Contacts of the helix formed by residues 305 - 330 (chain A) in PDB entry 4MDH
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 ASN 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ASN* 3.8 28.1 + - - +
303A PRO 4.0 6.2 - - - +
304A ILE* 1.3 69.7 - - - +
306A ASP* 1.3 66.8 + - - +
307A PHE* 3.5 9.5 - - + +
308A SER* 2.8 22.6 + - - +
309A ARG* 2.8 31.7 + - - +
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASN* 1.3 76.7 - - - +
307A PHE* 1.4 54.8 + - - +
309A ARG* 2.8 47.1 + - - +
310A GLU* 2.9 19.6 + - - +
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 3.4 27.8 - + - -
195A ASN* 5.8 0.2 - - - -
209A TYR* 5.3 2.9 - - - -
218A LEU 5.4 0.4 - - - -
219A LYS* 3.2 63.3 - - + -
223A ILE* 4.2 2.5 - - + -
305A ASN* 4.1 7.1 - - + +
306A ASP* 1.4 76.2 - - - +
308A SER* 1.3 64.0 + - - +
310A GLU* 3.2 20.2 - - + +
311A LYS* 3.0 47.2 + - - +
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 3.6 32.4 + - - -
193A ASP* 4.2 6.5 - - - -
195A ASN* 3.8 6.1 + - - -
304A ILE* 4.4 7.9 - - - -
305A ASN* 2.8 35.0 + - - -
306A ASP 3.1 0.4 - - - -
307A PHE* 1.3 77.3 - - - +
309A ARG* 1.3 65.8 + - - +
311A LYS* 3.3 2.1 + - - +
312A MET* 3.0 32.5 + - - +
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Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 3.0 38.7 + - + +
305A ASN* 2.8 21.4 + - - +
306A ASP* 2.8 34.5 + - - +
308A SER* 1.3 70.2 - - - +
310A GLU* 1.3 53.7 - - - +
312A MET* 2.9 9.1 + - - +
313A ASP* 2.6 45.2 + - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASP 2.9 9.4 + - - +
307A PHE* 3.2 17.8 - - - +
309A ARG* 1.3 80.7 - - - +
311A LYS* 1.3 62.1 + - + +
313A ASP* 3.4 5.2 + - - +
314A LEU* 3.0 41.8 + - - +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A THR 4.4 3.5 - - - +
190A GLN 5.4 2.0 - - - +
191A TYR* 3.5 41.1 - - + +
219A LYS 3.7 5.7 + - - -
223A ILE* 2.9 37.1 - - + +
307A PHE* 3.0 49.9 + - - +
308A SER 3.3 1.0 + - - +
309A ARG 3.2 0.6 - - - -
310A GLU* 1.3 82.5 - - + +
312A MET* 1.3 65.3 + - - +
314A LEU* 3.4 11.9 + - + +
315A THR* 3.3 24.1 + - - +
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TRP* 3.6 57.0 - - + -
191A TYR* 4.1 5.4 - - + -
277A TYR* 4.1 23.3 - - + +
279A VAL* 4.6 9.5 - - + +
285A TYR* 2.7 28.3 + - - +
304A ILE* 3.8 30.7 - - + -
308A SER* 3.0 20.2 + - - +
309A ARG* 2.9 8.2 + - - +
311A LYS* 1.3 78.1 - - - +
313A ASP* 1.4 58.3 + - - +
315A THR* 3.3 3.3 - - - +
316A ALA* 3.2 19.9 + - - +
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Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLY 4.2 14.9 - - - +
279A VAL* 5.7 2.3 - - - +
280A PRO* 5.5 2.6 - - - +
309A ARG* 2.6 26.8 + - - +
310A GLU* 4.0 4.8 - - - +
312A MET* 1.4 72.1 - - - +
314A LEU* 1.3 65.8 + - - +
315A THR 3.2 0.6 + - - -
316A ALA* 3.4 7.3 + - - +
317A LYS* 3.4 23.7 + - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A THR* 4.8 12.6 + - + +
310A GLU* 3.0 29.0 + - - +
311A LYS* 3.5 12.8 - - + +
313A ASP* 1.3 78.9 - - - +
315A THR* 1.3 59.9 + - - +
317A LYS* 3.5 25.9 + - + +
318A GLU* 3.5 18.5 + - - +
