Contacts of the helix formed by residues 398 - 418 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C LEU* 3.8 17.3 - - + +
185C TYR* 3.4 14.8 - - + +
266C MET* 3.5 29.6 - - + +
283C PHE* 3.8 24.5 - - + -
286C TRP* 3.9 15.7 - - + -
311C ILE* 3.9 11.0 - - + -
313C ARG* 4.5 4.7 - - - +
396C ASN 3.5 9.3 - - - +
397C ASP* 1.3 86.7 - - - +
399C ILE* 1.3 61.3 + - - +
400C PHE 3.1 0.7 - - - -
401C VAL* 3.2 19.3 + - - +
402C LEU* 3.9 3.8 + - - +
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Residues in contact with ILE 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C TRP* 3.6 31.4 - - + -
258C CYS* 4.0 7.4 - - - -
260C ILE* 4.0 4.9 - - + -
261C CYS* 3.7 22.2 - - - -
266C MET* 3.8 27.1 - - + -
313C ARG* 3.7 30.3 - - - +
384C LEU* 4.2 18.4 - - + -
397C ASP* 2.8 16.1 + - - +
398C PRO* 1.3 75.1 - - - +
400C PHE* 1.3 54.9 + - - +
402C LEU* 2.9 8.3 + - - +
403C LEU* 2.6 35.8 + - + +
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Residues in contact with PHE 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 4.6 0.7 - - - +
188C PHE* 3.6 34.3 - + - -
192C HIS* 3.7 26.9 - + - -
224C HIS* 4.0 2.9 - + - -
227C HIS* 3.7 8.7 - + - -
228C LEU* 5.6 0.2 - - + -
381C HIS* 3.8 14.1 - + - -
384C LEU* 5.8 1.2 - - - +
394C SER* 3.3 41.5 - - - +
395C PRO* 3.6 13.7 - - + +
397C ASP* 2.8 17.3 + - - +
398C PRO 4.5 0.2 - - - -
399C ILE* 1.3 76.3 - - - +
401C VAL* 1.3 65.4 + - - +
403C LEU* 3.2 10.2 + - - +
404C HIS* 2.9 55.6 + + + +
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Residues in contact with VAL 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PHE* 4.8 6.1 - - + -
148C LEU* 4.7 5.4 - - + -
185C TYR* 3.6 35.7 - - + +
188C PHE* 3.9 7.6 - - + -
228C LEU* 3.8 8.6 - - + +
231C LEU* 3.8 12.6 - - + -
246C LEU* 3.9 40.6 - - + -
247C PRO 5.0 0.2 - - - +
398C PRO 3.5 9.9 - - - +
399C ILE 3.2 1.0 + - - -
400C PHE* 1.3 78.9 - - - +
402C LEU* 1.3 69.4 + - + +
404C HIS 3.3 0.2 + - - -
405C THR* 3.0 30.4 + - + +
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Residues in contact with LEU 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 3.4 36.3 - - + -
144C PHE* 3.4 36.1 - - + -
247C PRO* 3.7 15.9 - - + +
248C TYR 4.1 0.7 - - - -
249C TRP* 3.1 33.5 + - + +
260C ILE* 3.7 21.5 - - + -
266C MET* 4.5 6.5 - - + -
398C PRO 4.2 10.8 - - - +
399C ILE* 2.9 8.3 + - - +
401C VAL* 1.3 80.8 - - + +
403C LEU* 1.3 65.9 + - - +
405C THR* 3.1 15.9 + - - -
406C PHE* 3.4 6.9 + - - +
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Residues in contact with LEU 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C TRP* 4.4 14.6 - - + -
251C PHE* 3.5 34.3 - - + -
377C HIS* 3.7 34.1 - - + +
380C ALA* 3.7 21.8 - - + +
381C HIS* 3.7 33.0 - - + +
384C LEU* 4.8 8.1 - - + -
399C ILE* 2.6 21.2 + - + +
400C PHE* 3.5 8.1 - - - +
402C LEU* 1.3 73.7 - - - +
404C HIS* 1.3 57.0 + - + +
406C PHE 3.4 1.2 + - - -
407C THR* 3.1 28.4 + - - +
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Residues in contact with HIS 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C PHE* 3.9 6.2 - + - -
224C HIS* 3.1 41.5 - + + +
228C LEU* 3.4 19.6 - - + +
377C HIS* 2.9 18.2 - + - -
381C HIS* 4.1 3.1 - - - -
400C PHE* 2.9 47.0 + + + +
