Contacts of the helix formed by residues 292 - 315 (chain A) in PDB entry 5ID3
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 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A THR* 3.0 9.5 + - - -
290A ASN* 3.8 2.4 - - - +
291A PHE* 1.4 123.3 - - + +
293A ILE* 1.4 87.3 + - - +
294A GLU 3.5 1.1 - - - -
295A LYS* 4.1 8.5 - - - +
296A TYR* 3.2 40.0 + - + +
293B ILE* 4.9 12.8 - - + -
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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
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260A TYR 5.6 4.9 - - - +
264A THR* 4.3 15.6 - - + +
265A GLN* 3.6 34.5 - - - +
292A ASP* 1.4 94.5 + - - +
294A GLU* 1.4 66.2 + - + +
297A ASN* 3.4 24.1 + - - +
291E PHE* 5.1 9.4 - - + +
292E ASP* 5.1 5.4 - - + +
295E LYS* 3.0 35.2 - - - +
296E TYR* 3.4 16.6 + - + +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 4.2 18.5 - - + +
264A THR* 3.9 22.8 - - + +
265A GLN* 5.5 1.7 - - - +
287A GLN* 3.9 33.4 - - - +
289A GLN 3.6 17.7 - - - +
290A ASN* 3.7 21.5 - - + +
293A ILE* 1.4 78.0 - - - +
295A LYS* 1.4 58.5 + - - +
297A ASN* 4.4 5.3 + - - +
298A ARG* 3.0 37.1 + - - +
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Residues in contact with LYS 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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192A LEU 4.9 15.7 - - - +
193A LEU* 5.6 0.2 - - - -
290A ASN* 3.6 20.0 - - - +
291A PHE 4.3 17.6 + - - -
292A ASP* 3.8 8.2 + - - +
293A ILE 3.5 0.2 - - - -
294A GLU* 1.4 79.5 - - - +
296A TYR* 1.4 61.0 + - + +
298A ARG* 4.5 0.6 - - - +
299A LEU* 2.9 35.8 + - + +
265B GLN* 5.6 2.4 - - - +
293B ILE* 4.6 10.1 - - - +
294B GLU* 3.9 20.8 + - - -
297B ASN* 3.6 41.3 + - + +
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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
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292A ASP* 3.2 26.7 + - + +
294A GLU 3.6 0.2 - - - -
295A LYS* 1.4 78.1 - - + +
297A ASN* 1.4 62.9 + - - +
299A LEU* 3.4 18.7 - - - +
300A VAL* 3.6 12.5 - - - +
292B ASP 3.3 22.9 + - - -
293B ILE* 3.5 35.1 + - + +
296B TYR* 3.5 27.4 - + + +
297B ASN* 3.9 21.8 - - + -
300B VAL* 5.7 0.2 - - - +
296E TYR* 3.9 25.4 - + + +
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Residues in contact with ASN 297 (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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293A ILE 3.4 15.2 + - - +
294A GLU* 4.4 5.7 + - - +
296A TYR* 1.4 77.1 - - - +
298A ARG* 1.3 98.2 + - - +
300A VAL* 3.1 21.4 - - - +
301A THR* 2.6 22.2 + - - -
295E LYS* 3.1 34.3 - - + +
296E TYR* 3.7 18.6 - - + -
299E LEU* 3.3 19.3 - - - +
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Residues in contact with ARG 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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190A GLU* 5.7 3.1 - - - -
191A THR* 3.2 46.1 - - + +
193A LEU* 3.9 21.8 - - + -
287A GLN* 5.6 7.0 + - - -
294A GLU* 3.0 23.7 + - - +
295A LYS* 4.5 0.9 - - - +
297A ASN* 1.3 104.8 + - - +
299A LEU* 1.4 57.0 + - - +
301A THR* 2.8 51.6 + - - +
192E LEU* 5.8 4.9 - - - +
299E LEU* 5.5 0.2 - - - +
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Residues in contact with LEU 299 (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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191A THR* 4.4 11.3 + - + +
192A LEU* 4.7 17.9 - - + +
295A LYS* 2.9 36.2 + - + +
296A TYR* 3.4 20.0 - - - +
298A ARG* 1.4 70.5 - - - +
300A VAL* 1.4 58.4 + - - +
301A THR 3.0 1.3 - - - -
302A GLU* 2.7 40.6 + - + +
303A VAL* 3.6 2.0 + - - +
297B ASN* 3.2 24.2 - - + +
300B VAL* 3.9 21.1 - - + -
301B THR* 3.1 43.1 - - + +
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Residues in contact with VAL 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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296A TYR 3.6 14.5 + - - +
