Contacts of the helix formed by residues 286 - 307 (chain A) in PDB entry 4WTM
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 THR 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLU* 4.4 0.2 + - - -
175A LEU* 4.1 16.6 - - + -
240A TYR* 3.4 26.7 - - + +
261A TYR* 3.4 38.8 - - + +
280A ARG* 4.5 7.7 + - - -
284A VAL* 3.6 10.5 - - - +
285A LEU* 1.3 77.0 - - + +
287A THR* 1.3 56.5 + - - +
288A SER 3.4 1.8 - - - -
289A MET* 3.6 23.3 - - + -
290A GLY* 2.7 33.9 + - - -
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Residues in contact with THR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ARG* 3.9 11.6 + - - +
281A ALA 3.2 9.4 + - - -
282A SER* 4.1 5.8 - - - -
283A GLY 3.1 15.6 + - - -
284A VAL* 2.7 21.9 + - - +
285A LEU 3.2 1.2 - - - -
286A THR* 1.3 76.1 + - - +
288A SER* 1.3 59.5 + - - +
291A ASN* 3.0 50.3 + - - +
605A UDP 3.3 31.4 - - - +
3T G 3.8 17.0 - - + +
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE* 4.9 14.4 - - - -
285A LEU 4.5 2.8 + - - -
286A THR 3.4 0.4 - - - -
287A THR* 1.3 74.2 - - - +
289A MET* 1.3 61.9 + - - +
291A ASN* 3.9 4.0 - - - +
292A THR* 2.8 37.1 + - - -
317A GLY* 6.0 0.9 - - - -
2P C 4.1 2.6 + - - -
3T G 2.8 28.3 + - - +
4T G 3.2 39.9 + - - -
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Residues in contact with MET 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.6 3.8 - - + -
178A ILE* 3.6 30.7 - - + +
179A THR* 3.7 35.2 - - + -
182A LEU* 4.1 6.3 - - - -
183A PRO* 3.9 17.0 - - + -
191A TYR* 6.5 0.2 - - - -
240A TYR* 3.3 34.8 - - + +
285A LEU 5.1 1.0 + - - -
286A THR* 3.5 22.5 + - + +
288A SER* 1.3 78.0 - - - +
290A GLY* 1.3 54.1 + - - +
292A THR* 3.2 4.1 + - - -
293A ILE* 2.9 52.0 + - + +
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Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLU* 3.2 21.6 - - - +
240A TYR* 4.1 8.7 + - - -
280A ARG* 3.1 15.7 - - - -
286A THR 2.7 22.6 + - - -
289A MET* 1.3 70.1 - - - +
291A ASN* 1.3 57.2 + - - +
293A ILE* 4.8 2.0 - - - -
294A THR* 2.8 29.1 + - - -
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Residues in contact with ASN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 3.1 29.3 - - + -
280A ARG* 2.8 27.2 + - - +
287A THR* 3.0 26.0 + - - +
288A SER* 3.9 4.6 - - - +
290A GLY* 1.3 73.7 - - - +
292A THR* 1.3 58.6 + - - +
295A CYS* 2.8 33.4 + - - +
317A GLY* 4.2 15.3 - - - -
318A ASP 4.7 0.4 - - - +
605A UDP 3.0 46.1 + - - -
2P C 4.7 1.8 + - - -
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PRO* 5.5 1.8 - - + -
187A MET* 3.7 27.1 - - + +
191A TYR* 4.1 20.9 - - + -
193A PHE* 3.9 9.2 - - - -
288A SER 2.8 22.8 + - - -
289A MET* 3.7 4.5 - - - -
291A ASN* 1.3 78.1 - - - +
293A ILE* 1.3 58.2 + - + +
295A CYS* 3.8 1.6 - - - +
296A TYR* 3.0 27.0 + - - +
315A VAL* 4.0 10.1 - - + +
316A CYS* 4.8 0.2 - - - -
317A GLY* 2.9 32.1 + - - +
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Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 5.0 6.3 - - + -
182A LEU* 3.8 28.7 - - + -
183A PRO* 4.6 8.5 - - + -
186A VAL* 4.3 17.5 - - + -
