Contacts of the helix formed by residues 382 - 405 (chain C) in PDB entry 5DO7
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 ASN 382 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C SER* 4.8 7.6 + - - -
378C ASN* 3.9 19.0 + - - -
379C LEU* 2.7 28.1 + - - +
380C VAL 3.0 5.4 + - - -
381C ARG* 1.3 78.0 - - - +
383C LYS* 1.3 67.6 + - - +
384C LEU* 3.1 16.9 - - + +
385C ALA* 2.8 29.9 + - - +
386C VAL* 3.3 7.1 + - - +
441C LEU* 6.0 2.0 - - - +
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Residues in contact with LYS 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C VAL 4.8 1.2 + - - -
382C ASN* 1.3 70.2 - - - +
384C LEU* 1.3 70.9 + - + +
385C ALA 2.9 0.9 + - - -
386C VAL* 3.4 9.9 + - - +
387C ILE* 3.3 20.6 + - + +
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ASN* 4.2 14.4 - - + +
383C LYS* 1.3 80.7 - - + +
385C ALA* 1.3 59.8 + - + +
387C ILE* 3.2 8.1 - - - +
388C THR* 3.2 18.7 + - - -
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Residues in contact with ALA 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C LEU* 4.6 2.5 - - + +
382C ASN* 2.8 35.5 + - - +
384C LEU* 1.3 75.5 - - + +
386C VAL* 1.3 68.4 + - - +
388C THR* 2.8 23.5 + - - -
389C ARG* 3.3 9.1 + - - +
441C LEU* 4.4 30.2 - - + +
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Residues in contact with VAL 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C LEU* 2.8 35.7 - - + +
380C VAL* 3.8 20.9 - - + +
382C ASN 3.3 10.7 + - - +
383C LYS* 4.4 3.6 - - - +
385C ALA* 1.3 78.4 - - - +
387C ILE* 1.3 68.2 + - - +
389C ARG* 2.8 23.0 + - - +
390C LEU* 3.3 33.0 + - + +
474C PHE* 3.9 19.1 - - + -
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Residues in contact with ILE 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C LYS 3.3 11.2 + - - +
384C LEU* 3.2 19.3 - - - +
386C VAL* 1.3 80.1 - - - +
388C THR* 1.3 72.7 + - - +
390C LEU* 3.3 11.6 + - + +
391C LEU* 2.8 65.9 + - + +
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Residues in contact with THR 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C LEU 3.2 17.7 + - - -
385C ALA* 2.8 9.7 + - - -
387C ILE* 1.3 80.7 - - - +
389C ARG* 1.3 63.6 + - - -
391C LEU* 2.9 1.7 + - - +
392C GLN* 2.8 65.6 + - + +
436C LEU* 4.5 11.2 - - + -
437C ASN* 5.4 0.9 - - - +
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Residues in contact with ARG 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C LEU* 3.0 41.9 - - + +
385C ALA 3.9 7.2 - - - +
386C VAL* 2.8 21.6 + - - +
388C THR* 1.3 74.7 - - - +
390C LEU* 1.3 62.5 + - + +
392C GLN* 3.2 18.3 + - - +
393C ASN 4.8 0.2 + - - -
437C ASN* 2.7 29.7 + - - +
441C LEU* 3.2 25.1 - - - +
467C TYR* 3.4 7.4 + - - -
470C HIS* 3.4 6.0 - - - -
471C VAL* 3.0 37.2 - - - +
474C PHE* 4.2 22.6 - - + +
475C SER* 5.1 0.3 - - - -
478C ALA* 3.2 15.7 - - - +
510C HIS* 4.2 6.2 + - - -
514C GLU* 2.8 25.3 + - - -
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Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C VAL* 3.3 38.6 - - + +
387C ILE* 3.5 13.0 - - + +
389C ARG* 1.3 76.7 - - + +
391C LEU* 1.3 70.4 + - + +
393C ASN* 4.4 1.6 + - - +
394C LEU 4.6 0.2 + - - -
474C PHE* 3.8 24.0 - - + -
477C VAL* 3.2 33.9 - - + -
478C ALA* 3.1 31.5 - - - +
481C ILE* 3.6 21.1 - - + +
