Contacts of the helix formed by residues 299 - 320 (chain B) in PDB entry 5M4G
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 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B GLY* 5.9 4.9 - - - -
295B ASN* 6.1 2.7 - - - +
297B LYS 4.6 4.0 - - - +
298B PHE* 1.3 77.0 - - - +
300B ALA* 1.3 59.5 + - - +
301B ASP* 3.6 6.7 + - - +
302B GLN* 3.0 41.7 + - - +
303B LYS* 2.8 28.1 + - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B THR* 1.3 74.3 - - - +
301B ASP* 1.3 65.9 + - - +
303B LYS* 3.4 9.5 + - - +
304B ALA* 3.0 24.1 + - - +
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B THR* 3.3 6.5 + - - +
300B ALA* 1.3 81.8 - - - +
302B GLN* 1.3 63.5 + - + +
304B ALA* 3.4 4.8 + - - +
305B VAL* 3.1 29.1 + - - +
344B MET* 5.3 0.5 - - - +
442B ARG* 2.9 51.2 + - - +
443B PHE* 3.5 27.5 - - + -
446B PHE* 4.3 6.1 - - + -
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Residues in contact with GLN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLY* 2.8 33.5 + - - -
271B ASP 4.0 2.2 + - - -
272B MET* 3.4 41.0 - - + +
293B PRO* 3.8 6.2 - - - +
297B LYS 3.8 4.3 - - - +
298B PHE* 3.6 14.8 - - + -
299B THR* 3.0 42.1 + - - +
301B ASP* 1.3 76.1 - - + +
303B LYS* 1.3 58.7 + - - +
305B VAL* 4.0 0.9 - - - +
306B TYR* 2.9 32.6 + - - +
446B PHE* 3.8 17.1 - - + -
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B PHE* 3.8 18.5 - - + -
299B THR 2.8 17.6 + - - +
300B ALA* 3.6 9.2 - - - +
302B GLN* 1.3 77.0 - - - +
304B ALA* 1.3 57.9 + - - +
306B TYR* 4.5 0.9 - - - -
307B GLU* 2.8 76.6 + - + +
472B VAL* 4.2 19.4 - - + +
473B GLU* 5.0 3.4 + - - -
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ALA 3.0 17.6 + - - +
301B ASP* 3.8 2.0 - - - +
303B LYS* 1.3 78.9 - - - +
305B VAL* 1.3 62.8 + - - +
307B GLU* 4.0 3.9 - - - +
308B ALA* 3.2 21.8 + - - +
340B GLU* 5.6 0.3 - - - +
344B MET* 3.7 36.4 - - + +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP 3.1 13.4 + - - +
302B GLN 4.1 0.2 - - - +
304B ALA* 1.3 75.5 - - - +
306B TYR* 1.3 66.0 + - - +
308B ALA* 3.1 16.1 + - - +
309B VAL* 3.3 12.0 + - - +
341B LEU* 5.4 0.7 - - + -
344B MET* 3.8 13.9 - - + -
415B ILE* 4.1 27.1 - - + +
417B PHE* 4.1 10.3 - - + -
443B PHE* 3.7 25.8 - - + -
446B PHE* 3.8 24.0 - - + -
449B VAL* 4.0 21.1 - - + -
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Residues in contact with TYR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B MET* 4.8 0.7 - - + -
291B SER* 3.4 30.1 + - - -
298B PHE* 3.7 18.2 - + + -
302B GLN 2.9 19.1 + - - +
303B LYS 3.9 2.2 - - - +
305B VAL* 1.3 77.7 - - - +
307B GLU* 1.3 62.5 + - + +
309B VAL* 3.1 6.2 + - - +
310B LEU* 2.9 31.7 + - + -
449B VAL* 3.7 26.2 - - + +
451B ILE* 3.5 34.5 - - + +
470B ARG* 2.6 41.5 + - - -
472B VAL* 4.2 17.9 - - + -
475B ILE* 3.2 17.2 - - + +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B LYS* 2.8 64.1 + - - +
304B ALA* 4.2 3.6 - - - +
306B TYR* 1.3 75.3 - - + +
308B ALA* 1.3 56.9 + - - +
310B LEU* 3.6 16.0 - - + +
311B ARG* 2.9 28.2 + - - +
340B GLU* 6.2 0.2 - - - -
472B VAL* 3.7 22.6 + - + +
473B GLU* 4.7 4.2 - - - +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ALA 3.2 13.3 + - - +
305B VAL* 3.1 12.2 + - - +
307B GLU* 1.3 77.9 - - - +
309B VAL* 1.3 62.1 + - - +
311B ARG* 3.3 4.0 + - - +
312B SER* 3.1 21.7 + - - -
336B ILE* 4.2 2.9 - - - +
337B HIS* 4.0 6.1 - - + -
340B GLU* 3.5 37.5 - - + -
341B LEU* 5.9 0.4 - - + -
344B MET* 5.6 2.5 - - - -
415B ILE* 3.8 18.4 - - + -
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B VAL 3.6 12.3 - - - +
306B TYR 3.1 6.1 + - - +
308B ALA* 1.3 72.8 - - - +
310B LEU* 1.3 61.4 + - - +
312B SER* 3.1 7.4 + - - -
313B SER* 2.9 27.9 + - - -
337B HIS* 4.3 1.3 - - - +
413B PRO* 3.3 36.1 - - + +
414B GLY* 4.0 1.6 - - - -
415B ILE* 3.7 37.2 - - + +
449B VAL* 3.8 18.2 - - + -
451B ILE* 3.9 20.6 - - + +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B TYR* 2.9 18.6 + - + +
