Contacts of the helix formed by residues 310 - 331 (chain X) in PDB entry 1FM6
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 310 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309X LEU* 1.3 78.3 - - - +
311X LEU* 1.3 67.9 + - - +
312X ASN* 2.5 45.1 + - - +
313X ASP* 3.3 13.9 + - - +
314X GLN* 3.1 19.2 + - - +
401X LEU* 4.1 12.9 - - + +
402X ASN* 4.4 20.4 + - + +
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Residues in contact with LEU 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309X LEU 3.4 2.2 + - - -
310X ASP* 1.3 77.8 + - - +
312X ASN* 1.3 64.1 + - - +
314X GLN* 3.2 12.7 + - + +
315X VAL* 3.1 17.5 + - - +
691Y HIS* 3.2 34.2 - - + +
694Y LEU* 3.4 31.2 - - + -
695Y GLN* 3.7 23.3 - - + +
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Residues in contact with ASN 312 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310X ASP* 2.5 22.5 + - - +
311X LEU* 1.3 74.8 - - - +
313X ASP* 1.3 58.4 + - - +
315X VAL* 3.3 6.1 + - - +
316X THR* 3.0 29.2 + - - -
401X LEU* 3.5 30.2 - - + +
684Y THR* 2.8 39.6 + - + +
691Y HIS* 5.4 0.3 + - - -
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Residues in contact with ASP 313 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309X LEU* 5.2 4.9 - - + -
310X ASP* 3.3 16.5 + - + +
312X ASN* 1.3 75.2 - - - +
314X GLN* 1.3 56.6 + - - +
315X VAL 3.1 0.9 - - - -
316X THR* 4.0 5.8 + - - -
317X LEU* 2.7 40.2 + - - +
399X GLY 4.2 1.2 - - - +
400X LEU* 3.4 20.7 - - + +
401X LEU* 2.7 35.2 + - - +
402X ASN* 2.8 37.9 + - - +
406X ILE* 4.1 10.5 - - + +
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Residues in contact with GLN 314 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306X PHE* 3.2 47.6 + - + +
307X VAL* 3.1 33.8 + - - +
309X LEU* 3.1 18.6 + - + +
310X ASP 3.1 12.0 + - - +
311X LEU* 3.4 19.0 - - - +
312X ASN 3.2 0.2 - - - -
313X ASP* 1.3 76.4 - - - +
315X VAL* 1.3 60.3 + - - +
317X LEU* 5.2 0.4 - - - -
318X LEU* 3.4 26.9 + - - +
694Y LEU* 3.3 36.9 - - + +
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Residues in contact with VAL 315 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311X LEU 3.1 4.7 + - - +
312X ASN 3.3 4.7 + - - +
313X ASP 3.1 0.4 - - - -
314X GLN* 1.3 77.1 - - - +
316X THR* 1.3 61.8 + - - +
317X LEU 3.3 0.2 - - - -
318X LEU* 3.6 5.6 - - + +
319X LYS* 2.8 27.9 + - - +
684Y THR* 3.4 23.8 - - - +
687Y HIS* 3.5 33.0 - - + -
690Y LEU* 4.2 10.0 - - + +
691Y HIS* 3.3 41.7 - - + +
694Y LEU* 3.8 14.1 - - + -
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Residues in contact with THR 316 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312X ASN* 3.0 21.0 + - - +
313X ASP* 3.2 5.2 + - - -
315X VAL* 1.3 77.3 - - - +
317X LEU* 1.3 64.6 + - - +
318X LEU 3.3 0.3 + - - -
319X LYS* 3.3 8.0 + - + +
320X TYR* 3.3 30.7 + - + +
397X ARG* 4.2 6.7 - - + -
398X PRO 3.5 25.1 + - - +
399X GLY 4.2 8.5 + - - -
400X LEU* 3.5 27.6 - - + +
684Y THR* 5.4 1.6 + - - -
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Residues in contact with LEU 317 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306X PHE* 4.3 14.6 - - + -
309X LEU* 4.0 18.2 - - + -
313X ASP 2.7 27.2 + - - +
314X GLN 4.2 3.8 - - - +
316X THR* 1.3 72.4 - - - +
318X LEU* 1.3 60.5 + - - +
320X TYR* 4.1 0.7 - - - +
321X GLY* 3.1 24.6 + - - -
392X ILE* 3.6 27.2 - - + +
393X LEU* 4.5 4.5 - - + -
394X SER 3.3 25.8 - - - +
397X ARG* 3.8 12.1 + - + -