187A MET* 4.8 6.3 - - - -
236A GLU* 5.4 3.8 - - + -
239A ILE* 3.8 33.0 - - + -
240A TYR* 4.9 5.8 - - + -
289A MET* 2.9 41.3 + - + +
290A GLY* 4.1 3.4 - - - +
292A THR* 1.3 75.2 - - - +
294A THR* 1.3 68.0 + - - +
296A TYR* 3.2 6.4 + - + +
297A VAL* 3.0 28.5 + - + +
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 4.3 13.0 - - + -
228A VAL* 5.0 3.6 - - + -
232A ASP* 4.3 15.5 + - + +
236A GLU* 2.4 36.4 + - - +
290A GLY 2.8 16.9 + - - -
291A ASN 4.2 1.1 - - - -
293A ILE* 1.3 70.3 - - - +
295A CYS* 1.3 66.4 + - - +
297A VAL* 3.3 6.3 + - + +
298A LYS* 3.1 52.9 + - + +
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Residues in contact with CYS 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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221A THR* 5.8 1.6 - - - -
224A PHE* 4.1 12.0 - - + -
291A ASN 2.8 20.5 + - - +
292A THR 3.8 2.5 - - - +
294A THR* 1.3 77.6 - - - +
296A TYR* 1.3 56.7 + - - +
298A LYS* 3.9 4.4 - - - +
299A ALA* 2.9 32.8 + - - +
315A VAL* 3.8 9.0 - - - -
317A GLY 3.3 20.6 - - - +
318A ASP* 3.9 17.3 - - - -
320A LEU* 3.4 30.3 - - - -
343A MET* 4.8 6.6 - - - +
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.7 26.9 - - + -
186A VAL* 3.7 26.4 + - + -
187A MET* 3.6 39.2 + - + -
190A SER* 4.2 21.0 + - - -
292A THR 3.0 20.4 + - - +
293A ILE* 3.5 6.7 - - + +
294A THR 3.2 0.4 - - - -
295A CYS* 1.3 75.2 - - - +
297A VAL* 1.3 59.6 + - - +
299A ALA* 4.4 4.0 - - - -
300A LEU* 3.0 50.8 + - + +
313A MET* 4.1 17.5 - - + -
315A VAL* 4.0 14.8 - - + +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.5 37.0 - - + +
67A VAL* 3.9 16.3 - - + +
68A LEU* 4.6 14.1 - - + +
71A ILE* 3.2 29.2 - - + -
235A THR* 6.2 0.4 - - + -
239A ILE* 4.7 7.9 - - + -
293A ILE* 3.0 30.4 + - + +
294A THR* 3.8 6.3 - - - +
296A TYR* 1.3 74.3 - - - +
298A LYS* 1.3 67.5 + - + +
301A ALA* 3.1 24.8 + - - +
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Residues in contact with LYS 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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58A GLN* 4.0 1.3 - - - +
64A TYR* 4.3 12.6 - - + -
224A PHE* 5.6 4.2 - - + -
227A THR* 4.4 2.6 + - - -
228A VAL* 5.0 2.6 - - - +
232A ASP* 2.9 37.5 + - - -
294A THR* 3.1 31.1 + - + +
295A CYS* 4.0 4.3 - - - +
297A VAL* 1.3 76.7 - - + +
299A ALA* 1.3 56.7 + - - +
301A ALA* 4.5 0.7 - - - -
302A ALA* 2.8 30.3 + - - +
343A MET* 3.6 15.9 - - + -
346A TYR* 2.9 51.7 + - + +
347A SER* 3.3 15.8 + - - -
348A ALA* 4.0 12.8 - - + +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A CYS 2.9 20.4 + - - +
296A TYR 4.1 0.2 - - - +
298A LYS* 1.3 75.1 - - - +
300A LEU* 1.3 60.0 + - - +
302A ALA 3.3 0.3 + - - -
303A CYS* 2.9 33.3 + - - -
313A MET* 3.7 23.6 - - + -
320A LEU* 3.8 20.4 - - + -
339A PHE* 3.4 11.3 - - + -
343A MET* 3.7 12.5 - - - -
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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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67A VAL* 4.0 26.0 - - + -
71A ILE* 5.6 0.4 - - + -
296A TYR* 3.0 47.2 + - + +
299A ALA* 1.3 73.7 - - - +
