Contacts of the helix formed by residues 306 - 331 (chain B) in PDB entry 5MDH
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 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ILE 5.1 0.7 - - - +
305B ASN* 1.3 70.7 - - - +
307B PHE* 1.3 67.6 + - - +
309B ARG* 2.8 19.4 + - - +
310B GLU* 3.3 14.3 + - - +
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 3.7 34.1 - + - -
195B ASN* 5.5 0.9 - - - -
209B TYR* 4.9 6.1 - - - -
218B LEU 5.4 0.2 - - - -
219B LYS* 3.6 64.2 - - + +
223B ILE* 3.9 12.6 - - + -
305B ASN* 3.4 10.9 - - - +
306B ASP* 1.3 76.1 - - - +
308B SER* 1.3 56.4 + - - +
310B GLU* 2.6 37.4 - - - +
311B LYS* 3.7 33.3 - - + +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 2.8 29.6 + - - -
193B ASP* 3.9 1.6 + - - -
195B ASN* 3.1 9.7 + - - -
196B HIS* 6.0 1.3 - - - -
304B ILE* 3.9 5.6 - - - -
305B ASN* 2.6 32.1 + - - +
307B PHE* 1.3 77.4 - - - +
309B ARG* 1.3 59.7 + - - +
311B LYS* 3.5 2.3 - - - +
312B MET* 3.0 53.1 + - - +
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Residues in contact with ARG 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TYR* 2.5 36.9 + - - +
278B GLY* 3.8 12.1 + - - -
279B VAL* 4.9 1.8 - - - +
304B ILE* 3.9 28.1 - - + +
305B ASN 3.0 11.2 + - - +
306B ASP* 2.8 16.0 + - - +
308B SER* 1.3 76.6 - - - +
310B GLU* 1.3 56.1 + - + +
312B MET* 4.0 18.5 - - - +
313B ASP* 2.6 87.1 + - - +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASP 3.3 9.6 + - - +
307B PHE* 2.6 26.1 - - - +
309B ARG* 1.3 73.1 - - - +
311B LYS* 1.3 100.8 + - - +
313B ASP* 4.3 7.6 - - + -
314B LEU* 3.9 14.2 - - + +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR 4.4 5.1 - - - +
190B GLN 5.7 0.4 - - - +
191B TYR* 3.4 38.6 - - + -
223B ILE* 5.0 5.4 - - + -
307B PHE* 3.7 37.5 - - + +
308B SER 3.5 8.7 - - - +
309B ARG 3.3 1.0 + - - -
310B GLU* 1.3 103.5 + - - +
312B MET* 1.3 55.5 + - - +
313B ASP 3.2 2.6 - - - +
314B LEU* 3.5 26.9 - - - +
315B THR* 2.7 39.6 + - - -
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TRP* 3.2 52.3 - - + +
191B TYR* 3.9 12.1 - - + -
193B ASP* 4.6 1.3 - - - +
196B HIS* 5.8 0.2 - - + -
277B TYR* 5.2 2.0 - - - +
279B VAL* 4.9 4.3 - - + +
285B TYR* 2.9 28.2 + - - +
304B ILE* 3.3 38.1 - - + -
308B SER* 3.0 34.7 + - - +
309B ARG* 4.0 19.7 - - - +
311B LYS* 1.3 80.2 - - - +
313B ASP* 1.3 56.9 + - - +
315B THR* 3.5 2.8 + - - -
316B ALA* 3.1 22.7 + - - +
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLY 4.1 7.3 - - - +
279B VAL* 5.7 0.3 - - - +
309B ARG* 2.6 67.3 + - - +
310B GLU* 4.3 5.7 - - + -
312B MET* 1.3 75.3 - - - +
314B LEU* 1.3 63.7 + - + +
316B ALA* 3.1 9.6 + - - +
317B LYS* 3.0 23.6 + - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 4.7 12.9 + - + +
310B GLU* 3.9 17.5 - - + +
311B LYS* 3.4 44.4 + - - +
313B ASP* 1.3 78.9 - - + +
315B THR* 1.4 62.5 + - - +
317B LYS* 3.3 25.9 + - + +
