Contacts of the helix formed by residues 398 - 418 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 4.0 11.5 - - + +
185A TYR* 3.3 16.2 - - + +
266A MET* 3.6 29.1 - - + +
283A PHE* 3.8 25.6 - - + -
286A TRP* 3.9 18.6 - - + -
311A ILE* 3.9 15.0 - - + -
313A ARG* 4.3 3.6 - - - +
396A ASN 3.4 9.1 - - - +
397A ASP* 1.3 88.8 - - - +
399A ILE* 1.3 61.6 + - - +
400A PHE 3.1 0.7 - - - -
401A VAL* 3.2 19.6 + - - +
402A LEU* 4.2 2.1 + - - +
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TRP* 3.6 31.2 - - + -
258A CYS* 4.1 6.5 - - - -
260A ILE* 4.2 4.7 - - + -
261A CYS* 3.7 20.4 - - - -
266A MET* 3.8 27.6 - - + -
313A ARG* 3.5 32.8 - - - +
384A LEU* 4.0 20.6 - - + -
397A ASP* 2.8 12.7 + - - +
398A PRO* 1.3 77.4 - - - +
400A PHE* 1.3 62.8 + - - +
402A LEU* 3.1 8.3 + - - +
403A LEU* 2.8 22.5 + - + +
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Residues in contact with PHE 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 4.6 0.7 - - - +
188A PHE* 3.5 20.4 - + - -
192A HIS* 3.8 18.4 - + - -
224A HIS* 3.9 2.2 - + - -
227A HIS* 3.4 34.1 - + - -
228A LEU* 5.5 0.2 - - + -
381A HIS* 3.7 15.0 - + + -
384A LEU* 5.6 1.4 - - - +
394A SER* 3.6 26.2 - - - +
395A PRO* 3.6 25.8 - - + +
397A ASP* 2.9 17.1 + - - +
398A PRO 4.6 0.2 - - - -
399A ILE* 1.3 76.2 - - - +
401A VAL* 1.3 65.6 + - - +
403A LEU* 3.6 9.5 - - - +
404A HIS* 2.9 55.7 + + + +
512A ZN 4.0 0.2 - - - -
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Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 5.0 8.7 - - + -
148A LEU* 4.7 7.2 - - + -
185A TYR* 3.5 36.6 - - + +
188A PHE* 3.9 6.7 - - + -
228A LEU* 3.7 9.6 - - + +
231A LEU* 3.9 15.7 - - + -
246A LEU* 4.1 37.0 - - + -
247A PRO 5.1 0.9 - - - +
398A PRO 3.7 9.2 - - - +
399A ILE 3.2 1.4 + - - -
400A PHE* 1.3 78.6 - - - +
402A LEU* 1.3 62.1 + - + +
404A HIS 3.4 0.2 + - - -
405A THR* 2.9 29.4 + - + +
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 4.0 11.4 - - + -
144A PHE* 4.0 20.6 - - + -
247A PRO* 3.3 36.1 - - + +
248A TYR* 3.9 4.7 - - - +
249A TRP* 3.1 34.7 + - + +
260A ILE* 3.9 19.1 - - + -
266A MET* 3.7 37.9 - - + -
398A PRO 4.3 4.9 - - - +
399A ILE* 3.1 5.4 + - - +
401A VAL* 1.3 73.3 - - + +
403A LEU* 1.3 65.9 + - - +
404A HIS 3.2 1.1 - - - -
405A THR* 3.3 11.9 + - - -
406A PHE* 3.3 7.4 + - - +
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Residues in contact with LEU 403 (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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249A TRP* 4.2 18.4 - - + -
251A PHE* 3.4 19.2 - - + -
377A HIS* 3.6 34.8 - - + +
380A ALA* 3.8 29.6 - - + +
381A HIS* 3.8 35.0 - - + +
384A LEU* 4.8 8.5 - - + -
399A ILE* 2.8 16.4 + - + +
400A PHE* 3.6 7.4 - - - +
402A LEU* 1.3 78.7 - - - +
404A HIS* 1.3 57.7 + - + +
407A THR* 3.0 28.1 + - - -
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Residues in contact with HIS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 4.1 7.2 - + - -
224A HIS* 3.0 41.3 - + + +
228A LEU* 3.3 21.5 - - + +
377A HIS* 3.2 16.0 - + - -
381A HIS* 4.1 2.2 - - - -
400A PHE* 2.9 46.2 + + + +
401A VAL 4.0 1.8 - - - +
403A LEU* 1.3 78.8 - - + +
405A THR* 1.3 60.1 + - - +
406A PHE 3.2 1.6 - - - -
407A THR* 3.7 9.0 - - - +
408A ASP* 2.8 29.5 + - - +
513A ZN 2.0 36.4 - - - -
