILE* 5.5 9.2 - - + -
268A LYS* 4.8 32.8 - - + -
277A TRP* 5.8 1.6 - - + -
298A GLN* 3.4 16.6 - - + +
299A LEU* 3.2 23.2 + - + +
301A ASP* 1.3 78.7 - - + +
303A GLN* 1.3 64.5 + - - +
304A PRO 3.4 0.2 - - - -
305A SER* 3.0 7.8 + - - +
306A HIS* 2.9 53.0 + - + +
307A SER 3.5 2.3 + - - -
311A LEU* 3.9 8.1 - - + -
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Residues in contact with GLN 303 (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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299A LEU 3.0 5.6 + - - +
300A LEU* 3.0 27.6 - - + +
302A LEU* 1.3 75.9 - - - +
304A PRO* 1.3 65.4 - - + +
307A SER* 2.9 32.1 + - - -
311A LEU* 3.7 17.1 - - - +
312A ILE* 3.0 36.3 - - - +
315A LEU* 3.5 22.7 - - - +
340A LEU* 5.1 4.5 - - - +
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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