401C VAL 4.0 1.6 - - - +
403C LEU* 1.3 74.8 - - + +
405C THR* 1.3 63.0 + - - +
406C PHE 3.2 1.3 - - - -
407C THR* 3.4 8.5 + - - +
408C ASP* 2.8 29.1 + - - +
513C ZN 2.1 37.0 - - - -
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Residues in contact with THR 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 4.1 11.2 - - - +
228C LEU* 3.6 24.5 - - + -
246C LEU* 4.0 21.8 - - + +
247C PRO 2.8 27.4 + - - +
248C TYR* 3.2 8.1 - - - -
401C VAL 3.0 20.9 + - - +
402C LEU 3.1 9.4 + - - -
404C HIS* 1.3 74.7 - - - +
406C PHE* 1.3 55.1 + - - +
409C ALA 2.9 21.0 + - - -
464C TYR* 3.1 22.6 + - - -
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Residues in contact with PHE 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C TYR* 3.7 24.8 - + + +
249C TRP 3.3 19.7 - - - +
250C ASN* 3.6 28.0 - - + -
251C PHE* 3.4 39.5 - + - -
252C ALA* 4.3 1.8 - - + -
333C VAL* 4.1 26.0 - - + -
376C LEU* 6.1 0.2 - - + -
402C LEU 3.4 4.9 + - - +
403C LEU 3.7 6.7 - - - +
404C HIS 3.2 0.8 - - - -
405C THR* 1.3 79.7 + - - +
407C THR* 1.3 64.4 + - - +
409C ALA* 3.1 4.5 + - - +
410C VAL* 3.1 32.6 + - + +
466C ILE* 3.8 24.5 - - + -
468C TRP* 4.4 7.4 - + - -
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Residues in contact with THR 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C PHE* 4.0 20.0 - - + -
221C LEU* 3.9 22.6 - - + +
251C PHE* 4.0 9.0 - - - -
359C VAL* 4.3 14.1 - - + +
377C HIS* 3.9 18.0 - - + +
403C LEU* 3.1 19.3 + - - +
404C HIS* 3.6 13.5 - - - +
406C PHE* 1.3 76.9 - - - +
408C ASP* 1.3 63.0 + - - +
410C VAL* 3.1 11.7 + - - +
411C PHE* 3.1 19.6 + - - +
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Residues in contact with ASP 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 4.6 2.9 - - - -
221C LEU* 4.4 2.5 - - - +
224C HIS 6.1 0.2 - - - -
225C ARG* 3.0 44.5 + - - +
228C LEU* 4.2 5.6 - - + -
404C HIS 2.8 22.1 + - - +
405C THR* 3.6 1.8 - - - +
407C THR* 1.3 73.9 - - - +
409C ALA* 1.3 55.5 + - - +
411C PHE* 3.2 9.4 + - - +
412C ASP* 2.8 27.7 + - - +
462C TYR* 3.0 20.7 + - - -
464C TYR* 2.7 29.1 + - - +
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C TYR* 5.4 0.7 - - + -
405C THR 2.9 15.0 + - - +
406C PHE* 3.1 12.5 + - + +
408C ASP* 1.3 75.1 - - - +
410C VAL* 1.3 62.0 + - - +
412C ASP* 3.6 1.6 + - - +
413C GLU 3.1 16.6 + - - -
464C TYR* 3.5 34.9 - - + -
466C ILE* 4.2 11.9 - - + -
468C TRP* 3.3 25.0 - - + -
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Residues in contact with VAL 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C PHE* 6.2 0.4 - - + -
333C VAL* 4.9 8.3 - - + -
336C CYS* 4.2 10.1 - - - -
337C LEU* 3.6 27.1 - - + +
355C PHE* 4.3 3.4 - - + -
359C VAL* 3.8 26.2 - - + -
376C LEU* 6.4 0.7 - - + -
406C PHE* 3.1 30.5 + - + +
407C THR* 3.1 10.5 + - - +
409C ALA* 1.3 76.3 - - - +
411C PHE* 1.3 56.8 + - - +
413C GLU* 3.2 5.3 + - - +
414C TRP* 2.9 24.7 + - - +
468C TRP* 3.7 22.0 - - + -
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Residues in contact with PHE 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C LEU* 3.6 44.4 - - + +
222C THR* 4.1 14.1 - - + -
225C ARG* 3.4 36.1 - - - -
342C PHE* 3.7 21.3 - + - -
355C PHE* 4.4 8.3 - + - -