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Residues in contact with THR 405 (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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130A ARG* 4.0 10.8 - - - +
228A LEU* 3.7 24.2 - - + -
246A LEU* 3.9 21.3 - - + +
247A PRO 2.6 29.4 + - - +
248A TYR* 3.1 16.0 - - - -
401A VAL 2.9 19.4 + - - +
402A LEU 3.3 2.4 + - - -
404A HIS* 1.3 75.1 - - - +
406A PHE* 1.3 56.4 + - - +
408A ASP 3.3 0.2 + - - -
409A ALA 2.8 22.5 + - - -
464A TYR* 3.1 20.5 + - - -
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Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 3.7 25.5 - + + +
249A TRP 3.2 22.9 - - - +
250A ASN* 3.5 30.1 - - + -
251A PHE* 3.5 34.1 - + + -
252A ALA* 4.3 2.2 - - + -
333A VAL* 4.3 22.7 - - + -
376A LEU* 5.9 0.7 - - + -
402A LEU 3.3 8.8 + - - +
403A LEU 4.0 2.7 - - - +
404A HIS 3.2 0.4 - - - -
405A THR* 1.3 78.9 + - - +
407A THR* 1.3 64.8 + - - +
409A ALA* 3.0 12.7 + - - +
410A VAL* 3.0 31.1 + - + +
466A ILE* 3.9 23.6 - - + -
468A TRP* 4.4 6.5 - + - -
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Residues in contact with THR 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 4.2 18.8 - - + -
221A LEU* 3.9 22.4 - - + +
224A HIS* 6.4 0.7 - - + -
251A PHE* 3.9 8.9 - - - -
359A VAL* 4.3 14.6 - - + +
377A HIS* 3.9 20.8 - - + +
403A LEU 3.0 17.2 + - - -
404A HIS* 3.4 14.3 + - - +
406A PHE* 1.3 78.5 - - - +
408A ASP* 1.3 57.2 + - - +
410A VAL* 3.4 10.6 + - - +
411A PHE* 3.1 24.1 + - - +
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 3.7 3.2 + - - -
221A LEU* 4.5 1.9 - - - +
225A ARG* 2.8 45.9 + - - +
228A LEU* 4.1 7.9 - - + -
404A HIS 2.8 18.5 + - - +
405A THR 3.6 0.2 - - - +
407A THR* 1.3 74.1 - - - +
409A ALA* 1.3 59.7 + - - +
411A PHE* 3.3 10.4 + - - +
412A ASP* 2.8 24.9 + - - +
462A TYR* 2.8 20.1 + - - -
464A TYR* 2.7 25.4 + - - +
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Residues in contact with ALA 409 (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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248A TYR* 5.4 0.7 - - + -
405A THR 2.8 12.4 + - - +
406A PHE* 3.0 11.4 + - - +
408A ASP* 1.3 74.4 - - - +
410A VAL* 1.3 60.1 + - - +
412A ASP* 3.1 2.3 + - - +
413A GLU 2.9 25.3 + - - -
464A TYR* 3.4 38.7 - - + -
466A ILE* 4.1 21.8 - - + -
468A TRP* 3.5 10.3 - - + -
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Residues in contact with VAL 410 (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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333A VAL* 4.5 7.2 - - + -
336A CYS* 3.9 28.0 - - - -
337A LEU* 3.7 17.9 - - + +
355A PHE* 4.2 4.5 - - + -
359A VAL* 4.0 16.6 - - + -
376A LEU* 6.1 1.1 - - + -
406A PHE* 3.0 31.9 + - + +
407A THR* 3.6 9.0 - - - +
408A ASP 3.3 0.2 - - - -
409A ALA* 1.3 74.4 - - - +
411A PHE* 1.3 58.2 + - - +
413A GLU* 3.3 1.1 + - - -
414A TRP* 2.9 27.2 + - - +
468A TRP* 3.6 25.1 - - + -
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Residues in contact with PHE 411 (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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221A LEU* 3.8 46.9 - - + -
222A THR* 4.1 14.6 - - + -
225A ARG* 3.6 35.7 - - - -
342A PHE* 3.6 23.1 - + - -
355A PHE* 4.3 12.1 - + - -
359A VAL* 6.0 0.2 - - + -
407A THR 3.1 14.3 + - - +
408A ASP* 3.5 14.6 - - - +
410A VAL* 1.3 77.6 - - - +
412A ASP* 1.3 54.9 + - - +
414A TRP* 3.2 2.9 + + + +