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TRP* 4.0 3.4 - - + +
184A GLY* 3.2 25.6 - - - +
185A ASN* 2.9 22.5 + - - +
189A THR* 2.7 41.8 + - - +
191A TYR* 5.3 0.9 - - + +
285A TYR* 3.2 17.0 - - - +
311A LYS 3.3 8.9 + - - +
312A MET* 3.3 5.6 - - - +
314A LEU* 1.3 76.4 - - - +
316A ALA* 1.3 59.4 + - - +
317A LYS 3.0 4.5 - - - -
318A GLU* 3.4 1.8 + - - +
319A LEU* 2.9 30.1 + - - +
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Residues in contact with ALA 316 (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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279A VAL* 4.0 5.4 - - + -
280A PRO* 4.0 29.1 - - + +
283A LEU* 4.0 7.4 - - + +
285A TYR* 3.5 23.8 - - + -
312A MET 3.2 13.1 + - - +
313A ASP* 3.4 8.9 + - - +
315A THR* 1.3 77.1 - - - +
317A LYS* 1.3 56.9 + - - +
319A LEU* 3.8 8.0 - - - +
320A ALA* 3.2 23.6 + - - +
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Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP 3.4 15.6 + - - +
314A LEU* 3.6 25.8 - - + +
315A THR 3.0 0.4 - - - -
316A ALA* 1.3 77.7 - - - +
318A GLU* 1.3 56.7 + - - +
319A LEU 3.2 0.9 - - - -
320A ALA* 3.3 6.3 + - + +
321A GLU* 2.7 55.3 + - + +
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASN* 2.3 30.8 + - - +
187A SER* 2.4 24.2 + - - -
188A SER* 5.1 1.9 + - - -
189A THR* 3.0 30.0 + - + +
314A LEU 3.5 10.2 + - - +
315A THR 3.4 6.7 + - - +
317A LYS* 1.3 76.5 - - - +
319A LEU* 1.3 59.2 + - - +
321A GLU* 3.1 20.6 + - + +
322A GLU* 2.8 42.3 + - + +
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Residues in contact with LEU 319 (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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133A ASN* 4.7 5.4 - - + +
134A THR* 4.4 4.1 + - - +
184A GLY 4.1 4.9 - - - -
185A ASN* 2.9 48.7 - - + +
283A LEU* 4.1 16.3 - - + +
284A LEU 3.7 21.8 - - - +
285A TYR* 2.9 41.5 - - + -
315A THR 2.9 21.3 + - - +
316A ALA* 3.8 6.7 - - - +
318A GLU* 1.3 76.3 - - - +
320A ALA* 1.3 56.9 + - - +
322A GLU* 3.3 8.8 - - - +
323A LYS* 2.9 26.5 + - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A PRO* 6.3 1.3 - - + -
283A LEU* 4.1 10.7 - - + +
316A ALA 3.2 13.1 + - - +
317A LYS* 3.3 11.4 - - + +
319A LEU* 1.3 76.1 - - - +
321A GLU* 1.3 68.5 + - - +
323A LYS* 3.2 10.6 + - - +
324A GLU* 3.0 31.9 + - + +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LYS* 2.7 39.6 + - + +
318A GLU* 3.1 28.3 + - + +
320A ALA* 1.3 76.2 - - - +
322A GLU* 1.4 59.0 + - + +
324A GLU* 3.0 33.8 + - - +
325A THR* 3.2 11.2 + - - -
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 5.6 10.5 - - + -
131A PRO* 4.1 21.1 - - + +
134A THR* 2.8 32.4 + - + +
185A ASN* 3.1 33.2 + - - +
187A SER* 4.3 2.9 + - - -
318A GLU* 2.8 22.0 + - + +
319A LEU* 3.3 7.4 - - - +
321A GLU* 1.4 74.8 - - + +
323A LYS* 1.3 62.7 + - - +
325A THR* 3.4 9.7 + - - +
326A ALA* 3.1 23.6 + - - +
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Residues in contact with LYS 323 (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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134A THR* 4.4 7.1 + - + +
