Contacts of the helix formed by residues 272 - 294 (chain A) in PDB entry 3D5K
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 ARG 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU* 3.0 20.5 + - + +
270A GLN 3.8 0.2 - - - -
271A ARG* 1.3 78.8 - - - +
273A PRO* 1.4 74.0 - - + +
274A ASP* 2.8 48.6 + - - -
275A ILE* 3.2 18.1 + - + +
276A LEU* 3.0 23.3 + - - +
361A ALA 4.9 1.6 + - - -
364A THR* 5.4 3.6 - - - +
365A ALA* 3.6 25.9 - - - +
368A GLU* 2.4 35.2 + - - -
444A LYS 4.6 3.1 + - - +
445A ALA* 2.8 43.9 + - - +
446A LEU 4.4 1.3 - - - +
447A GLY* 4.2 8.3 - - - +
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Residues in contact with PRO 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLN* 3.5 37.5 - - - +
151A ARG* 4.0 17.5 - - + +
152A SER* 3.6 22.9 - - - +
155A THR* 4.5 3.8 - - + +
271A ARG 3.7 8.5 - - - +
272A ARG* 1.4 90.4 - - + +
274A ASP* 1.3 52.0 + - - +
276A LEU* 3.1 2.5 + - + +
277A GLU* 2.7 36.2 + - - +
444A LYS 5.8 0.4 - - - +
447A GLY* 4.0 19.7 - - - +
450A TRP* 6.0 1.1 - - + -
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Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER* 3.8 19.2 + - - +
272A ARG* 2.8 41.1 + - - -
273A PRO* 1.3 76.5 - - - +
275A ILE* 1.3 68.6 + - - +
277A GLU* 3.8 21.4 - - - +
278A ALA* 3.3 22.9 + - - +
361A ALA* 4.3 9.5 - - - +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 3.8 35.9 - - + +
269A LEU* 4.2 13.2 - - - +
272A ARG* 3.2 14.2 + - + +
274A ASP* 1.3 90.1 + - - +
276A LEU* 1.3 63.8 + - + +
278A ALA* 3.3 2.8 + - - +
279A GLU 3.1 16.3 + - - -
358A TYR* 3.5 26.5 - - + +
361A ALA* 3.9 19.7 - - + +
362A ILE* 4.0 23.8 - - + -
365A ALA* 3.7 25.4 - - + -
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 4.8 4.0 - - - +
148A GLN* 3.4 30.7 - - + +
269A LEU 3.5 24.7 - - - +
270A GLN* 3.4 26.7 - - - +
271A ARG 4.7 2.2 - - - -
272A ARG 3.0 22.6 + - - +
273A PRO* 3.5 6.1 - - + +
275A ILE* 1.3 72.8 - - + +
277A GLU* 1.3 65.4 + - - +
279A GLU* 3.2 18.4 + - + +
280A HIS* 3.2 35.4 + - + -
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA* 3.3 27.4 - - + +
148A GLN* 3.7 16.0 - - + +
149A ALA* 3.5 28.9 - - - +
152A SER* 4.8 1.4 - - - -
273A PRO 2.7 18.8 + - - +
274A ASP* 3.8 22.0 - - - +
276A LEU* 1.3 72.9 - - - +
278A ALA* 1.3 61.1 + - - +
279A GLU 3.4 0.2 + - - -
280A HIS 3.4 1.2 + - - -
281A GLN* 3.2 30.0 + - + +
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Residues in contact with ALA 278 (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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274A ASP 3.3 13.7 + - - +
275A ILE 3.5 9.6 - - - +
276A LEU 3.3 0.2 - - - -
277A GLU* 1.3 79.3 - - - +
279A GLU* 1.3 56.7 + - - +
281A GLN* 3.5 8.6 + - - +
282A LEU* 3.0 27.0 + - - +
354A ASN* 4.7 2.4 - - - +
357A GLN* 4.4 5.4 - - + +
358A TYR* 4.0 30.0 - - + +
361A ALA* 4.3 9.4 - - + -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 2.6 38.9 + - - +
9A ARG* 2.8 40.3 + - - -
269A LEU 6.0 0.2 - - - -
275A ILE 3.1 7.0 + - - +
276A LEU* 3.2 19.8 + - + +
278A ALA* 1.3 76.2 - - - +
280A HIS* 1.3 65.6 + - - +
282A LEU* 3.4 5.4 + - + +
283A MET* 2.9 41.2 + - - +
358A TYR* 3.6 30.0 - - + -
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Residues in contact with HIS 280 (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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141A GLU* 3.3 34.5 - - + +