318B GLU* 3.4 12.8 + - - +
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Residues in contact with THR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TRP 3.6 10.9 + - - -
184B GLY* 3.9 9.9 - - - -
185B ASN* 3.3 30.3 - - + +
189B THR* 3.0 44.1 + - - +
190B GLN* 3.8 2.9 - - - +
191B TYR* 4.3 1.7 + - - +
285B TYR* 4.0 2.2 + - - -
311B LYS 2.7 32.7 + - - -
312B MET* 3.7 7.8 + - - -
314B LEU* 1.4 70.9 - - - +
316B ALA* 1.3 62.5 + - - +
317B LYS 3.5 0.2 + - - -
318B GLU* 3.5 3.5 + - - +
319B LEU* 3.1 23.6 + - - +
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B VAL* 4.9 2.2 - - + -
280B PRO* 4.2 25.6 - - + +
283B LEU* 4.2 4.7 - - + +
285B TYR* 3.9 16.1 - - + -
312B MET 3.1 16.2 + - - +
313B ASP* 3.2 14.6 - - - +
315B THR* 1.3 75.1 - - - +
317B LYS* 1.3 60.5 + - - +
319B LEU* 3.3 6.5 + - - +
320B ALA* 2.8 29.9 + - - +
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Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP 3.0 12.0 + - - +
314B LEU* 3.7 21.9 - - + +
315B THR 3.3 0.4 - - - -
316B ALA* 1.3 74.0 - - - +
318B GLU* 1.3 54.9 + - - +
320B ALA* 2.7 30.3 + - - +
321B GLU* 3.0 36.2 + - + +
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LYS* 3.7 23.4 + - + +
185B ASN* 2.5 31.3 + - - -
187B SER* 2.8 14.9 + - - -
188B SER* 5.1 1.4 + - - -
189B THR* 2.9 34.4 + - + +
314B LEU 3.4 7.4 + - - +
315B THR 3.6 7.6 - - - +
316B ALA 3.4 0.2 - - - -
317B LYS* 1.3 78.3 - - - +
319B LEU* 1.3 55.6 + - - +
321B GLU* 3.2 17.5 - - - +
322B GLU* 2.9 42.9 + - + +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 3.6 19.1 - - + -
134B THR* 4.9 4.9 + - - +
184B GLY 3.8 3.8 - - - +
185B ASN* 3.7 36.1 - - + +
283B LEU* 4.1 16.3 - - + +
284B LEU 3.3 28.0 - - - +
285B TYR* 3.5 31.4 - - + -
315B THR 3.1 12.6 + - - +
316B ALA 3.6 5.2 - - - +
317B LYS 3.3 0.2 - - - -
318B GLU* 1.3 78.7 - - - +
320B ALA* 1.4 61.0 + - - +
322B GLU* 4.0 10.8 - - - +
323B LYS* 3.1 22.9 + - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B PRO* 5.8 5.2 - - + -
283B LEU* 4.6 11.9 - - + +
316B ALA 2.8 12.0 + - - +
317B LYS* 2.7 19.8 + - - +
319B LEU* 1.4 71.8 - - - +
321B GLU* 1.3 54.6 + - + +
323B LYS* 3.1 10.1 - - - +
324B GLU* 2.9 37.4 + - - +
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Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LYS* 3.3 43.4 + - + +
318B GLU* 3.2 19.7 - - + +
320B ALA* 1.3 72.8 - - + +
322B GLU* 1.3 65.6 + - + +
324B GLU* 3.1 21.5 + - - +
325B THR* 2.9 26.6 + - - -
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LYS* 3.2 33.9 + - - +
101B LEU* 3.6 22.0 - - + +
131B PRO* 4.1 10.1 - - - +
134B THR* 2.5 36.8 + - - +
185B ASN* 3.4 29.0 + - - +
318B GLU* 2.9 22.1 + - + +
319B LEU* 4.1 6.7 - - - +
321B GLU* 1.3 76.1 - - + +
323B LYS* 1.3 57.0 + - - +
325B THR* 4.5 4.3 - - - -
326B ALA* 2.8 34.5 + - - +