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Residues in contact with LEU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C ILE* 2.8 44.0 + - + +
388C THR* 4.7 1.1 - - - -
390C LEU* 1.3 94.2 - - + +
392C GLN* 1.3 67.9 + - - +
393C ASN 3.1 2.9 - - - -
394C LEU* 2.8 32.5 + - + +
395C ILE* 3.1 19.6 + - + +
481C ILE* 4.2 17.9 - - + -
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Residues in contact with GLN 392 (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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388C THR* 2.8 54.0 + - + +
389C ARG* 3.2 11.9 + - - +
391C LEU* 1.3 71.0 - - - +
393C ASN* 1.3 72.5 + - - +
395C ILE* 2.5 31.8 + - + +
396C MET* 2.9 8.5 + - - +
433C THR* 3.8 26.2 + - + -
436C LEU* 3.3 25.3 - - + +
437C ASN* 2.7 29.4 + - - +
510C HIS* 4.3 3.8 - - - -
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Residues in contact with ASN 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG 4.8 0.2 + - - -
390C LEU 4.4 0.4 + - - -
391C LEU 3.1 0.4 - - - -
392C GLN* 1.3 88.8 - - - +
394C LEU* 1.3 52.4 + - - +
396C MET* 2.8 31.2 + - - +
429C ALA 5.8 0.2 - - - -
430C THR* 3.7 24.6 - - - +
433C THR* 4.1 11.1 - - - +
478C ALA* 4.2 12.1 - - + +
479C THR* 4.0 21.6 + - - +
482C PHE* 3.2 29.9 - - + +
506C LEU 4.5 2.0 + - - -
510C HIS* 3.1 38.8 + - + +
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Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU 4.6 0.8 + - - -
391C LEU* 2.8 21.7 + - + +
393C ASN* 1.3 70.2 - - - +
395C ILE* 1.3 79.7 + - + +
397C GLY* 2.8 3.5 + - - -
398C LEU* 2.8 57.4 + - + +
481C ILE* 3.2 36.6 - - + +
482C PHE* 3.6 16.9 - - - +
485C VAL* 3.7 26.9 - - + -
486C CYS* 5.0 0.7 - - - -
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Residues in contact with ILE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C LEU* 3.3 33.7 - - + +
392C GLN* 2.5 24.1 + - + +
394C LEU* 1.3 85.2 - - + +
396C MET* 1.3 65.0 + - + +
398C LEU* 3.3 6.6 + - + +
399C PHE* 2.8 33.2 + - + +
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Residues in contact with MET 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C GLN 2.9 5.5 + - - +
393C ASN* 2.8 31.3 + - - +
395C ILE* 1.3 75.5 - - + +
397C GLY* 1.3 55.2 + - - +
399C PHE* 3.3 7.5 + - + +
400C LEU* 3.0 47.3 + - + +
425C GLN* 4.9 6.1 - - - +
426C PHE* 4.9 7.9 - - + -
429C ALA* 3.8 33.0 - - + +
430C THR* 6.2 0.7 - - + -
432C TYR* 6.3 2.5 - - + -
433C THR* 5.1 11.0 - - + -
482C PHE* 4.5 1.6 - - + -
568D ASN* 4.2 24.2 - - - +
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Residues in contact with GLY 397 (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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393C ASN 3.4 2.8 + - - -
394C LEU 2.8 10.4 + - - -
396C MET* 1.3 73.5 - - - +
398C LEU* 1.3 60.6 + - - +
400C LEU* 3.5 2.2 + - - +
401C LEU* 2.8 30.5 + - - +
426C PHE* 4.3 9.6 - - - -
482C PHE* 3.7 11.2 - - - -
486C CYS* 3.5 25.2 - - - +
490C LEU* 5.0 1.6 - - - +
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Residues in contact with LEU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 2.8 46.7 + - + +
395C ILE* 3.7 9.9 - - + +
397C GLY* 1.3 75.9 - - - +
399C PHE* 1.3 56.7 + - - +
401C LEU* 2.7 36.4 + - + +
402C PHE* 2.8 15.7 + - - +
