Contacts of the helix formed by residues 380 - 393 (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 380 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230X LYS* 4.6 5.2 - - - +
378X GLU 4.1 0.6 + - - +
379X LEU* 1.3 73.8 - - - +
381X ASP* 1.3 60.2 + - - +
382X SER* 2.3 31.0 + - - -
383X ASP* 2.8 32.6 + - - +
384X LEU* 3.0 19.1 + - - +
424X ASN* 2.9 22.6 + - - +
425X HIS* 4.6 2.4 + - + -
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Residues in contact with ASP 381 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219X TYR* 4.0 17.6 - - + -
222X TYR* 2.5 40.1 + - + -
223X ILE* 4.9 1.3 - - + -
229X THR* 3.7 8.8 - - - -
230X LYS* 2.9 24.4 + - - +
231X ALA* 2.9 36.3 + - - +
380X ASP* 1.3 75.6 - - - +
382X SER* 1.3 57.7 + - - +
384X LEU* 3.8 4.1 - - - +
385X ALA* 2.9 29.6 + - - +
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Residues in contact with SER 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215X ALA 5.6 0.2 - - - +
219X TYR* 3.7 29.4 - - - +
380X ASP* 2.3 30.8 + - - -
381X ASP* 1.3 75.4 - - - +
383X ASP* 1.3 66.5 + - - +
385X ALA* 3.7 5.5 + - - +
386X ILE* 3.6 20.4 + - - +
420X GLN* 3.5 22.6 + - - -
424X ASN* 4.1 1.7 + - - -
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Residues in contact with ASP 383 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379X LEU* 3.3 16.3 - - + -
380X ASP* 2.8 29.0 + - - +
382X SER* 1.3 74.1 + - - +
384X LEU* 1.3 66.3 + - - +
386X ILE* 3.0 8.3 + - - +
387X PHE* 2.9 21.2 + - - +
417X LEU* 4.5 3.5 - - + +
420X GLN* 2.9 35.0 + - - +
421X LEU* 4.1 14.5 - - + +
424X ASN* 3.2 4.7 + - - -
425X HIS* 2.8 31.1 + - - -
435X LEU* 5.7 0.9 - - + -
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Residues in contact with LEU 384 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222X TYR* 4.0 20.6 - - + +
230X LYS* 4.2 11.7 - - + -
328X THR* 4.0 17.9 - - + +
329X MET* 5.9 4.0 - - + -
332X SER* 3.7 22.7 - - - +
374X PHE* 4.0 30.3 - - + -
379X LEU* 4.3 12.6 - - + +
380X ASP 3.0 22.0 + - - +
381X ASP* 3.8 7.4 - - - +
383X ASP* 1.3 79.3 - - - +
385X ALA* 1.3 64.7 + - - +
387X PHE* 3.0 8.0 + - + -
388X ILE* 2.7 35.0 + - + +
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Residues in contact with ALA 385 (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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218X LEU* 4.0 1.8 - - + -
219X TYR* 3.7 20.6 - - - +
222X TYR* 3.5 36.3 - - + -
299X TYR* 2.6 23.9 + - - +
381X ASP 2.9 18.2 + - - +
382X SER 3.8 6.3 - - - +
383X ASP 3.2 0.2 + - - -
384X LEU* 1.3 77.9 - - - +
386X ILE* 1.3 62.9 + - + +
388X ILE* 3.6 1.5 + - - +
389X ALA* 3.3 10.7 + - - +
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Residues in contact with ILE 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215X ALA* 3.8 26.2 - - + +
218X LEU* 4.2 27.6 - - + -
382X SER 3.6 10.8 - - - +
383X ASP 3.0 4.9 + - - +
385X ALA* 1.3 72.4 - - + +
387X PHE* 1.3 67.9 + - - +
389X ALA* 3.0 4.5 + - - +
390X VAL* 3.0 20.5 + - - +
413X LEU* 3.6 28.0 - - + +
416X ALA* 4.0 9.0 - - + +
417X LEU* 3.7 16.4 - - + +
420X GLN* 3.5 40.2 - - + -
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Residues in contact with PHE 387 (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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328X THR* 4.0 20.6 - - + -
374X PHE* 4.0 18.2 - + - -
379X LEU* 5.8 0.7 - - + -
383X ASP 2.9 13.2 + - - +
384X LEU* 3.4 13.2 - - + +
386X ILE* 1.3 76.2 - - - +