297A ASN* 3.1 24.2 - - - +
299A LEU* 1.4 77.6 - - + +
301A THR* 1.4 55.2 + - - +
303A VAL* 3.0 37.9 + - + +
304A ASP 3.6 2.1 + - - -
300B VAL* 4.5 13.5 - - + -
296E TYR* 5.7 2.5 - - + -
299E LEU* 3.6 22.7 - - + -
300E VAL* 4.3 33.0 - - + -
302E GLU* 3.8 4.6 - - - +
303E VAL* 4.6 8.3 - - + -
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Residues in contact with THR 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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191A THR* 4.8 3.4 - - - -
297A ASN* 2.6 27.2 + - - -
298A ARG* 2.8 37.2 + - - +
299A LEU 3.0 0.8 + - - -
300A VAL* 1.4 71.9 - - - +
302A GLU* 1.4 54.2 + - - +
303A VAL 3.0 2.0 - - - -
304A ASP* 2.6 52.8 + - - +
305A GLU* 5.1 0.2 - - - -
192E LEU* 4.3 19.7 - - + -
299E LEU* 3.1 17.3 - - + +
302E GLU* 3.7 12.1 - - - +
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Residues in contact with GLU 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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188A ASN* 2.7 39.8 + - - +
191A THR* 3.8 18.5 - - + +
298A ARG 3.4 4.9 + - - -
299A LEU* 2.7 25.1 + - + +
301A THR* 1.4 70.3 - - - +
303A VAL* 1.4 69.6 + - + +
305A GLU* 3.0 23.3 + - - +
306A LEU* 3.6 1.0 + - - +
301B THR* 6.3 0.7 - - - -
303B VAL* 4.6 1.6 - - - +
304B ASP* 3.8 24.5 - - + +
307B ARG* 2.7 47.7 + - - +
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Residues in contact with VAL 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 LEU 4.2 2.5 - - - +
300A VAL* 3.0 29.8 + - + +
302A GLU* 1.4 86.7 - - + +
304A ASP* 1.4 51.9 + - - +
306A LEU* 2.7 66.5 + - + +
300B VAL* 4.3 10.3 - - + +
303B VAL* 3.9 28.3 - - + -
303E VAL* 3.8 31.4 - - + -
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Residues in contact with ASP 304 (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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300A VAL 3.6 1.8 + - - -
301A THR* 2.6 40.2 + - - +
303A VAL* 1.4 72.0 - - - +
305A GLU* 1.4 81.0 + - - +
307A ARG* 3.0 28.6 + - - +
308A ASN* 3.6 10.2 + - - +
188E ASN* 3.6 25.6 + - - +
192E LEU* 5.1 3.7 - - - +
302E GLU* 3.3 37.5 + - - +
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Residues in contact with GLU 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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184A LEU* 4.7 11.0 - - + +
187A GLU* 4.2 22.6 - - + +
191A THR* 5.7 1.1 - - - +
301A THR 4.2 1.8 - - - +
302A GLU* 3.0 17.4 + - - +
304A ASP* 1.4 102.1 - - - +
306A LEU* 1.4 56.0 + - - +
308A ASN* 3.0 39.2 + - - +
309A GLN* 3.5 9.4 + - - +
307B ARG* 3.5 37.0 - - - +
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Residues in contact with LEU 306 (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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302A GLU* 6.0 0.2 - - - +
303A VAL* 2.7 55.3 + - + +
305A GLU* 1.4 71.9 - - - +
307A ARG* 1.4 80.7 + - + +
309A GLN* 3.2 14.2 + - - +
310A LEU* 3.1 21.0 + - + +
303B VAL* 4.4 8.7 - - + -
306B LEU* 3.5 32.3 - - + -
307B ARG* 3.6 24.7 - - + +
310B LEU* 3.9 15.0 - - + -
306D LEU* 5.5 4.0 - - + -
303E VAL* 5.2 1.6 - - + -
306E LEU* 3.8 39.0 - - + -
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Residues in contact with ARG 307 (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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304A ASP* 3.0 19.5 + - - +
306A LEU* 1.4 86.2 - - + +
308A ASN* 1.4 57.8 + - - +
311A LYS* 3.3 17.4 + - - +
184E LEU* 2.7 41.0 + - - +
185E GLN* 3.0 27.0 + - - +
188E ASN* 3.5 28.4 - - - +
302E GLU 3.6 21.8 - - - +
303E VAL* 5.3 0.4 - - - -
305E GLU* 3.8 22.4 - - + -
306E LEU* 3.7 12.8 - - + +
309E GLN* 2.7 40.5 + - - +
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Residues in contact with ASN 308 (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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184A LEU* 5.8 4.9 - - + -
