Contacts of the helix formed by residues 321 - 346 (chain A) in PDB entry 3WOO
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 TYR 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 3.6 29.2 - - + -
317A ILE* 2.9 29.6 + - + +
318A GLN 4.0 1.8 - - - +
320A LYS* 1.3 79.1 - - + +
322A ALA* 1.3 59.8 + - - +
323A ALA 3.3 2.8 + - - -
324A THR* 3.3 22.8 + - + -
325A MET* 2.8 31.3 + - + +
328A TRP* 5.3 0.2 - + - -
403A ALA* 5.7 0.3 - - - +
447A ARG 3.7 15.7 + - - -
448A TYR* 3.5 6.9 - - - -
449A VAL* 3.0 48.0 + - + -
452A MET* 3.6 27.1 - - + +
453A ASP* 3.7 11.3 + - - +
456A LEU* 4.3 13.9 - - + -
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.6 20.0 - - + +
93A GLN* 4.3 0.2 - - + -
103A ILE* 3.9 16.8 - - + -
318A GLN 3.3 17.3 + - - +
319A VAL 3.4 9.4 + - - +
320A LYS 3.4 2.8 - - - -
321A TYR* 1.3 78.5 - - - +
323A ALA* 1.3 57.9 + - - +
325A MET* 4.4 2.0 - - - -
326A ALA* 2.9 18.2 + - - +
804A GOL 2.8 24.8 + - - +
807A GOL 4.0 9.4 - - - +
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.8 23.5 - - + -
90A GLY* 4.3 15.7 - - - +
93A GLN* 4.0 21.5 - - + +
320A LYS 5.0 0.2 + - - -
321A TYR 3.3 0.6 - - - -
322A ALA* 1.3 76.0 - - - +
324A THR* 1.3 64.5 + - - +
326A ALA* 3.3 4.0 + - - +
327A GLY* 3.2 17.8 + - - -
447A ARG* 4.5 10.1 - - + +
805A GOL 5.9 0.4 - - - +
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LYS 5.3 1.2 + - - -
321A TYR* 3.3 25.4 + - + -
323A ALA* 1.3 73.7 - - - +
325A MET* 1.3 62.4 + - - +
327A GLY* 3.2 3.1 + - - -
328A TRP* 2.9 69.1 + - + +
447A ARG* 5.3 11.5 + - - +
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Residues in contact with MET 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 3.8 34.1 - - + +
307A VAL* 3.6 32.3 - - + -
308A GLU* 3.7 36.3 - - + +
321A TYR* 2.8 23.0 + - + +
322A ALA* 3.7 5.4 - - - +
324A THR* 1.3 81.1 - - - +
326A ALA* 1.3 63.8 + - - +
328A TRP* 3.8 11.7 - - + -
329A ASN* 3.0 35.2 + - - +
804A GOL 3.8 14.6 - - - +
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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
----------------------------------------------------------
89A TYR* 4.2 13.9 - - + -
208A LYS* 3.5 23.5 + - - +
212A ASP* 5.0 0.3 - - - +
322A ALA 2.9 18.1 + - - +
323A ALA* 3.6 5.8 - - - +
324A THR 3.3 0.4 - - - -
325A MET* 1.3 75.0 - - - +
327A GLY* 1.3 57.7 + - - +
329A ASN* 3.5 1.7 + - - +
330A ASN* 2.9 32.4 + - - +
804A GOL 3.4 14.9 + - - +
3C ILE* 5.6 2.0 - - - -
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Residues in contact with GLY 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 5.4 0.9 - - - -
323A ALA 3.2 9.4 + - - -
324A THR* 3.2 7.0 + - - -
325A MET 3.1 0.4 - - - -
326A ALA* 1.3 74.5 - - - +
328A TRP* 1.3 66.7 + - - +
330A ASN* 3.3 4.5 + - - +
331A THR* 3.0 30.8 + - - -
3C ILE* 5.1 9.4 - - - +
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Residues in contact with TRP 328 (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 TYR* 3.7 42.9 - + + -
303A GLN* 3.7 48.6 + - + +
304A ILE* 3.6 23.7 - - + +
307A VAL* 3.7 27.6 - - + -
321A TYR* 5.3 1.3 - + - -
324A THR* 2.9 44.3 + - + +
325A MET* 3.8 22.7 - - + +
327A GLY* 1.3 75.6 - - - +
329A ASN* 1.3 51.7 + - - +
332A SER* 2.8 39.5 + - - -
456A LEU* 4.2 14.4 - - + -
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Residues in contact with ASN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASP* 3.3 39.4 + - - +