144A LEU* 3.5 41.5 + - + +
145A ALA* 3.6 10.5 - - + -
148A GLN* 3.8 24.0 - - + +
276A LEU* 3.2 25.2 + - + +
277A GLU 3.4 0.2 + - - -
279A GLU* 1.3 79.3 + - - +
281A GLN* 1.3 60.6 + - - +
283A MET* 4.1 16.5 - - + -
284A ALA* 2.8 29.6 + - - +
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Residues in contact with GLN 281 (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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73A PHE* 6.0 2.6 - - - -
142A GLN* 4.5 25.0 + - - +
145A ALA* 3.5 18.8 - - + +
146A THR* 5.2 2.0 + - - -
277A GLU* 3.2 25.8 + - + +
278A ALA* 3.6 10.8 - - - +
279A GLU 3.3 0.2 - - - -
280A HIS* 1.3 75.2 - - - +
282A LEU* 1.3 61.1 + - - +
284A ALA* 3.4 6.5 + - - +
285A ALA* 3.1 23.0 + - - +
354A ASN* 3.7 20.6 + - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.0 21.1 - - + +
8A GLN 5.4 0.2 - - - +
10A PRO* 4.0 33.9 - - + -
278A ALA 3.0 14.2 + - - +
279A GLU* 3.5 7.4 - - + +
281A GLN* 1.3 73.5 - - - +
283A MET* 1.3 59.4 + - - +
285A ALA* 3.2 2.9 + - - +
286A ASN* 3.0 25.1 + - - +
351A LYS* 3.5 39.9 - - + +
354A ASN* 3.6 14.3 - - + +
355A VAL* 3.6 24.2 - - + +
358A TYR* 4.4 11.7 - - + -
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Residues in contact with MET 283 (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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7A TYR* 3.7 43.1 - - + -
141A GLU* 3.2 40.8 - - + +
279A GLU* 2.9 30.0 + - - +
280A HIS* 3.6 24.2 - - + +
282A LEU* 1.3 76.6 - - - +
284A ALA* 1.3 60.8 + - - +
286A ASN* 3.3 11.4 + - - +
287A ALA* 3.1 19.1 + - - +
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Residues in contact with ALA 284 (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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138A GLN* 3.3 48.9 - - + +
141A GLU* 3.8 11.2 - - + +
142A GLN* 3.9 18.6 - - + +
280A HIS 2.8 17.2 + - - +
281A GLN* 3.5 8.7 - - - +
283A MET* 1.3 76.8 - - - +
285A ALA* 1.3 60.1 + - - +
287A ALA* 3.4 3.1 + - - +
288A SER 3.3 10.2 + - - -
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Residues in contact with ALA 285 (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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138A GLN* 5.5 1.1 - - - +
281A GLN 3.1 5.8 + - - +
282A LEU 3.2 7.2 + - - +
284A ALA* 1.3 74.2 - - - +
286A ASN* 1.3 63.9 + - - +
288A SER* 2.8 26.0 + - - +
289A ILE* 3.5 12.0 + - - +
347A ALA 4.4 2.1 - - - +
350A GLN* 4.2 5.6 - - + +
351A LYS* 3.9 21.8 - - - +
354A ASN* 3.3 30.1 - - - +
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Residues in contact with ASN 286 (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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4A ILE* 3.9 6.9 - - - +
5A PRO* 3.1 43.4 + - - +
7A TYR* 3.8 26.5 - - + +
282A LEU 3.0 13.2 + - - +
283A MET* 3.4 13.9 + - - +
284A ALA 3.3 0.2 - - - -
285A ALA* 1.3 76.7 - - - +
287A ALA* 1.3 60.8 + - - +
289A ILE* 3.5 22.7 + - - +
351A LYS* 2.8 37.9 + - - +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.0 19.0 - - + +
134A SER* 3.4 35.9 - - - +
137A ASP* 4.1 13.0 - - + +
138A GLN* 3.8 12.1 - - - +
141A GLU* 5.0 2.2 - - - +
283A MET 3.1 12.1 + - - +
284A ALA 3.6 9.4 - - - +
285A ALA 3.3 0.2 - - - -
286A ASN* 1.3 76.2 - - - +
288A SER* 1.3 58.9 + - - +
290A GLY* 3.0 15.8 + - - -
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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