415A LEU* 2.9 52.7 + - + +
452A MET 4.6 1.3 - - - -
453A PHE* 4.0 17.7 - + - -
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Residues in contact with ASP 412 (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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225A ARG* 3.0 18.7 + - - +
408A ASP 2.8 19.5 + - - +
409A ALA 3.1 4.7 + - - +
411A PHE* 1.3 72.9 - - - +
413A GLU* 1.3 62.5 + - - +
415A LEU* 3.2 5.0 + - - +
416A ARG* 3.1 22.0 + - - +
455A THR* 3.8 5.8 - - - +
456A ALA* 2.8 32.9 + - - +
457A PRO* 3.5 21.7 - - - +
462A TYR 5.0 0.2 - - - +
463A THR* 5.2 1.4 + - - -
464A TYR* 4.2 19.0 + - + -
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Residues in contact with GLU 413 (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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337A LEU* 3.8 22.4 - - + +
409A ALA 2.9 16.2 + - - +
410A VAL 3.7 3.4 - - - +
412A ASP* 1.3 75.0 - - - +
414A TRP* 1.3 60.0 + - - +
416A ARG* 2.7 44.0 + - - +
417A ARG* 2.9 41.3 + - - +
468A TRP* 3.6 43.7 + - + +
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Residues in contact with TRP 414 (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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337A LEU* 3.7 11.6 - - + +
339A VAL 2.9 20.7 + - - -
340A GLY 3.4 22.9 - - - -
342A PHE* 3.6 36.1 - + + -
355A PHE* 3.4 50.3 - + + -
410A VAL 2.9 7.0 + - - +
411A PHE* 3.2 8.3 + + - +
413A GLU* 1.3 76.5 - - - +
415A LEU* 1.3 77.7 + - + +
417A ARG* 4.5 0.2 - - - -
418A TYR* 3.0 54.1 + + + +
421A ASP* 3.8 23.6 - - + -
453A PHE* 4.0 20.9 - + - -
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Residues in contact with LEU 415 (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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225A ARG* 3.6 19.1 - - - +
411A PHE* 2.9 48.1 + - + +
412A ASP* 3.2 8.2 + - - +
414A TRP* 1.3 85.8 - - + +
416A ARG* 1.3 60.6 + - - +
419A ASN* 3.2 3.1 + - - -
420A ALA* 2.8 35.4 + - + +
453A PHE* 3.7 31.6 - - + -
454A VAL 3.3 29.2 - - - +
455A THR* 3.7 17.2 - - + +
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Residues in contact with ARG 416 (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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412A ASP 3.1 12.6 + - - +
413A GLU* 2.7 42.8 + - - +
415A LEU* 1.3 75.8 - - - +
417A ARG* 1.3 83.3 + - - +
418A TYR 3.3 0.7 + - - -
419A ASN* 3.4 10.0 + - - -
455A THR* 3.8 13.4 - - + +
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Residues in contact with ARG 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ALA* 5.1 1.6 + - - +
337A LEU* 3.5 34.9 + - - +
338A GLU* 2.6 35.2 + - - -
413A GLU* 2.9 30.9 + - - +
414A TRP 3.3 0.2 + - - -
416A ARG* 1.3 98.3 - - - +
418A TYR* 1.3 90.2 + - + +
419A ASN 3.5 0.6 + - - -
58C SER 5.6 3.2 + - - -
61C GLY* 5.7 8.7 - - - -
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Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 2.5 31.6 + - - -
338A GLU* 3.7 11.8 + - - -
340A GLY* 4.0 16.4 - - - +
414A TRP* 3.0 61.4 + + + +
417A ARG* 1.3 106.8 + - + +
419A ASN* 1.3 69.4 + - - +
420A ALA 3.2 3.3 + - - -
421A ASP* 3.4 18.0 + - + +
61C GLY* 4.4 8.1 - - - -
102C ASN* 3.6 36.4 + - + -
504C NAG 4.8 1.7 - - - +
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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