215A ASN* 4.8 0.4 - - - -
304A ILE* 3.9 31.8 - - - +
325A MET* 3.0 30.8 + - - +
326A ALA 3.8 1.1 - - - +
328A TRP* 1.3 76.7 - - - +
330A ASN* 1.3 63.9 + - - +
332A SER* 3.3 5.6 + - - -
333A LYS* 3.0 27.5 + - - +
804A GOL 3.6 14.5 + - - +
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Residues in contact with ASN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASP* 4.7 0.2 + - - -
215A ASN* 2.9 23.0 + - - +
216A TRP* 3.0 19.9 + - - -
326A ALA 2.9 19.1 + - - +
327A GLY* 3.8 4.9 - - - +
329A ASN* 1.3 76.5 - - - +
331A THR* 1.3 62.7 + - - +
334A ASN* 3.0 26.0 + - - +
1C VAL* 2.8 57.5 + - + +
3C ILE* 3.5 22.5 + - + +
5C PRO* 6.0 2.2 - - - +
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 4.6 0.2 - - + -
300A TYR* 3.7 25.9 - - + -
327A GLY* 3.0 17.7 + - - -
330A ASN* 1.3 78.0 + - - +
332A SER* 1.3 66.7 + - - +
334A ASN* 3.2 6.1 + - - +
335A TYR* 2.9 53.8 + - + +
5C PRO* 3.4 30.3 - - + +
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA* 4.1 23.1 - - - +
300A TYR* 4.0 19.2 - - - -
301A LYS* 4.1 12.9 - - - +
304A ILE* 3.9 9.0 - - - +
328A TRP 2.8 24.5 + - - -
329A ASN* 3.3 7.4 + - - -
331A THR* 1.3 76.2 - - - +
333A LYS* 1.3 64.6 + - - +
335A TYR* 3.3 3.6 + - - +
336A ASP* 3.0 28.4 + - - +
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Residues in contact with LYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASP* 2.9 28.9 + - + +
213A ILE* 3.0 16.2 + - - +
215A ASN* 2.7 32.5 + - + +
216A TRP* 3.8 13.9 - - + -
217A MET* 3.9 7.0 - - - +
301A LYS* 6.0 0.2 - - - +
329A ASN 3.0 19.0 + - - +
330A ASN* 4.9 0.2 - - - -
332A SER* 1.3 74.5 + - - +
334A ASN* 1.3 66.7 + - - +
336A ASP* 3.4 9.5 + - + +
337A GLY 3.0 18.7 + - - -
677A TRP* 3.6 27.5 - - + -
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Residues in contact with ASN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TRP* 3.3 39.6 - - + +
330A ASN 3.0 20.5 + - - +
331A THR* 3.4 7.2 - - - +
333A LYS* 1.3 75.8 - - - +
335A TYR* 1.3 71.3 + - - +
337A GLY* 3.1 2.6 + - - -
338A GLN* 2.9 51.8 + - - +
680A VAL* 3.6 18.0 - - - +
2C TYR* 5.3 0.9 - - - -
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Residues in contact with TYR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 5.9 0.2 - - - +
293A TYR* 3.4 70.6 - + + +
296A ILE* 3.6 40.9 - - + +
297A ALA* 4.4 6.5 - - + -
331A THR* 2.9 34.1 + - + +
332A SER 3.7 4.7 - - - +
333A LYS 3.2 0.2 - - - -
334A ASN* 1.3 92.0 - - - +
336A ASP* 1.3 65.4 + - - +
338A GLN* 3.2 5.7 + - - +
339A LEU* 3.0 30.0 + - - +
5C PRO* 5.5 7.1 - - + +
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Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA* 4.1 9.5 - - - +
301A LYS* 2.6 38.9 + - - -
332A SER 3.0 15.8 + - - +
333A LYS* 3.5 14.5 - - + +
335A TYR* 1.3 75.8 - - - +
337A GLY* 1.3 60.8 + - - +
339A LEU* 3.4 12.2 + - - +
340A GLU* 3.1 24.4 + - - +
677A TRP* 4.0 11.7 - - + -
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Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LYS 3.0 10.7 + - - -
334A ASN 3.1 3.5 + - - -
336A ASP* 1.3 73.3 - - - +
338A GLN* 1.3 60.5 + - - +
340A GLU* 3.3 2.6 + - - +
341A GLY* 2.9 26.5 + - - -
677A TRP* 3.4 34.6 - - - +
680A VAL* 3.3 16.6 - - - +
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Residues in contact with GLN 338 (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 TYR* 3.4 28.0 + - + -