485C VAL* 3.8 22.7 - - + -
486C CYS* 4.3 1.8 - - - -
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Residues in contact with PHE 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C ILE* 2.8 27.2 + - + +
396C MET* 3.5 9.9 - - - +
398C LEU* 1.3 73.5 - - - +
400C LEU* 1.3 60.1 + - + +
402C PHE* 3.7 12.5 - + - +
403C PHE* 3.1 39.6 - + - -
565D ALA* 4.0 11.7 - - + -
568D ASN* 3.5 42.2 - - + -
569D SER* 3.7 31.2 - - - -
572D LEU* 4.2 9.0 - - + -
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Residues in contact with LEU 400 (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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396C MET* 3.0 24.4 + - + +
397C GLY 3.7 3.6 - - - +
399C PHE* 1.3 74.8 - - + +
401C LEU* 1.3 66.9 + - - +
402C PHE 2.9 2.0 - - - -
403C PHE* 2.8 16.8 + - - +
404C VAL* 2.8 22.4 + - + +
422C LEU* 4.5 19.5 - - + +
425C GLN* 3.8 35.7 - - + -
426C PHE* 3.5 38.8 - - + -
490C LEU* 5.9 0.4 - - + -
568D ASN* 5.7 1.1 - - - +
572D LEU* 3.7 30.7 - - + -
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Residues in contact with LEU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C GLY 2.8 20.9 + - - +
398C LEU* 2.7 29.3 + - + +
400C LEU* 1.3 71.4 - - - +
402C PHE* 1.3 53.5 + - - +
404C VAL 4.6 0.2 - - - +
405C LEU* 2.8 52.9 + - - +
406C ARG* 5.7 1.1 - - + -
485C VAL* 5.0 2.9 - - + -
486C CYS* 4.9 8.5 - - - -
489C THR* 3.8 42.0 - - + +
490C LEU* 3.9 20.6 - - + +
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Residues in contact with PHE 402 (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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398C LEU 2.8 13.2 + - - +
399C PHE* 3.7 11.9 - + - +
400C LEU 2.9 0.4 + - - -
401C LEU* 1.3 76.7 - - - +
403C PHE* 1.3 83.3 + + - +
405C LEU* 4.1 8.1 - - - +
586D VAL* 3.7 35.1 - - + +
587D PRO* 3.8 32.1 - - + +
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Residues in contact with PHE 403 (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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399C PHE* 3.1 47.8 - + - -
400C LEU 2.8 10.3 + - - +
402C PHE* 1.3 89.0 - + - +
404C VAL* 1.3 67.3 + - + +
405C LEU* 3.2 8.3 + - - +
569D SER* 3.2 42.0 - - - -
572D LEU* 3.5 30.7 - - + -
573D ALA* 4.3 8.7 - - - -
578D ILE* 5.4 4.7 - - + -
583D LEU* 3.6 27.1 - - + +
587D PRO* 3.8 28.7 - - + -
590D ILE* 4.2 11.9 - - + -
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Residues in contact with VAL 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C LEU* 2.8 27.7 + - + +
403C PHE* 1.3 76.2 - - + +
405C LEU* 1.3 76.3 + - - +
406C ARG 3.5 7.5 - - - +
407C VAL* 4.9 8.3 - - + -
418C ASP* 4.7 24.2 - - + +
422C LEU* 3.9 31.2 - - + -
490C LEU* 4.2 4.0 - - + -
572D LEU* 5.7 1.1 - - + -
578D ILE* 4.0 30.3 - - + -
582D SER 5.3 4.9 - - - +
583D LEU* 5.4 4.7 - - - -
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C LEU* 2.8 25.1 + - - +
402C PHE 4.1 6.3 - - - +
403C PHE 3.2 14.7 - - - +
404C VAL* 1.3 82.3 - - - +
406C ARG* 1.3 86.3 + - + +
490C LEU* 3.2 23.4 - - - +
583D LEU* 4.7 1.8 - - - -
584D TRP* 3.9 46.7 - - + +
585D THR 5.1 0.2 - - - +
586D VAL* 3.6 28.5 - - + +
587D PRO* 5.2 0.4 - - + -
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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