359C VAL* 5.6 0.2 - - - +
407C THR 3.1 11.7 + - - +
408C ASP* 3.2 13.0 + - - +
410C VAL* 1.3 76.4 - - - +
412C ASP* 1.3 57.9 + - - +
414C TRP* 2.9 9.7 + + + +
415C LEU* 2.8 57.3 + - + +
452C MET 4.1 7.2 - - - -
453C PHE* 4.0 15.3 - + - -
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Residues in contact with ASP 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C ARG* 3.0 22.6 + - - +
408C ASP 2.8 16.2 + - - +
409C ALA 3.9 4.5 - - - +
411C PHE* 1.3 72.9 - - - +
413C GLU* 1.3 58.0 + - - +
415C LEU* 3.4 4.7 + - - +
416C ARG* 3.0 28.1 + - - +
454C VAL 3.7 0.2 - - - +
455C THR* 3.6 5.6 - - - +
456C ALA* 2.7 35.0 + - - +
457C PRO* 3.4 22.7 - - - +
463C THR* 5.6 1.2 - - - -
464C TYR* 4.4 16.8 + - + -
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Residues in contact with GLU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C LEU* 3.9 26.4 - - + +
409C ALA 3.1 15.0 + - - +
410C VAL 3.3 8.1 - - - +
411C PHE 3.1 0.2 - - - -
412C ASP* 1.3 74.5 - - - +
414C TRP* 1.3 59.4 + - - +
416C ARG* 2.2 47.4 + - - +
417C ARG* 2.8 48.5 + - + +
468C TRP* 3.3 38.3 + - + +
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Residues in contact with TRP 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C LEU* 4.2 9.6 - - + -
339C VAL 3.2 19.1 + - - -
340C GLY 3.7 15.9 - - - -
342C PHE* 3.5 39.0 - + + -
355C PHE* 3.4 53.3 - + + +
410C VAL 2.9 7.8 + - - +
411C PHE* 2.9 7.8 + + - +
413C GLU* 1.3 78.2 - - - +
415C LEU* 1.3 74.4 + - + +
417C ARG* 4.5 1.6 - - - +
418C TYR* 2.9 62.7 + + + -
421C ASP* 3.6 21.1 - - + -
453C PHE* 3.9 21.1 - + - -
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Residues in contact with LEU 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C ARG* 3.8 15.0 - - - +
411C PHE* 2.8 52.6 + - + +
412C ASP* 3.7 7.4 - - - +
414C TRP* 1.3 77.2 - - + +
416C ARG* 1.3 68.6 + - - +
419C ASN* 3.1 3.6 + - - -
420C ALA* 2.9 31.6 + - - +
453C PHE* 3.4 39.7 - - + +
454C VAL 3.1 29.4 - - - +
455C THR* 4.2 13.9 - - + +
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Residues in contact with ARG 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 5.0 6.8 + - - -
175B ASN* 2.6 35.6 + - - +
412C ASP* 3.0 15.6 + - - +
413C GLU* 2.2 53.0 + - - +
415C LEU* 1.3 78.1 - - - +
417C ARG* 1.3 72.6 + - - +
419C ASN* 3.4 8.7 + - - +
455C THR* 4.1 16.4 - - + +
468C TRP* 4.8 4.2 - - - -
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Residues in contact with ARG 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 5.6 2.8 + - - -
173B ASP* 4.7 21.6 + - - +
175B ASN* 4.0 32.3 + - + +
334C ALA 5.1 2.6 + - - -
337C LEU* 3.7 33.9 + - - +
338C GLU* 4.3 21.4 + - - +
413C GLU* 2.8 37.0 + - - +
416C ARG* 1.3 86.8 - - - +
418C TYR* 1.3 84.3 + - + +
419C ASN 3.5 0.6 + - - -
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Residues in contact with TYR 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU 2.8 29.0 + - - -
338C GLU* 3.4 19.8 + - - +
339C VAL 4.1 0.7 - - - -
340C GLY* 3.5 30.7 - - - +
414C TRP* 2.9 58.6 + + + +
417C ARG* 1.3 98.5 + - + +
419C ASN* 1.3 70.1 + - - +
420C ALA 3.2 2.7 + - - -
421C ASP* 3.4 17.2 + - + +
1T NAG 6.6 0.2 - - - -
2T NAG 4.7 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