334A ASN* 2.9 37.5 + - - +
335A TYR* 3.2 8.2 + - - +
337A GLY* 1.3 75.5 - - - +
339A LEU* 1.4 51.5 + - - +
341A GLY* 3.0 2.1 + - - -
342A PHE* 2.7 52.8 + - + -
680A VAL* 3.3 33.7 + - + +
681A SER* 3.9 4.2 - - - +
683A ASN* 3.7 9.4 + - - +
684A TRP* 3.2 32.9 - - - -
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA* 3.3 36.3 - - + +
293A TYR* 4.2 11.7 - - + -
294A PRO* 4.1 28.9 - - + -
297A ALA* 5.9 0.7 - - + -
335A TYR 3.0 23.2 + - - +
336A ASP* 3.7 13.5 - - - +
338A GLN* 1.4 75.4 - - - +
340A GLU* 1.3 62.8 + - - +
342A PHE* 3.4 14.7 + - + +
343A LYS* 3.3 27.5 + - + +
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Residues in contact with GLU 340 (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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336A ASP 3.1 16.9 + - - +
337A GLY 3.8 4.0 - - - +
339A LEU* 1.3 75.1 - - - +
341A GLY* 1.4 59.8 + - - +
343A LYS* 3.2 12.2 + - - +
344A ARG* 2.9 28.5 + - + +
677A TRP* 3.1 40.0 + - + +
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Residues in contact with GLY 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLY 2.9 17.3 + - - -
338A GLN 3.6 1.3 - - - -
340A GLU* 1.4 68.5 - - - +
342A PHE* 1.3 66.3 + - - +
344A ARG* 3.1 20.3 + - - +
345A ILE* 3.0 27.7 + - - +
678A GLU* 5.2 2.2 - - - -
681A SER* 3.5 23.3 - - - -
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Residues in contact with PHE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 3.6 33.2 - + + -
288A THR* 5.6 0.2 - - + -
289A ALA* 3.8 21.3 - - + -
293A TYR* 4.1 9.9 - + - -
338A GLN* 2.7 37.4 + - + -
339A LEU* 3.6 19.5 - - + +
340A GLU 3.2 0.2 - - - -
341A GLY* 1.3 77.2 - - - +
343A LYS* 1.3 57.8 + - + +
346A ASP* 3.0 10.7 + - - -
347A ALA* 2.9 42.4 + - + +
348A ALA 5.5 0.2 - - - +
681A SER* 3.7 20.0 - - - -
684A TRP* 3.5 37.9 - + + -
685A VAL 5.9 0.2 - - - -
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Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.3 15.0 + - + +
340A GLU* 3.2 10.4 + - - +
342A PHE* 1.3 78.0 - - + +
344A ARG* 1.3 64.3 + - - +
345A ILE 3.4 0.5 + - - -
346A ASP* 3.4 10.3 + - - +
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Residues in contact with ARG 344 (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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340A GLU* 2.9 16.1 + - + +
341A GLY* 3.1 15.0 + - - +
343A LYS* 1.3 80.3 - - - +
345A ILE* 1.3 72.4 + - + +
678A GLU* 2.7 52.4 + - - +
681A SER* 3.6 15.8 + - - -
687A ASP* 2.9 28.5 + - - +
690A MET* 3.9 27.5 - - - +
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Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLY 3.0 12.9 + - - +
342A PHE 4.1 0.2 - - - +
344A ARG* 1.3 109.2 - - + +
346A ASP* 1.3 64.4 + - - +
347A ALA* 4.0 13.0 - - + +
350A GLN* 2.8 36.3 - - - +
681A SER* 4.5 10.8 - - - +
685A VAL* 3.8 39.0 - - + +
687A ASP* 3.8 18.6 - - + +
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PHE 3.0 9.3 + - - -
343A LYS* 3.4 10.0 + - - +
344A ARG 3.5 0.4 + - - -
345A ILE* 1.3 80.5 - - - +
347A ALA* 1.3 64.5 + - - +
348A ALA* 3.2 6.3 + - - +
349A GLY* 3.1 25.9 + - - -
350A GLN* 2.9 20.0 + - + +
353A ARG* 3.9 15.5 + - - +
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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
------------------------------------------------------------
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