Contacts of the helix formed by residues 293 - 306 (chain A) in PDB entry 5E9W
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 SER 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A SER 3.5 2.6 + - - +
291A PHE 3.2 0.6 - - - -
292A GLU* 1.3 79.6 - - - +
294A TYR* 1.3 65.9 + - - +
295A GLU* 3.7 13.2 + - - +
296A GLN* 2.8 35.1 + - - +
297A ALA* 3.2 19.6 + - - +
354A PHE* 3.8 13.7 - - - -
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Residues in contact with TYR 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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293A SER* 1.3 73.4 - - - +
295A GLU* 1.3 81.6 + - + +
297A ALA* 3.3 2.4 + - - +
298A ASP* 2.9 51.0 + - + +
354A PHE* 3.5 44.5 - + + +
381A MET* 3.7 22.9 - - + -
384A LYS* 4.0 12.2 + - - +
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Residues in contact with GLU 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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263A SER 4.4 0.7 - - - -
293A SER* 3.3 11.8 + - - +
294A TYR* 1.3 102.3 + - + +
296A GLN* 1.3 58.2 + - + +
298A ASP* 3.5 3.9 + - - +
299A MET* 2.8 32.2 + - - +
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Residues in contact with GLN 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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261A ASP* 5.2 0.6 + - - -
263A SER* 3.2 48.5 + - - +
264A LYS* 3.7 27.8 - - + +
289A TYR 4.9 4.2 + - - -
290A SER 3.1 16.4 - - - +
292A GLU* 3.0 43.2 + - - +
293A SER* 2.8 22.8 + - - +
294A TYR 3.4 0.4 - - - -
295A GLU* 1.3 78.4 - - + +
297A ALA* 1.3 55.2 + - - +
299A MET* 3.4 0.3 + - - +
300A MET* 2.9 26.3 + - - +
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Residues in contact with ALA 297 (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* 2.9 21.0 + - - +
291A PHE* 4.0 24.0 - - + -
293A SER 3.2 10.7 + - - +
294A TYR 3.6 7.4 - - - +
296A GLN* 1.3 72.6 - - - +
298A ASP* 1.3 64.9 + - - +
300A MET* 3.3 3.5 + - - +
301A LEU* 3.0 25.8 + - - +
354A PHE* 4.0 10.1 - - + -
381A MET* 3.8 15.9 - - + -
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Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 2.9 39.7 + - + +
295A GLU* 3.8 4.0 - - - +
297A ALA* 1.3 75.5 - - - +
299A MET* 1.3 51.5 + - - +
301A LEU* 3.2 5.1 + - - +
302A ARG* 2.8 32.7 + - - +
381A MET* 3.7 13.7 - - + +
384A LYS* 2.6 34.0 + - - +
385A TYR* 2.7 32.4 + - - -
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Residues in contact with MET 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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262A SER 3.5 5.6 - - - +
263A SER 3.2 29.8 - - - +
264A LYS* 4.0 20.6 - - - +
265A GLU 3.6 19.3 - - - +
266A LEU* 4.0 23.6 - - + +
295A GLU 2.8 19.6 + - - +
296A GLN 3.6 0.2 - - - +
298A ASP* 1.3 74.5 - - - +
300A MET* 1.3 60.0 + - - +
302A ARG* 3.2 12.2 + - - +
303A ASN* 2.8 37.0 + - - +
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Residues in contact with MET 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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204A LEU* 4.1 16.2 - - + +
262A SER* 3.2 14.7 + - - +
263A SER 4.0 8.3 - - - +
283A CYS* 4.6 4.3 - - - -
286A VAL* 3.9 24.7 - - + +
287A CYS* 4.0 15.9 - - - -
289A TYR 5.5 0.2 - - - -
290A SER* 3.6 31.4 - - - +
296A GLN 2.9 17.5 + - - +
