Contacts of the helix formed by residues 491 - 514 (chain C) in PDB entry 4DAJ
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 THR 491 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.4 26.4 - - + +
165C ARG* 5.6 1.3 - - - -
489C ALA 3.7 2.4 + - - -
490C GLN* 1.3 79.3 + - - +
492C LEU* 1.3 60.7 + - - +
493C SER* 3.5 1.5 - - - -
494C ALA* 3.8 3.3 - - + +
495C ILE* 3.2 38.1 + - + +
542C CYS 5.2 0.2 - - - +
543C TYR* 4.4 12.7 + - + -
546C CYS* 3.1 44.8 - - + +
547C ASN* 3.4 16.3 + - - +
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Residues in contact with LEU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU 5.5 0.2 - - - +
161C ILE* 4.3 20.4 - - + -
162C SER* 3.8 24.7 - - - +
165C ARG* 5.1 11.0 - - - +
250C TYR* 3.8 30.3 - - + -
253C ILE* 4.2 33.0 - - + -
489C ALA* 4.2 11.7 - - - +
490C GLN 2.8 8.5 + - - +
491C THR* 1.3 76.8 - - - +
493C SER* 1.3 68.6 + - - +
495C ILE* 5.1 3.1 - - + -
496C LEU* 2.9 38.6 + - + +
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Residues in contact with SER 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C TYR* 2.5 41.9 + - - -
254C TYR* 4.9 2.3 - - - -
489C ALA* 3.6 16.8 + - - +
491C THR 3.5 0.4 - - - -
492C LEU* 1.3 76.2 - - - +
494C ALA* 1.3 57.7 + - - +
496C LEU* 3.9 1.3 - - - +
497C LEU* 2.9 41.8 + - - +
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Residues in contact with ALA 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C THR* 3.7 5.2 + - - +
492C LEU 3.1 0.2 - - - -
493C SER* 1.3 79.1 - - - +
495C ILE* 1.3 64.0 + - - +
497C LEU* 4.1 1.4 - - - +
498C ALA* 2.9 26.1 + - - +
542C CYS* 4.2 21.9 - - + +
545C LEU* 5.6 7.4 - - + -
546C CYS* 3.6 28.6 - - - -
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Residues in contact with ILE 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 5.1 3.6 - - + -
109C LEU* 4.4 7.9 - - + -
158C LEU* 3.8 31.6 - - + -
161C ILE* 5.9 0.7 - - + -
491C THR* 3.2 30.2 + - + +
492C LEU* 4.3 3.8 - - + +
494C ALA* 1.3 74.3 - - - +
496C LEU* 1.3 64.1 + - - +
498C ALA* 3.6 4.3 - - - +
499C PHE* 2.9 22.6 + - + +
535C ASN* 4.7 0.9 + - - +
539C ASN* 3.5 25.1 - - - +
542C CYS* 3.2 31.6 - - + -
543C TYR* 3.9 22.9 - - + -
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Residues in contact with LEU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 5.4 3.6 - - + -
162C SER* 5.3 2.7 - - - +
243C VAL* 5.3 3.1 - - + +
246C MET* 3.7 49.4 - - + +
247C THR* 4.6 9.2 - - - +
250C TYR* 3.5 44.6 - - + -
492C LEU* 2.9 27.9 + - + +
493C SER 3.9 2.2 - - - +
495C ILE* 1.3 77.5 - - - +
497C LEU* 1.3 65.1 + - + +
499C PHE* 3.0 12.8 + - + +
500C ILE* 3.0 29.7 + - + +
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Residues in contact with LEU 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C TYR* 5.7 6.3 - - + +
493C SER* 2.9 27.8 + - - +
494C ALA* 4.1 2.2 - - - +
496C LEU* 1.3 75.2 - - + +
498C ALA* 1.3 63.2 + - - +
500C ILE* 3.4 15.9 - - + +
501C ILE* 2.9 49.9 + - + +
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Residues in contact with ALA 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ALA 2.9 18.6 + - - +
495C ILE* 3.6 4.9 - - - +
497C LEU* 1.3 75.3 - - - +
499C PHE* 1.3 55.8 + - - +
501C ILE* 3.9 2.6 - - - -
502C THR* 2.5 43.0 + - + +
535C ASN* 3.5 8.3 - - - +
538C VAL* 4.5 12.6 - - + -
539C ASN* 4.9 2.2 - - - +
542C CYS* 4.1 20.2 - - - -
