Contacts of the helix formed by residues 398 - 418 (chain B) in PDB entry 5M8L
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 PRO 398 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.9 15.1 - - + +
185B TYR* 3.3 18.2 - - + +
266B MET* 3.5 29.8 - - + +
283B PHE* 3.7 25.1 - - + -
286B TRP* 3.8 14.8 - - + -
311B ILE* 3.9 11.2 - - + -
313B ARG* 4.6 3.8 - - - +
396B ASN 3.6 8.5 - - - +
397B ASP* 1.3 87.8 - - - +
399B ILE* 1.3 60.1 + - - +
400B PHE 3.0 0.7 - - - -
401B VAL* 3.1 20.1 + - - +
402B LEU* 3.9 3.1 + - - +
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Residues in contact with ILE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TRP* 3.6 32.8 - - + -
258B CYS* 4.1 3.8 - - - -
260B ILE* 4.4 5.4 - - + -
261B CYS* 3.7 22.0 - - - -
266B MET* 3.9 23.1 - - + -
313B ARG* 3.6 29.4 - - - +
384B LEU* 4.0 23.6 - - + -
397B ASP* 2.9 15.2 + - - +
398B PRO* 1.3 74.5 - - - +
400B PHE* 1.3 54.9 + - - +
402B LEU* 3.1 8.2 + - - -
403B LEU* 2.7 35.7 + - + +
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Residues in contact with PHE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 4.6 0.9 - - - +
188B PHE* 3.6 35.0 - + - -
192B HIS* 3.7 28.7 - + - -
224B HIS* 4.0 2.7 - + - -
227B HIS* 3.6 10.1 - + - -
228B LEU* 5.7 0.7 - - + -
381B HIS* 3.7 13.7 - + - -
384B LEU* 5.7 1.2 - - - +
394B SER* 3.4 33.9 - - - +
395B PRO* 3.5 21.8 - - + +
397B ASP* 2.9 17.3 + - - +
398B PRO 4.5 0.2 - - - -
399B ILE* 1.3 75.9 - - - +
401B VAL* 1.3 63.1 + - - +
403B LEU* 3.2 10.1 + - - +
404B HIS* 2.8 54.7 + + + +
517B ZN 4.0 0.2 - - - -
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 4.8 8.7 - - + -
148B LEU* 4.7 6.7 - - + -
185B TYR* 3.4 36.6 - - + +
188B PHE* 3.8 7.4 - - + -
228B LEU* 3.8 9.2 - - + +
231B LEU* 3.8 12.1 - - + -
246B LEU* 4.1 39.7 - - + -
247B PRO 4.9 1.1 - - - +
398B PRO 3.1 10.0 + - - +
400B PHE* 1.3 79.5 - - - +
402B LEU* 1.3 64.2 + - + +
404B HIS 3.3 0.7 + - - -
405B THR* 3.0 29.3 + - + +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.1 10.5 - - + -
144B PHE* 3.9 14.6 - - + -
247B PRO* 3.1 48.2 - - + +
248B TYR* 3.9 4.7 - - - +
249B TRP* 3.1 35.2 + - + +
260B ILE* 4.1 11.2 - - + -
266B MET* 3.8 42.8 - - + -
398B PRO 4.3 5.6 - - - +
399B ILE* 3.1 5.6 + - - +
401B VAL* 1.3 74.8 - - + +
403B LEU* 1.3 67.0 + - - +
405B THR* 3.2 11.8 + - - -
406B PHE* 3.3 6.2 + - - +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TRP* 4.2 18.2 - - + -
251B PHE* 3.5 27.1 - - + -
377B HIS* 3.4 39.0 - - + +
380B ALA* 3.8 22.7 - - + +
381B HIS* 3.8 31.4 - - + +
384B LEU* 5.0 4.3 - - + -
399B ILE* 2.7 25.6 + - + +
400B PHE* 3.5 7.6 - - - +
402B LEU* 1.3 74.2 - - - +
404B HIS* 1.3 57.6 + - + +
406B PHE 3.6 0.2 + - - -
407B THR* 3.1 26.5 + - - -
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Residues in contact with HIS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 4.0 6.7 - + - -
224B HIS* 3.1 39.1 - + + +