388X ILE* 1.3 64.4 + - - +
390X VAL* 2.9 20.3 + - + +
391X ILE* 3.0 38.2 + - + +
417X LEU* 4.4 13.2 - - + +
435X LEU* 3.4 61.9 - - + -
436X LEU* 4.9 2.2 - - + -
438X LYS* 4.5 1.6 - - + -
439X MET* 3.9 24.2 - - + -
442X LEU* 4.3 6.5 - - + -
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Residues in contact with ILE 388 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222X TYR* 3.8 26.2 - - + -
226X PHE* 4.6 5.4 - - + -
296X ILE* 5.6 0.4 - - + -
299X TYR* 4.3 12.3 - - + -
325X ILE* 3.5 31.2 - - + -
328X THR* 4.9 12.1 - - + -
329X MET* 3.6 38.1 - - + -
384X LEU* 2.7 24.9 + - + +
385X ALA 3.8 4.3 - - - +
387X PHE* 1.3 74.2 - - + +
389X ALA* 1.3 62.6 + - - +
391X ILE* 3.4 11.4 + - + +
392X ILE* 3.1 28.9 + - + +
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Residues in contact with ALA 389 (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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218X LEU* 4.3 6.3 - - + -
299X TYR* 4.1 8.3 - - - +
303X ILE* 3.9 24.9 - - + -
385X ALA 3.3 10.5 + - - +
386X ILE 3.0 10.4 + - - +
388X ILE* 1.3 76.0 - - - +
390X VAL* 1.3 66.7 + - - +
392X ILE* 3.2 1.6 + - - +
393X LEU* 3.1 30.0 + - - +
413X LEU* 3.5 24.9 - - + +
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Residues in contact with VAL 390 (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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420U LEU* 5.1 0.2 - - + -
386X ILE 3.0 14.2 + - - +
387X PHE* 2.9 12.0 + - + +
389X ALA* 1.3 76.9 - - - +
391X ILE* 1.3 62.9 + - - +
393X LEU 3.4 5.9 + - - -
410X GLN* 2.8 41.0 + - + +
413X LEU* 3.8 28.0 - - + +
414X LEU* 3.8 28.0 - - + +
417X LEU* 3.9 21.1 - - + -
436X LEU* 4.8 2.9 - - + -
439X MET* 4.0 19.5 - - - -
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Residues in contact with ILE 391 (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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321X GLY* 4.2 3.6 - - - +
324X GLU* 3.4 26.5 - - + +
325X ILE* 3.9 24.7 - - + -
328X THR* 4.0 7.0 - - - +
387X PHE* 3.0 50.7 + - + +
388X ILE* 3.5 9.9 - - + +
390X VAL* 1.3 78.4 - - - +
392X ILE* 1.3 63.3 - - - +
394X SER* 2.6 21.7 + - - -
397X ARG* 3.4 10.8 + - - +
439X MET* 3.7 22.2 - - + -
442X LEU* 3.9 18.2 - - + -
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Residues in contact with ILE 392 (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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296X ILE* 4.4 7.2 - - + -
299X TYR* 4.3 6.3 - - + -
300X ALA* 3.9 22.2 - - + -
303X ILE* 3.9 17.9 - - + -
306X PHE* 4.1 25.1 - - + -
317X LEU* 3.6 29.7 - - + +
318X LEU* 4.5 9.6 - - + -
321X GLY* 5.2 3.1 - - - -
325X ILE* 3.3 24.7 - - + -
388X ILE* 3.1 22.9 + - + +
389X ALA 3.2 6.0 + - - +
391X ILE* 1.3 79.4 - - - +
393X LEU* 1.3 64.9 + - + +
394X SER* 3.1 5.7 + - - -
397X ARG* 5.2 0.7 + - - -
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Residues in contact with LEU 393 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303X ILE* 3.7 28.5 - - + -
306X PHE* 4.8 7.2 - - + -
309X LEU* 4.7 10.8 - - + -
317X LEU* 4.5 4.0 - - + -
389X ALA 3.1 27.1 + - - +
390X VAL 3.4 4.9 + - - -
391X ILE 3.3 0.4 - - - -
392X ILE* 1.3 82.9 - - + +
394X SER* 1.3 58.7 + - - +
395X GLY 3.7 1.2 + - - -
406X ILE* 3.9 20.8 - - + +
409X ILE* 3.4 42.6 - - + -
410X GLN* 3.0 36.4 - - + +
413X LEU* 3.7 14.8 - - + -
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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