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Residues in contact with PHE 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C SER* 5.9 1.1 - - - -
155C VAL* 3.5 28.7 - - + -
158C LEU* 3.6 28.9 - - + -
239C PHE* 3.8 11.0 - + - -
242C PRO* 6.3 0.9 - - + -
243C VAL* 3.5 27.4 - - + -
246C MET* 4.1 15.3 - - + -
495C ILE* 2.9 14.3 + - + +
496C LEU* 3.2 11.9 - - + +
498C ALA* 1.3 76.8 - - - +
500C ILE* 1.3 79.9 + - + +
502C THR* 3.1 1.0 + - - -
503C TRP* 2.9 68.2 + + - +
535C ASN* 2.9 21.7 - - - +
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Residues in contact with ILE 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C VAL* 4.4 21.3 - - + -
247C THR* 5.4 6.5 - - - +
496C LEU* 3.0 23.0 + - + +
497C LEU* 3.4 24.2 - - + +
499C PHE* 1.3 88.8 - - + +
501C ILE* 1.3 57.7 + - + +
503C TRP* 4.9 0.2 - - - -
504C THR* 2.5 63.0 + - + +
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Residues in contact with ILE 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C LEU* 2.9 42.4 + - + +
498C ALA* 4.1 2.5 - - - +
500C ILE* 1.3 80.2 - - + +
502C THR* 1.3 67.0 + - + +
504C THR* 4.0 2.9 + - - -
505C PRO* 3.2 23.9 - - - +
531C LEU* 5.7 0.2 - - - +
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Residues in contact with THR 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C ALA* 2.5 30.6 + - + +
499C PHE 3.1 4.9 + - - -
501C ILE* 1.3 84.9 - - + +
503C TRP* 1.3 62.2 + - - +
505C PRO* 4.1 2.8 - - - +
531C LEU* 3.1 46.7 - - - +
532C CYS* 3.6 0.9 + - - -
534C ILE* 3.9 24.2 - - + +
535C ASN* 2.9 28.0 - - - +
538C VAL* 5.4 4.7 - - + -
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Residues in contact with TRP 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 6.5 1.1 - - + -
151C SER* 4.1 19.5 - - - -
154C SER* 5.7 3.6 - - - -
155C VAL* 3.4 32.3 - - + -
239C PHE* 3.4 32.5 - + + -
499C PHE* 2.9 30.9 + + - +
502C THR* 1.3 87.4 - - - +
504C THR* 1.3 69.5 + - - +
505C PRO* 2.7 8.2 - - - +
506C TYR* 2.7 22.1 + - - +
507C ASN* 4.0 1.5 + - - +
532C CYS* 3.1 47.1 + - + +
535C ASN* 3.5 15.3 + - + +
536C SER* 5.8 2.0 - - - -
2000C 0HK 3.5 47.1 - - + -
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Residues in contact with THR 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C PHE* 3.1 35.4 - - + -
240C TYR* 6.3 0.4 - - + -
243C VAL* 5.2 2.0 - - + -
500C ILE* 2.5 52.8 + - + +
501C ILE* 4.0 2.9 + - - -
503C TRP* 1.3 72.1 - - - +
505C PRO* 1.3 73.6 - - - +
507C ASN* 2.9 4.8 + - - +
508C ILE* 2.8 37.4 + - - +
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Residues in contact with PRO 505 (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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501C ILE 3.2 19.1 - - - +
502C THR 4.1 0.7 - - - +
503C TRP 2.7 6.3 - - - +
504C THR* 1.3 97.6 - - - +
506C TYR* 1.3 61.6 + - - +
508C ILE* 3.4 15.9 + - + +
509C MET* 2.9 23.7 + - - +
528C GLY* 5.6 1.8 - - - -
531C LEU* 4.3 25.4 - - + -
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Residues in contact with TYR 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C TYR* 4.7 4.3 + - - -
231C THR* 6.0 0.9 - - - +
503C TRP 2.7 18.6 + - - +
505C PRO* 1.3 73.5 - - - +
507C ASN* 1.3 60.1 + - - +
509C MET* 2.8 35.5 + - + +
510C VAL* 2.9 24.6 + - + +
525C TRP* 4.0 27.3 - + + -
528C GLY* 3.9 8.3 - - - +
529C TYR* 3.8 48.2 - + - -