228B LEU* 3.6 21.1 - - + +
377B HIS* 3.0 17.8 - + - -
381B HIS* 4.1 2.2 - - - -
400B PHE* 2.8 48.3 + + + +
401B VAL 4.0 1.6 - - - +
403B LEU* 1.3 77.5 - - + +
405B THR* 1.3 60.2 + - - +
406B PHE 3.2 1.1 - - - -
407B THR* 3.2 9.2 + - - +
408B ASP* 2.7 30.0 + - - +
517B ZN 2.0 37.5 - - - -
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Residues in contact with THR 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 3.9 15.7 - - - +
228B LEU* 3.7 24.9 - - + -
246B LEU* 4.0 15.5 - - + -
247B PRO 2.8 28.2 + - - +
248B TYR* 3.1 16.9 - - - -
401B VAL 3.0 18.7 + - - +
402B LEU 3.2 2.6 + - - -
404B HIS* 1.3 75.1 - - - +
406B PHE* 1.3 56.7 + - - +
409B ALA* 2.9 22.0 + - - +
464B TYR* 3.3 20.7 + - - -
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B TYR* 3.7 20.3 - + - +
249B TRP 3.0 28.9 - - - +
250B ASN* 3.7 27.6 - - + -
251B PHE* 3.6 35.0 - + + -
252B ALA* 4.2 13.9 - - + -
333B VAL* 4.3 6.7 - - + -
402B LEU 3.3 12.2 + - - +
403B LEU 3.8 3.8 - - - +
404B HIS 3.2 0.8 - - - -
405B THR* 1.3 75.2 + - - +
407B THR* 1.3 65.9 + - - +
409B ALA* 3.1 4.6 + - + +
410B VAL* 3.1 33.8 + - + +
466B ILE* 3.9 23.8 - - + -
468B TRP* 4.2 15.0 - + - -
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Residues in contact with THR 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 4.3 16.6 - - + -
221B LEU* 3.9 23.5 - - + +
224B HIS* 6.3 0.7 - - + -
251B PHE* 4.0 8.4 - - - -
359B VAL* 4.3 15.0 - - + +
377B HIS* 3.8 25.0 - - + +
403B LEU 3.1 16.1 + - - -
404B HIS* 3.2 15.9 + - - +
406B PHE* 1.3 78.3 - - - +
408B ASP* 1.3 62.8 + - - +
410B VAL* 3.3 9.0 + - - +
411B PHE* 3.1 19.8 + - - +
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Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 3.9 3.3 + - - -
221B LEU* 4.4 2.0 - - - +
225B ARG* 2.6 47.2 + - - +
228B LEU* 4.2 7.6 - - + -
404B HIS 2.7 19.9 + - - +
405B THR* 4.2 2.2 - - - -
407B THR* 1.3 73.7 - - - +
409B ALA* 1.3 55.8 + - - +
411B PHE* 3.4 10.1 - - - +
412B ASP* 2.8 26.5 + - - +
462B TYR* 2.6 24.7 + - - -
464B TYR* 2.7 23.4 + - - +
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B TYR* 5.5 0.7 - - + -
405B THR 2.9 14.5 + - - +
406B PHE* 3.1 12.5 + - + +
408B ASP* 1.3 74.8 - - - +
410B VAL* 1.3 61.5 + - - +
412B ASP* 3.2 1.7 + - - +
413B GLU* 2.9 23.7 + - - +
464B TYR* 3.5 36.0 - - + -
466B ILE* 4.4 7.6 - - + -
468B TRP* 3.5 24.3 - - + -
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B VAL* 4.3 9.6 - - + -
336B CYS* 4.0 26.7 - - - -
337B LEU* 3.7 15.5 - - + +
355B PHE* 4.3 3.6 - - + -
359B VAL* 4.0 16.6 - - + -
376B LEU* 6.1 0.9 - - + -
406B PHE* 3.1 30.7 + - + +
407B THR* 3.3 8.3 + - - +
409B ALA* 1.3 74.5 - - - +
411B PHE* 1.3 56.6 + - - +
413B GLU* 3.3 3.8 + - - +
414B TRP* 2.9 27.0 + - - +
468B TRP* 3.7 26.5 - - + -
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.7 52.0 - - + -
222B THR* 4.0 18.2 - - + -
225B ARG* 3.5 36.3 - - - -
342B PHE* 3.8 22.9 - + - -