301A ALA* 1.3 65.5 + - - +
303A CYS* 3.3 12.5 + - + +
304A LYS* 3.2 33.0 + - + +
311A PRO* 4.8 12.8 - - + -
313A MET* 4.0 21.4 - - + -
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Residues in contact with ALA 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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63A HIS* 3.6 7.8 - - - +
64A TYR* 3.5 35.2 - - + +
67A VAL* 3.7 10.0 - - + +
297A VAL 3.1 19.2 + - - +
298A LYS* 3.5 4.5 - - - +
300A LEU* 1.3 76.8 - - - +
302A ALA* 1.3 58.4 + - - +
304A LYS* 3.1 5.2 + - - +
305A ALA* 2.8 28.1 + - - +
346A TYR* 3.6 13.7 - - + +
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Residues in contact with ALA 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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298A LYS 2.8 18.4 + - - +
299A ALA 3.7 0.4 - - - +
300A LEU 3.3 0.2 - - - -
301A ALA* 1.3 76.1 - - - +
303A CYS* 1.3 55.7 + - - +
305A ALA* 3.6 1.6 - - - +
306A ALA* 2.9 32.1 + - - +
339A PHE* 3.6 33.5 - - + +
342A ALA* 3.9 16.8 - - + -
343A MET* 3.7 21.1 - - + +
346A TYR* 3.7 1.7 - - + -
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Residues in contact with CYS 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 ALA 2.9 22.2 + - - -
300A LEU* 3.5 16.6 - - + +
301A ALA 3.2 0.4 - - - -
302A ALA* 1.3 76.6 - - - +
304A LYS* 1.3 59.6 + - + +
306A ALA 3.5 0.2 + - - -
307A GLY* 3.1 6.6 + - - -
308A ILE* 2.9 57.1 + - + +
311A PRO* 4.5 11.9 - - + -
313A MET* 4.7 5.6 - - - -
322A VAL* 4.1 26.0 - - - -
339A PHE* 3.6 14.6 - - - -
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A HIS* 3.7 38.1 + - + +
66A SER* 4.6 13.6 + - - -
67A VAL* 3.5 26.7 - - + -
300A LEU* 3.2 22.8 + - + +
301A ALA* 3.1 6.6 + - - +
303A CYS* 1.3 75.0 - - + +
305A ALA* 1.3 66.4 + - - +
306A ALA 3.2 0.7 + - - -
307A GLY* 3.2 11.4 + - - +
308A ILE 5.7 0.7 - - - -
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Residues in contact with ALA 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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61A ASP* 5.0 0.2 - - - +
63A HIS* 3.7 28.0 + - + -
301A ALA 2.8 18.7 + - - +
302A ALA 3.6 4.7 - - - +
304A LYS* 1.3 73.3 - - - +
306A ALA* 1.3 58.4 + - - +
307A GLY 3.6 0.2 + - - -
338A ALA* 4.9 4.2 - - - +
342A ALA* 3.9 23.1 - - + -
345A ARG* 4.6 8.1 - - - +
346A TYR* 4.3 3.8 - - - +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA 2.9 17.9 + - - +
303A CYS 4.1 2.9 - - - +
305A ALA* 1.3 75.9 - - - +
307A GLY* 1.3 58.2 + - - +
308A ILE* 4.3 8.1 - - + -
335A ASN* 3.1 53.8 - - - +
338A ALA* 3.9 10.1 - - - +
339A PHE* 3.5 18.4 - - + +
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Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A CYS 3.1 4.9 + - - -
304A LYS* 3.2 10.1 + - - -
305A ALA 3.4 0.8 + - - -
306A ALA* 1.3 80.0 - - - +
308A ILE* 1.3 67.5 + - - +
309A VAL* 3.2 15.9 + - - +
327A GLN* 5.0 0.3 - - - +
331A GLU* 4.9 2.1 - - - +
335A ASN* 4.0 11.6 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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