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134A SER 5.0 0.2 - - - -
135A LEU* 5.9 0.4 - - - -
138A GLN* 3.4 35.6 + - - -
284A ALA 3.3 5.4 + - - -
285A ALA* 2.8 23.2 + - - +
287A ALA* 1.3 75.3 - - - +
289A ILE* 1.3 63.0 + - - +
291A ALA* 3.3 10.2 + - - +
292A ALA* 3.2 20.3 + - - +
347A ALA* 4.1 16.2 + - - +
350A GLN* 5.6 1.9 - - - +
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Residues in contact with ILE 289 (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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5A PRO* 3.9 20.2 - - + -
285A ALA 3.6 11.7 - - - +
286A ASN* 3.5 13.7 - - - +
287A ALA 3.2 0.6 - - - -
288A SER* 1.3 76.7 + - - +
290A GLY* 1.3 55.8 + - - +
292A ALA* 3.2 2.0 + - - +
293A ARG* 2.9 43.4 + - - +
344A LEU* 4.1 13.7 - - + -
347A ALA* 3.8 23.8 - - - +
348A LYS* 4.2 19.1 - - + -
351A LYS* 3.6 40.4 - - + +
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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
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3A LEU* 3.7 33.0 + - - +
4A ILE* 3.9 2.9 - - - -
5A PRO* 4.4 1.0 - - - +
130A GLY 4.4 1.2 - - - +
134A SER* 3.4 16.0 + - - -
286A ASN 3.9 2.0 + - - -
287A ALA 3.0 12.6 + - - -
289A ILE* 1.3 79.4 - - - +
291A ALA* 1.3 55.4 + - - +
294A ALA* 3.3 26.5 + - - +
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Residues in contact with ALA 291 (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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131A ARG* 3.6 45.8 + - + +
134A SER* 3.4 12.4 - - - -
135A LEU* 3.9 24.2 - - + +
287A ALA 3.5 0.4 + - - +
288A SER* 3.3 11.3 + - - +
289A ILE 3.3 0.2 - - - -
290A GLY* 1.3 74.8 - - - +
292A ALA* 1.3 63.5 - - - +
293A ARG 3.4 0.2 - - - -
294A ALA 3.8 4.4 + - - -
295A ALA* 3.8 8.0 + - - +
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Residues in contact with ALA 292 (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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288A SER 3.2 12.1 + - - +
289A ILE 3.2 8.0 + - - +
291A ALA* 1.3 76.5 - - - +
293A ARG* 1.3 62.4 + - - +
295A ALA* 3.5 18.4 - - - +
296A PHE* 3.8 12.0 - - - -
340A LEU 4.8 1.6 - - - +
343A SER* 3.9 12.0 - - - +
344A LEU* 3.8 33.1 - - + +
347A ALA* 3.9 7.6 - - + -
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Residues in contact with ARG 293 (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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3A LEU* 3.2 50.2 + - + +
4A ILE 4.7 0.2 - - - -
5A PRO* 3.8 30.3 - - - +
289A ILE* 2.9 25.6 + - - +
290A GLY 4.0 0.2 - - - +
292A ALA* 1.3 74.2 - - - +
294A ALA* 1.3 54.7 + - - +
295A ALA 3.0 9.8 + - - -
296A PHE* 3.2 23.3 + - - +
297A PHE* 3.6 13.9 - - + -
344A LEU* 3.8 20.0 - - + +
348A LYS* 4.7 13.9 - - - +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.3 8.7 - - + +
129A PHE* 3.5 28.6 - - + +
131A ARG* 3.8 31.0 - - + +
290A GLY 3.3 17.0 + - - +
291A ALA 3.8 2.2 + - - -
292A ALA 3.4 0.8 - - - -
293A ARG* 1.3 77.4 - - - +
295A ALA* 1.3 58.2 + - - +
296A PHE 3.3 0.9 - - - -
297A PHE* 3.7 19.5 + - - +
298A PRO 5.3 1.0 - - - +
299A SER* 6.1 0.5 - - - -
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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
------------------------------------------------------------
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