355B PHE* 4.3 12.5 - + - -
359B VAL* 5.6 0.4 - - - +
407B THR 3.1 13.3 + - - +
408B ASP* 3.4 16.8 - - - +
410B VAL* 1.3 74.0 - - - +
412B ASP* 1.3 64.0 + - - +
414B TRP* 3.1 3.6 + + + +
415B LEU* 2.9 44.9 + - + +
452B MET 4.4 1.6 - - - -
453B PHE* 4.2 7.0 - + - -
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Residues in contact with ASP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ARG* 3.1 22.7 + - - +
408B ASP 2.8 16.6 + - - +
409B ALA 3.2 4.7 + - - +
411B PHE* 1.3 72.2 - - - +
413B GLU* 1.3 62.8 + - - +
415B LEU* 3.1 5.0 + - - +
416B ARG* 3.0 23.7 + - - +
454B VAL 4.1 0.2 - - - +
455B THR* 3.7 7.8 - - - +
456B ALA* 2.8 32.9 + - - +
457B PRO* 3.5 21.3 - - - +
463B THR* 5.3 1.7 + - - -
464B TYR* 4.3 17.0 - - + -
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU* 3.9 18.8 - - + -
409B ALA 2.9 15.6 + - - +
410B VAL* 3.6 4.5 - - - +
411B PHE 3.2 0.2 - - - -
412B ASP* 1.3 75.4 - - - +
414B TRP* 1.3 65.0 + - - +
416B ARG* 3.0 41.1 + - - +
417B ARG* 2.9 31.8 + - + +
468B TRP* 3.5 44.7 + - + +
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Residues in contact with TRP 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU* 3.8 11.4 - - + +
339B VAL 3.1 22.2 + - - -
340B GLY 3.5 21.3 - - - -
342B PHE* 3.6 33.9 - + + -
355B PHE* 3.3 54.4 - + + -
410B VAL 2.9 8.1 + - - +
411B PHE* 3.4 7.9 - + - +
413B GLU* 1.3 76.8 - - - +
415B LEU* 1.3 88.9 + - + +
417B ARG* 3.2 1.0 + - - -
418B TYR* 3.0 52.0 + + + -
421B ASP* 3.7 24.2 - - + -
453B PHE* 3.9 10.8 - + - -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ARG* 3.6 17.7 - - - +
411B PHE* 2.9 38.5 + - + +
412B ASP* 3.1 7.6 + - - +
414B TRP* 1.3 87.0 - - + +
416B ARG* 1.3 62.5 + - - +
419B ASN* 3.1 3.6 + - - -
420B ALA* 2.8 34.6 + - + +
453B PHE* 3.6 43.1 - - + -
454B VAL 3.4 27.8 - - - +
455B THR* 3.9 17.4 - - + +
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Residues in contact with ARG 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ASP* 3.0 14.9 + - - +
413B GLU* 3.0 37.7 + - - +
415B LEU* 1.3 76.7 - - - +
417B ARG* 1.3 82.5 + - - +
418B TYR 3.2 0.9 + - - -
419B ASN* 3.3 15.5 + - - +
455B THR* 3.9 14.5 - - + +
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ALA* 4.7 3.8 + - - +
337B LEU* 3.3 50.3 + - - +
338B GLU* 3.8 22.0 - - - +
413B GLU* 2.9 27.5 + - - +
414B TRP* 3.2 3.1 + - - +
416B ARG* 1.3 99.9 - - - +
418B TYR* 1.3 77.5 + - + +
419B ASN* 4.0 4.7 + - - -
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Residues in contact with TYR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU 2.8 29.6 + - - -
338B GLU* 3.5 18.9 + - - -
339B VAL 4.2 0.2 - - - -
340B GLY* 3.7 25.6 - - - +
414B TRP* 3.0 58.1 + + + +
417B ARG* 1.3 100.1 + - + +
419B ASN* 1.3 75.4 + - - +
420B ALA 3.1 2.8 + - - -
421B ASP* 3.4 17.7 + - + +
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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