297A ALA 3.9 1.1 - - - +
299A MET* 1.3 76.3 - - - +
301A LEU* 1.3 57.8 + - - +
303A ASN* 3.3 2.4 + - - +
304A ALA* 2.8 28.7 + - + +
314A PHE* 6.4 0.7 - - + -
500A SAH 3.7 38.1 - - + +
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Residues in contact with LEU 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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287A CYS* 6.3 0.2 - - - -
291A PHE* 5.8 1.1 - - + -
297A ALA 3.0 15.7 + - - +
298A ASP* 3.4 9.2 - - - +
300A MET* 1.3 78.4 - - - +
302A ARG* 1.3 50.7 + - - +
304A ALA* 3.2 1.9 + - - -
305A CYS* 2.7 46.7 + - - +
314A PHE* 3.6 34.5 - - + -
378A LEU* 4.0 22.4 - - + -
381A MET* 3.6 39.9 - - + +
382A ALA* 3.7 21.5 - - + +
385A TYR* 4.0 10.5 - - + -
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Residues in contact with ARG 302 (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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266A LEU* 3.3 44.3 - - + +
268A ILE* 4.1 6.5 - - - +
298A ASP 2.8 10.8 + - - +
299A MET* 3.2 13.6 + - - +
301A LEU* 1.3 75.8 - - - +
303A ASN* 1.3 60.0 + - - +
306A GLU* 2.8 66.4 + - + +
385A TYR* 3.4 42.3 - - + +
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Residues in contact with ASN 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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202A LEU* 3.4 18.2 - - - +
204A LEU* 4.1 7.4 - - + -
262A SER* 2.7 31.2 + - - +
265A GLU 2.8 21.0 + - - +
266A LEU* 3.6 10.6 - - - +
267A LEU* 2.9 45.8 + - + +
268A ILE 4.8 0.3 + - - -
271A PHE* 5.7 0.9 - - - -
278A PHE* 5.6 1.0 - - - -
299A MET* 2.8 20.7 + - - +
300A MET 3.6 4.7 - - - +
302A ARG* 1.3 76.7 - - - +
304A ALA* 1.3 60.5 + - - +
306A GLU* 4.8 5.7 + - - +
307A ARG* 5.4 4.0 + - - +
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Residues in contact with ALA 304 (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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202A LEU* 4.6 1.7 - - - +
204A LEU* 3.9 7.4 - - + +
278A PHE* 5.8 1.9 - - - -
281A CYS* 3.3 35.8 - - - +
283A CYS* 5.7 0.4 - - + -
300A MET* 2.8 19.1 + - + +
301A LEU 3.7 4.7 - - - +
302A ARG 3.1 0.2 - - - -
303A ASN* 1.3 79.6 - - - +
305A CYS* 1.3 59.3 + - - +
307A ARG 5.3 0.6 + - - -
308A LEU* 3.7 10.7 + - - +
314A PHE* 3.6 35.4 - - + -
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Residues in contact with CYS 305 (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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301A LEU* 2.7 30.9 + - - +
304A ALA* 1.3 77.6 - - - +
306A GLU* 1.3 61.4 + - - +
307A ARG 3.3 2.7 - - - -
308A LEU* 3.3 10.2 + - - +
314A PHE* 3.8 29.2 - - - -
382A ALA* 5.6 0.2 - - - -
385A TYR* 3.8 21.8 - - + -
387A MET* 3.7 30.7 - - - -
474A LYS* 2.8 27.6 + - - -
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Residues in contact with GLU 306 (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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266A LEU* 3.5 9.0 - - - +
268A ILE* 3.3 33.9 - - + +
302A ARG* 2.8 62.7 + - + +
303A ASN* 4.9 4.5 - - - +
304A ALA 3.9 0.2 - - - -
305A CYS* 1.3 74.2 - - - +
307A ARG* 1.3 79.7 + - + +
308A LEU 3.3 3.0 + - - +
385A TYR* 5.0 9.0 - - + -
474A LYS* 4.2 9.1 + - - +
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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