532C CYS* 3.8 14.4 - - - -
2000C 0HK 3.5 55.6 - - + +
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Residues in contact with ASN 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ALA* 3.5 18.4 - - - +
239C PHE* 3.2 42.3 - - + +
240C TYR* 2.5 34.9 + - + +
503C TRP* 4.3 6.9 + - - +
504C THR 2.9 8.4 + - - +
506C TYR* 1.3 71.9 - - - +
508C ILE* 1.3 60.0 + - + +
509C MET 3.0 1.6 - - - -
510C VAL* 2.9 8.8 + - - +
511C LEU 2.8 21.8 + - - -
2000C 0HK 3.0 41.0 + - - +
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Residues in contact with ILE 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C TYR* 4.1 6.7 - - + +
504C THR* 2.8 30.3 + - - +
505C PRO* 3.4 18.2 - - + +
507C ASN* 1.3 76.4 - - + +
509C MET* 1.3 58.5 + - - +
511C LEU* 3.8 10.4 - - + +
512C VAL* 2.9 44.9 + - + +
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Residues in contact with MET 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C PRO 2.9 10.9 + - - +
506C TYR* 2.8 38.1 + - + +
508C ILE* 1.3 76.8 - - - +
510C VAL* 1.3 57.4 + - - +
512C VAL* 3.8 6.6 - - - +
513C ASN* 2.9 26.8 + - - +
520C ILE* 3.4 42.1 - - + +
524C TYR* 3.5 35.9 - - - +
525C TRP* 3.5 29.7 - - + +
528C GLY* 4.4 4.0 - - - -
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Residues in contact with VAL 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PRO 5.0 0.9 - - - +
231C THR* 4.0 19.1 - - + -
232C PHE* 3.7 33.9 - - + +
235C ALA* 4.0 10.1 - - + -
506C TYR* 2.9 38.5 + - + +
507C ASN* 2.9 17.5 + - - +
509C MET* 1.3 73.9 - - - +
511C LEU* 1.3 58.2 + - - +
512C VAL 2.9 3.4 - - - -
513C ASN* 2.6 29.1 + - + +
514C THR* 2.9 13.5 + - - +
525C TRP* 4.2 9.4 - - + -
2000C 0HK 4.7 2.5 - - + -
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Residues in contact with LEU 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C PHE* 3.3 38.1 - - + -
240C TYR* 3.6 25.1 - - + +
507C ASN 2.8 10.0 + - - +
508C ILE* 3.9 10.3 - - + +
510C VAL* 1.3 73.0 - - - +
512C VAL* 1.3 59.1 + - + +
514C THR* 3.8 1.1 - - - -
515C PHE* 3.1 43.5 - - + -
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Residues in contact with VAL 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ILE* 2.9 37.4 + - + +
509C MET* 3.8 6.1 - - - +
511C LEU* 1.3 80.1 - - + +
513C ASN* 1.3 66.7 + - - +
515C PHE* 3.1 15.3 + - - +
516C CYS* 3.2 22.5 + - - -
519C CYS* 4.5 1.1 - - + -
520C ILE* 3.9 24.2 - - + -
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Residues in contact with ASN 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PRO* 4.0 21.7 - - - +
231C THR* 5.6 5.4 - - - +
509C MET 2.9 20.2 + - - +
510C VAL* 2.6 12.5 + - - +
512C VAL* 1.3 75.7 - - - +
514C THR* 1.3 62.5 + - - +
516C CYS* 2.8 27.9 + - - +
517C ASP* 4.9 7.5 + - - +
519C CYS* 5.1 1.6 - - - -
520C ILE* 4.6 6.2 - - + +
525C TRP* 3.6 28.6 - - + +
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Residues in contact with THR 514 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PRO* 3.2 22.0 + - - +
229C THR* 4.5 17.7 - - + -
232C PHE* 3.1 31.6 - - + +
510C VAL 2.9 12.0 + - - -
511C LEU 3.8 3.1 - - - -
512C VAL 3.1 0.2 - - - -
513C ASN* 1.3 77.5 - - - +
515C PHE* 1.3 79.6 - - + +
516C CYS 5.3 0.2 - - - -
248D ILE* 4.3 15.5 - - + -
252D ARG* 2.8 34.8 + - - +
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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