137A LEU* 3.1 31.0 - - + -
281A ASP 4.7 1.4 + - - -
282A ASP* 2.3 55.5 + - - +
283A LEU* 4.2 12.1 - - + +
319A LEU 2.9 13.8 + - - +
320A ALA* 3.2 11.2 - - - +
322A GLU* 1.3 73.4 - - - +
324A GLU* 1.4 65.1 + - + +
326A ALA* 3.2 6.7 + - - +
327A PHE* 3.1 50.2 + - + +
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Residues in contact with GLU 324 (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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320A ALA* 3.0 27.3 + - + +
321A GLU* 3.1 18.0 - - - +
323A LYS* 1.4 78.7 - - + +
325A THR* 1.3 60.5 + - - +
327A PHE* 4.1 3.0 - - - +
328A GLU* 3.3 27.6 + - - +
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Residues in contact with THR 325 (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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100A LEU* 3.9 24.8 - - + +
102A LYS* 3.9 29.6 - - + -
321A GLU 3.2 13.4 + - - -
322A GLU* 3.5 11.1 - - - -
323A LYS 3.3 0.2 - - - -
324A GLU* 1.3 79.2 - - - +
326A ALA* 1.3 62.1 + - - +
328A GLU* 3.8 4.7 - - - +
329A PHE* 3.2 21.3 + - - +
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Residues in contact with ALA 326 (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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102A LYS* 6.2 1.3 - - - -
105A VAL* 4.0 22.6 - - + +
134A THR* 3.7 22.4 - - + -
138A THR* 4.4 0.2 - - - +
322A GLU 3.1 14.3 + - - +
323A LYS* 3.2 4.4 + - - +
325A THR* 1.3 74.7 - - - +
327A PHE* 1.3 66.5 + - + +
328A GLU 3.0 4.3 - - - -
329A PHE* 3.0 22.7 + - - +
330A LEU* 3.0 18.5 + - - +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 6.1 1.1 - - + -
137A LEU* 4.1 13.2 - - + -
138A THR* 3.9 29.2 - - + -
141A LYS* 3.6 35.7 - - + -
323A LYS* 3.1 41.7 + - + +
324A GLU* 4.1 2.9 - - - +
326A ALA* 1.3 79.0 - - + +
328A GLU* 1.3 57.1 + - - +
330A LEU* 4.1 16.8 - - + -
331A SER* 3.0 23.0 + - - -
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLU* 3.3 19.5 + - - +
325A THR* 3.8 5.8 - - - +
326A ALA 3.0 1.0 - - - -
327A PHE* 1.3 77.4 - - - +
329A PHE* 1.3 63.4 - - - +
330A LEU 3.3 0.4 - - - -
331A SER* 3.5 3.5 + - - -
332A SER* 2.8 31.3 + - - -
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS* 3.4 62.6 - - + -
103A ALA* 5.9 0.4 - - - -
105A VAL* 4.1 14.1 - - + -
106A LYS* 5.3 10.7 - - + -
325A THR 3.2 10.2 + - - +
326A ALA* 3.0 11.8 + - - +
328A GLU* 1.3 81.1 - - - +
330A LEU* 1.3 65.2 + - + +
332A SER* 3.3 21.5 + - - +
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Residues in contact with LEU 330 (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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105A VAL* 3.8 22.9 - - + -
106A LYS* 3.9 44.7 + - + +
109A LYS* 4.1 26.0 + - + +
138A THR* 3.3 34.5 - - + +
326A ALA 3.0 15.2 + - - +
327A PHE* 4.1 18.4 - - + -
329A PHE* 1.3 80.6 - - + +
331A SER* 1.3 61.7 + - - +
332A SER 3.2 5.2 + - - +
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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