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 4.6 4.6 - - - +
137B LEU* 3.5 15.9 - - + -
141B LYS* 4.4 0.4 - - - +
281B ASP 4.3 3.2 + - - -
282B ASP* 2.8 52.9 + - - +
283B LEU* 4.0 11.7 - - + +
319B LEU 3.1 14.6 + - - +
320B ALA* 3.1 11.4 - - - +
322B GLU* 1.3 73.0 - - - +
324B GLU* 1.3 70.5 + - - +
326B ALA* 4.7 2.7 - - - -
327B PHE* 3.1 62.1 + - + -
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Residues in contact with GLU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ALA* 2.9 25.0 + - - +
321B GLU* 3.1 22.4 + - - +
323B LYS* 1.3 81.2 - - + +
325B THR* 1.3 64.2 + - - +
327B PHE* 3.1 10.8 + - - +
328B GLU* 3.2 17.6 + - - +
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Residues in contact with THR 325 (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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101B LEU* 3.7 23.1 - - + -
102B LYS* 4.1 25.0 - - + +
321B GLU 2.9 15.6 + - - -
322B GLU* 3.9 4.0 - - - -
324B GLU* 1.3 77.5 - - - +
326B ALA* 1.3 62.9 + - - +
328B GLU* 4.0 7.0 + - - +
329B PHE* 3.6 19.2 + - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.1 27.6 - - + -
102B LYS* 6.0 0.2 - - - +
105B VAL* 4.0 16.6 - - + +
134B THR* 3.7 16.8 - - + -
138B THR* 4.7 0.2 - - - +
322B GLU 2.8 17.2 + - - +
323B LYS 4.0 2.0 - - - +
325B THR* 1.3 73.9 - - - +
327B PHE* 1.3 66.9 + - + +
329B PHE* 3.5 5.3 - - - +
330B LEU* 3.2 30.4 + - - +
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 5.4 0.7 - - + -
137B LEU* 3.2 28.0 - - + -
138B THR* 4.3 20.9 - - + -
141B LYS* 3.3 27.6 - - + -
323B LYS* 3.1 50.9 + - + +
324B GLU* 3.9 2.7 - - - +
326B ALA* 1.3 81.2 - - + +
328B GLU* 1.3 54.4 + - - +
330B LEU* 4.0 10.4 - - + +
331B SER* 2.5 39.0 + - - -
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Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLU 3.2 14.9 + - - +
325B THR* 4.4 7.4 - - - +
327B PHE* 1.3 74.4 - - - +
329B PHE* 1.3 58.5 + - - +
331B SER* 3.1 6.0 + - - +
332B SER* 2.7 45.3 + - - +
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 3.5 44.2 - - + -
105B VAL* 4.6 4.0 - - + -
106B LYS* 4.8 12.1 - - + -
325B THR 3.6 12.1 + - - +
326B ALA* 3.5 9.6 + - - +
328B GLU* 1.3 76.0 - - - +
330B LEU* 1.3 76.8 + - + +
332B SER* 2.7 34.8 + - - -
333B ALA 3.3 4.7 + - - +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.3 37.5 - - + -
106B LYS* 4.0 26.1 + - + +
109B LYS* 4.2 35.8 - - + -
138B THR* 3.4 28.0 - - + +
326B ALA 3.2 11.2 + - - +
327B PHE* 4.2 10.5 - - + +
329B PHE* 1.3 92.0 - - + +
331B SER* 1.3 57.6 + - - +
333B ALA* 4.1 8.2 + - - +
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B PHE 2.5 24.7 + - - -
328B GLU* 3.1 9.0 + - - -
330B LEU* 1.3 73.8 - - - +
332B SER* 1.3 71.7 + - - +
333B ALA* 3.3 5.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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