400X LEU* 3.5 24.2 - - + -
406X ILE* 3.5 26.7 - - + -
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Residues in contact with LEU 318 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296X ILE* 4.8 13.5 - - + -
297X THR* 3.9 24.0 - - + +
300X ALA* 3.9 23.8 - - + -
306X PHE* 4.2 7.9 - - + -
314X GLN 3.4 19.3 + - - +
315X VAL* 3.3 7.8 + - - +
316X THR 3.1 0.4 - - - -
317X LEU* 1.3 79.8 - - - +
319X LYS* 1.3 66.5 + - - +
321X GLY* 6.3 0.4 - - - -
322X VAL* 3.0 38.2 + - + +
392X ILE* 4.5 8.7 - - + -
690Y LEU* 4.4 17.7 - - + +
694Y LEU* 3.8 30.5 - - + -
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Residues in contact with LYS 319 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315X VAL 2.8 17.2 + - - +
316X THR* 3.3 9.2 + - - +
318X LEU* 1.3 79.7 - - - +
320X TYR* 1.3 84.5 + - + +
322X VAL* 4.3 2.8 + - - +
323X HIS* 5.0 2.4 + - - +
471X GLU 3.1 4.2 + - - -
472X ILE* 2.8 54.9 + - + +
474X LYS 2.7 29.1 + - - -
475X ASP* 4.6 1.6 - - - -
476X LEU* 4.3 16.5 - - + +
686Y ARG* 4.4 5.2 - - - +
687Y HIS* 3.1 37.3 - - + +
690Y LEU* 4.2 12.8 - - + +
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Residues in contact with TYR 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316X THR* 3.3 20.4 + - + +
319X LYS* 1.3 99.3 - - + +
321X GLY* 1.3 61.0 + - - +
322X VAL 3.6 0.4 - - - -
323X HIS* 4.8 1.9 + - - +
324X GLU* 3.8 5.5 + - - +
397X ARG* 3.4 39.2 + - + +
398X PRO* 3.6 46.7 + - + +
475X ASP 3.6 18.5 + - - -
476X LEU* 3.1 38.5 - - + -
477X TYR* 3.4 46.6 + + - -
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Residues in contact with GLY 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317X LEU 3.1 19.3 + - - -
318X LEU* 3.4 0.4 + - - -
320X TYR* 1.3 78.7 - - - +
322X VAL* 1.3 67.0 + - - +
323X HIS 3.4 0.7 - - - -
324X GLU* 3.2 5.1 + - - +
325X ILE* 3.0 32.6 + - - +
391X ILE* 4.2 6.9 - - - +
392X ILE* 5.2 2.5 - - - -
397X ARG* 3.5 15.2 - - - +
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Residues in contact with VAL 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293X VAL* 3.8 34.5 - - + +
296X ILE* 3.8 28.4 - - + +
318X LEU* 3.0 29.1 + - + +
319X LYS 4.5 2.9 - - - +
320X TYR 3.6 0.6 - - - -
321X GLY* 1.3 76.5 - - - +
323X HIS* 1.3 75.0 + - + +
325X ILE* 3.2 5.9 + - - +
326X ILE* 2.9 49.3 + - + +
472X ILE* 4.5 9.0 - - + -
690Y LEU* 5.9 1.1 - - + -
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Residues in contact with HIS 323 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289X SER* 4.8 0.2 - - - -
319X LYS 5.0 1.8 + - - +
320X TYR 4.8 3.7 + - - +
321X GLY 3.4 0.4 - - - -
322X VAL* 1.3 80.4 - - + +
324X GLU* 1.3 67.2 + - - +
326X ILE* 3.3 16.7 + - + +
327X TYR* 3.0 47.0 + + + -
446X VAL* 4.0 21.5 - - + -
469X LEU* 4.4 9.7 - - + +
472X ILE* 3.9 28.1 - - + +
473X TYR* 3.2 37.8 + + - -
476X LEU* 4.4 6.4 - - + +
504X BRL 2.6 31.5 + - + -
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Residues in contact with GLU 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320X TYR 3.8 4.2 + - - +
321X GLY 3.2 7.3 + - - +
323X HIS* 1.3 76.4 - - - +
325X ILE* 1.3 57.5 + - - +
327X TYR* 4.8 0.4 - - - -
328X THR* 2.9 31.3 + - - -
391X ILE* 3.4 15.9 - - + +
397X ARG* 2.8 44.9 + - - -
439X MET* 5.0 7.1 - - - +
442X LEU* 3.6 34.2 - - + +
443X ARG* 2.9 18.5 + - - -
446X VAL* 4.0 12.6 - - + -
477X TYR* 2.9 22.0 + - - +