304A ASP* 3.9 9.8 + - - +
305A GLU* 3.0 37.0 + - - +
307A ARG* 1.4 85.2 - - - +
309A GLN* 1.4 67.1 + - + +
311A LYS* 3.1 28.3 + - + +
312A ARG* 3.6 1.7 + - - +
314B ARG* 5.4 1.7 - - - +
185E GLN* 2.7 47.4 + - - +
188E ASN* 5.3 4.2 - - - +
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Residues in contact with GLN 309 (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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184A LEU* 4.1 10.8 - - + +
305A GLU 3.7 10.3 - - - +
306A LEU* 3.2 7.2 + - - +
308A ASN* 1.4 76.0 - - + +
310A LEU* 1.4 61.1 + - - +
312A ARG 3.4 3.3 + - - -
313A LEU* 3.4 19.9 + - - +
307B ARG* 2.7 59.9 + - - +
310B LEU* 3.3 14.8 - - + +
311B LYS* 3.1 35.4 - - - +
314B ARG* 3.6 40.2 - - - +
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Residues in contact with LEU 310 (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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306A LEU* 3.1 33.8 + - + +
308A ASN 3.5 0.2 - - - -
309A GLN* 1.4 71.9 - - - +
311A LYS* 1.4 58.4 + - - +
313A LEU* 3.0 11.7 + - - +
314A ARG* 2.8 35.3 + - - +
310B LEU* 3.7 35.4 - - + -
306E LEU* 3.5 38.6 - - + +
309E GLN* 3.6 19.3 - - + +
310E LEU* 3.8 37.0 - - + +
313E LEU* 4.6 6.8 - - + +
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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
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307A ARG* 3.3 13.4 + - - +
308A ASN* 3.1 19.5 - - + +
309A GLN 3.4 0.4 - - - -
310A LEU* 1.4 75.3 - - - +
312A ARG* 1.4 101.2 + - + +
314A ARG* 3.6 15.8 + - - +
315A ASP* 3.6 15.6 + - - +
181E LYS* 3.6 58.4 - - - +
184E LEU* 4.4 6.3 - - + -
185E GLN* 3.6 26.7 - - - +
309E GLN* 3.1 25.5 - - - +
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Residues in contact with ARG 312 (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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308A ASN 4.6 1.3 - - - +
309A GLN 3.4 8.3 + - - +
310A LEU 3.3 0.6 - - - -
311A LYS* 1.4 109.6 - - + +
313A LEU* 1.4 63.7 + - - +
315A ASP* 3.3 6.4 + - - +
316A PRO* 3.1 19.8 - - - +
314B ARG* 4.0 29.8 - - + +
318B GLU* 2.7 59.6 + - - +
181E LYS* 4.3 12.8 - - - +
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Residues in contact with LEU 313 (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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309A GLN 3.4 12.5 + - - +
310A LEU* 3.0 9.5 + - - +
312A ARG* 1.4 75.6 - - - +
314A ARG* 1.4 61.7 + - - +
316A PRO* 3.3 19.8 - - + +
317A LEU 3.5 14.9 - - - +
318A GLU* 3.3 31.3 - - + +
310B LEU* 3.6 40.8 - - + +
313B LEU* 3.6 26.2 - - + +
314B ARG* 3.7 27.9 - - + +
318B GLU 4.6 2.7 - - - +
313E LEU* 4.0 19.9 - - + +
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Residues in contact with ARG 314 (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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310A LEU 2.8 20.1 + - - +
311A LYS* 3.8 12.0 + - - +
312A ARG 3.3 0.2 - - - -
313A LEU* 1.4 72.5 - - - +
315A ASP* 1.4 66.3 + - - +
316A PRO 3.3 7.3 - - - +
317A LEU 4.7 1.0 - - - +
180E LYS* 3.9 31.5 + - - +
181E LYS* 4.6 6.5 - - - +
184E LEU* 3.4 28.0 - - - +
309E GLN* 3.5 40.9 - - + +
312E ARG* 3.0 60.2 - - + +
313E LEU* 3.8 26.5 - - + +
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Residues in contact with ASP 315 (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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311A LYS 3.6 7.5 + - - +
312A ARG 3.3 8.9 + - - +
314A ARG* 1.4 79.7 - - - +
316A PRO* 1.4 71.7 - - + +
318B GLU* 4.0 9.8 - - - +
181E LYS* 3.4 40.3 + - + +
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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
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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