307B GLU* 3.7 20.2 - - + +
308B ALA 3.3 0.2 - - - -
309B VAL* 1.3 75.6 - - - +
311B ARG* 1.3 63.3 - - - +
313B SER* 3.4 3.7 + - - -
314B ARG* 3.0 70.6 + - - +
451B ILE* 3.5 18.5 - - + +
470B ARG* 3.9 33.2 - - + +
471B THR* 4.2 17.9 - - + -
472B VAL 5.3 0.4 - - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B GLU 2.9 18.0 + - - +
308B ALA* 3.6 6.7 - - - +
309B VAL 3.2 0.2 - - - -
310B LEU* 1.3 78.2 - - - +
312B SER* 1.3 55.8 + - - +
314B ARG* 3.4 4.3 + - - +
315B ALA* 2.9 28.5 + - + +
336B ILE* 3.8 30.9 - - + +
339B GLU* 3.0 31.7 + - - +
340B GLU* 2.5 46.0 + - - +
343B HIS* 5.2 1.0 + - - -
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ALA 3.1 5.1 + - - -
309B VAL 3.1 8.8 + - - -
311B ARG* 1.3 74.0 - - - +
313B SER* 1.3 67.8 + - - +
315B ALA* 3.2 0.5 + - - +
316B VAL* 2.9 29.7 + - - +
333B ALA* 4.1 17.5 - - - -
336B ILE* 3.8 19.7 - - - +
337B HIS* 2.8 39.5 + - - -
413B PRO* 3.3 9.5 - - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B VAL 2.9 18.8 + - - -
310B LEU* 3.5 9.6 - - - +
312B SER* 1.3 77.6 + - - +
314B ARG* 1.3 61.1 + - - +
316B VAL* 3.4 1.9 + - - +
317B MET* 2.9 47.8 + - - +
411B VAL* 4.4 5.7 - - - +
413B PRO* 3.8 19.5 - - - -
451B ILE* 4.1 20.8 + - - +
453B GLU* 4.3 7.3 + - - +
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Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B LEU* 3.0 54.6 + - + +
311B ARG* 4.1 4.3 - - - +
313B SER* 1.3 76.5 + - - +
315B ALA* 1.3 60.4 + - - +
317B MET* 3.8 23.9 - - + +
318B GLY* 2.9 25.6 + - - -
453B GLU* 4.6 2.2 + - - -
470B ARG* 4.1 18.2 - - - +
471B THR* 4.3 19.0 - - - +
474B GLU* 5.1 2.6 + - - -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ARG* 2.9 14.9 + - + +
312B SER 3.2 1.1 + - - +
314B ARG* 1.3 78.1 - - - +
316B VAL* 1.3 61.5 + - - +
318B GLY* 3.3 3.1 + - - -
319B ALA* 3.1 24.1 + - - +
332B LEU* 4.1 10.0 - - + +
336B ILE* 3.3 34.5 - - + -
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B SER 2.9 19.8 + - - +
313B SER* 3.9 2.9 - - - +
315B ALA* 1.3 76.9 - - - +
317B MET* 1.3 64.2 + - - +
319B ALA* 3.1 2.3 + - - +
320B MET* 3.0 49.2 + - + +
326B TRP* 4.3 0.7 - - + -
329B MET* 3.7 31.2 - - + +
332B LEU* 4.3 14.8 - - + -
333B ALA* 4.3 12.3 - - + +
368B LEU* 3.9 21.8 - - + -
411B VAL* 3.9 17.3 - - + -
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Residues in contact with MET 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B SER* 2.9 38.4 + - - +
314B ARG* 4.0 22.2 - - + +
316B VAL* 1.3 77.9 - - - +
318B GLY* 1.3 60.8 + - - +
319B ALA 3.4 0.2 + - - -
320B MET* 3.7 11.6 + - - +
411B VAL* 4.3 18.6 - - + -
453B GLU* 4.0 30.1 - - - +
455B VAL* 4.2 4.0 - - - -
462B ILE* 3.7 42.6 - - + +
464B LEU* 4.2 20.0 - - + -
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Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ARG 2.9 17.6 + - - -
315B ALA* 3.7 2.7 - - - -
316B VAL 3.2 0.2 - - - -
317B MET* 1.3 76.3 - - - +
319B ALA* 1.3 57.5 + - - +
320B MET 4.8 1.7 - - - +
321B LYS* 5.1 5.7 - - - -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ALA 3.1 14.5 + - - +
316B VAL 3.1 1.6 + - - -
318B GLY* 1.3 78.5 - - - +
320B MET* 1.3 63.9 + - - +
321B LYS* 3.4 13.7 + - - +
324B VAL* 3.5 14.6 - - - +
329B MET* 3.7 27.6 - - + -
332B LEU* 4.3 7.2 - - + -
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Residues in contact with MET 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B VAL* 3.0 28.1 + - + +
317B MET* 3.7 10.8 + - - +
318B GLY 3.6 2.4 - - - +
319B ALA* 1.3 78.1 - - - +
321B LYS* 1.3 63.5 + - - +
324B VAL* 4.6 2.7 - - - -
326B TRP* 3.6 27.4 - - + -
329B MET* 4.2 5.6 - - - -
403B LEU* 3.9 23.1 - - + -
409B LEU* 4.4 9.4 - - + -
411B VAL* 3.7 23.3 - - + -
455B VAL* 3.7 24.5 - - + -
457B VAL* 4.6 4.7 - - + -
461B GLY* 3.3 17.8 - - - -
462B ILE* 3.6 21.7 + - + +
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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