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Residues in contact with ILE 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226X PHE* 5.3 0.2 - - + -
296X ILE* 3.4 32.5 - - + -
321X GLY 3.0 21.1 + - - +
322X VAL 3.6 6.5 - - - +
324X GLU* 1.3 75.5 - - - +
326X ILE* 1.3 58.4 + - - +
328X THR* 3.6 6.0 - - - -
329X MET* 2.9 43.8 + - - +
388X ILE* 3.5 33.0 - - + +
391X ILE* 3.9 17.5 - - + -
392X ILE* 3.3 37.5 - - + -
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Residues in contact with ILE 326 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288X ARG* 6.4 1.1 - - + -
289X SER* 3.7 34.1 - - - +
292X ALA* 3.6 31.9 - - + -
293X VAL* 4.6 1.1 - - + -
296X ILE* 4.0 5.6 - - + -
322X VAL* 2.9 39.8 + - + +
323X HIS* 3.3 16.1 + - + +
325X ILE* 1.3 76.6 - - - +
327X TYR* 1.3 67.8 + - + +
329X MET* 3.7 4.9 - - - +
330X LEU* 2.8 29.6 + - + +
504X BRL 4.1 18.6 - - + -
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Residues in contact with TYR 327 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323X HIS* 3.0 44.2 + + + +
324X GLU* 4.1 3.4 - - - +
326X ILE* 1.3 77.3 - - + +
328X THR* 1.3 67.6 + - - +
330X LEU* 3.3 19.4 + - + +
331X ALA* 3.3 8.3 + - - +
367X LYS* 3.7 36.3 - - + -
370X PHE* 3.8 16.6 - - + -
442X LEU* 4.2 11.0 - - + -
445X ILE* 4.0 24.9 - - + -
446X VAL* 4.2 15.5 - - + -
449X HIS* 3.6 27.6 + + + -
504X BRL 3.4 38.4 - + + +
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Residues in contact with THR 328 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324X GLU 2.9 23.1 + - - -
325X ILE* 3.3 7.4 + - - -
327X TYR* 1.3 77.5 - - - +
329X MET* 1.3 68.5 + - + +
331X ALA* 3.2 17.5 + - - +
332X SER* 3.9 3.8 + - - -
370X PHE* 4.2 10.1 - - - -
374X PHE* 3.8 30.8 - - + -
384X LEU* 4.0 15.1 - - + +
387X PHE* 4.0 12.3 - - + -
388X ILE* 4.9 6.1 - - + -
391X ILE* 4.0 2.5 - - - +
442X LEU* 3.2 22.9 - - - +
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Residues in contact with MET 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222X TYR* 3.8 24.2 - - + +
226X PHE* 3.5 53.2 - - + -
228X LEU 5.2 7.0 - - - +
229X THR* 6.0 0.2 - - - -
296X ILE* 5.2 1.6 - - - -
325X ILE* 2.9 26.3 + - - +
326X ILE* 4.0 4.3 - - - +
328X THR* 1.3 74.3 - - + +
330X LEU* 1.3 65.2 + - - +
331X ALA 3.1 2.0 - - - -
332X SER* 3.0 25.3 + - - -
333X LEU* 3.8 8.1 + - - +
384X LEU* 5.9 3.8 - - + -
388X ILE* 3.6 24.9 - - + -
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Residues in contact with LEU 330 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326X ILE* 2.8 20.0 + - + +
327X TYR* 3.5 16.8 - - + +
328X THR 3.2 0.6 - - - -
329X MET* 1.3 76.8 - - - +
331X ALA* 1.3 61.9 + - - +
333X LEU* 3.0 20.5 + - + +
334X MET* 3.2 34.7 - - + +
339X VAL* 3.8 26.2 - - + -
364X MET* 4.4 0.2 - - + -
367X LYS* 4.3 13.9 - - + -
504X BRL 4.1 41.3 - - + +
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Residues in contact with ALA 331 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327X TYR 3.3 7.1 + - - +
328X THR 3.2 14.0 + - - +
329X MET 3.1 0.4 - - - -
330X LEU* 1.3 77.1 - - - +
332X SER* 1.3 63.3 + - - +
333X LEU 3.2 0.2 - - - -
334X MET* 3.3 9.8 + - - +
370X PHE* 4.4 4.0 - - + -
371X ALA* 3.8 33.4 - - + -
374X PHE* 4.3 14.1 - - + -
375X ASN* 3.1 34.7 + - - +
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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) + - + + + + + -
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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