Contacts of the helix formed by residues 491 - 510 (chain C) in PDB entry 3QHE
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 ASP 491 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489C THR* 3.0 22.2 + - + +
490C ASN* 1.3 75.2 + - - +
492C HIS* 1.3 65.9 + - - +
493C TYR* 3.0 21.8 + - - +
494C SER* 3.0 22.8 + - - -
495C ILE* 2.8 28.0 + - - +
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Residues in contact with HIS 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C ASN* 4.2 2.0 + - - -
491C ASP* 1.3 73.3 + - - +
493C TYR* 1.3 62.2 + - - +
495C ILE* 4.0 7.4 - - - +
496C THR* 2.9 51.9 + - + -
499C ARG* 6.0 0.7 - - - -
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Residues in contact with TYR 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C PRO* 3.5 19.3 + - + -
442C VAL* 3.4 52.7 + - + -
445C GLN* 3.8 2.9 - - - -
446C ILE 3.3 11.1 + - - -
447C CYS* 2.9 45.5 + - + +
448C PRO* 3.7 6.5 - - + +
491C ASP* 3.0 12.1 + - - +
492C HIS* 1.3 80.3 + - - +
494C SER* 1.3 61.4 + - - +
496C THR* 4.0 3.9 - - - -
497C LEU* 3.1 25.7 + - + +
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Residues in contact with SER 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C PRO* 5.9 2.9 - - - -
482C ASP* 3.3 23.0 + - - +
486C TYR* 5.4 2.2 - - - +
489C THR* 3.5 15.9 - - - +
491C ASP* 3.0 29.5 + - - -
493C TYR* 1.3 81.5 - - - +
495C ILE* 1.3 60.2 + - - +
497C LEU* 3.4 7.4 + - - +
498C ARG* 3.0 40.2 + - - +
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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
----------------------------------------------------------
489C THR* 3.6 24.7 - - + +
490C ASN* 4.2 11.0 - - - +
491C ASP 2.8 26.7 + - - +
492C HIS* 4.0 6.7 - - - +
494C SER* 1.3 76.0 - - - +
496C THR* 1.3 57.7 + - - +
498C ARG* 3.3 10.1 + - - +
499C ARG* 2.9 41.6 + - - +
535C SER* 5.1 2.9 - - - +
537C SER* 3.7 34.5 - - - +
540C LEU* 4.1 16.6 - - + +
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Residues in contact with THR 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C CYS* 4.1 7.0 - - - -
492C HIS* 2.9 44.6 + - + -
493C TYR* 4.0 4.5 - - - -
495C ILE* 1.3 74.6 - - - +
497C LEU* 1.3 59.4 + - - +
499C ARG* 3.2 19.5 + - - +
500C TYR* 2.9 68.6 + - + +
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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
----------------------------------------------------------
441C PRO* 3.7 35.4 - - + -
446C ILE* 3.9 15.9 - - + -
447C CYS* 3.8 22.8 - - - +
450C VAL* 3.9 13.4 - - + +
478C LEU* 4.1 26.5 - - + +
479C LEU* 5.3 2.5 - - - -
482C ASP* 4.8 12.1 - - + +
493C TYR* 3.1 18.6 + - + +
494C SER* 3.4 9.6 - - - +
495C ILE 3.3 0.2 - - - -
496C THR* 1.3 77.7 - - - +
498C ARG* 1.3 71.3 + - + +
500C TYR* 3.5 2.0 + - - -
501C ALA* 3.1 24.8 + - + +
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Residues in contact with ARG 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C LEU* 4.4 15.7 - - + +
482C ASP* 2.7 46.5 + - + +
483C CYS* 3.6 22.4 - - - +
486C TYR* 3.8 9.1 - - - +
487C GLY 2.8 29.1 + - - -
488C LEU* 4.4 2.4 - - - +
489C THR* 3.9 7.3 + - - +
494C SER* 3.0 32.0 + - - +
495C ILE* 3.8 3.3 - - - +
497C LEU* 1.3 81.4 - - + +
499C ARG* 1.3 58.2 + - - +
501C ALA* 3.4 5.8 + - - +
502C GLY* 2.8 26.2 + - - -
532C GLN* 2.8 39.1 + - + +
540C LEU* 3.8 26.0 - - + +
543C VAL* 4.6 0.3 - - - +
544C ILE* 5.4 2.2 - - + +
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Residues in contact with ARG 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C HIS* 6.0 0.8 - - - -
495C ILE* 2.9 29.5 + - - +
496C THR* 3.2 31.9 + - - +
498C ARG* 1.3 73.2 - - - +
500C TYR* 1.3 72.9 + - + +
502C GLY 3.2 0.9 + - - -
503C MET* 2.9 43.7 + - - +
539C ASP* 3.7 22.9 + - - +
540C LEU* 3.7 35.9 - - + +
543C VAL* 3.4 19.4 - - + +
389D GLN* 3.8 20.4 + - - -
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Residues in contact with TYR 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C CYS* 4.0 13.5 - - - -
450C VAL* 3.7 17.4 - - + +
451C CYS* 3.6 44.8 - - + -
454C MET* 3.5 40.8 - - + +
455C LYS* 5.9 0.3 + - - -
496C THR* 2.9 47.3 + - + +
497C LEU 3.9 0.4 - - - +
499C ARG* 1.3 83.0 + - + +
501C ALA* 1.3 65.6 + - - +
503C MET* 3.5 11.8 + - + -
504C ALA* 3.1 19.1 + - - +
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Residues in contact with ALA 501 (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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450C VAL* 3.4 12.7 - - + +
475C ILE* 3.7 20.8 - - + +
478C LEU* 5.6 1.8 - - + -
479C LEU* 4.2 23.1 - - + +
497C LEU* 3.1 21.7 + - + +
498C ARG* 3.6 5.8 - - - +
500C TYR* 1.3 78.6 - - - +
502C GLY* 1.3 58.2 + - - +
504C ALA* 3.1 5.1 + - - +
505C LEU* 2.9 32.8 + - - +
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Residues in contact with GLY 502 (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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479C LEU* 4.4 8.0 - - - +
498C ARG 2.8 14.6 + - - -
499C ARG 3.2 0.2 + - - -
501C ALA* 1.3 77.6 - - - +
503C MET* 1.3 55.5 + - - +
505C LEU* 3.2 3.2 + - - -
506C THR* 2.8 31.7 + - - -
543C VAL* 3.4 22.0 - - - -
544C ILE* 5.7 2.0 - - - -
547C VAL* 3.4 14.2 - - - +
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Residues in contact with MET 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C MET* 3.3 43.5 - - + -
457C SER* 4.6 0.2 - - - -
458C PHE* 4.5 5.8 - - + -
499C ARG* 2.9 31.8 + - - +
500C TYR* 3.7 19.7 - - + +
502C GLY* 1.3 75.0 - - - +
504C ALA* 1.3 57.6 + - - +
506C THR* 3.3 8.6 + - - -
507C ASN* 3.0 34.1 + - - +
543C VAL* 4.3 5.2 - - + -
387D TYR* 3.5 55.8 - - + +
389D GLN* 5.5 1.1 - - - +
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Residues in contact with ALA 504 (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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450C VAL* 5.5 0.7 - - + +
453C LEU* 3.9 27.4 - - + -
454C MET* 4.0 6.0 - - - +
457C SER* 3.5 20.2 - - - +
475C ILE* 4.3 8.7 - - + -
500C TYR 3.1 12.9 + - - +
501C ALA* 3.1 9.9 + - - +
503C MET* 1.3 74.1 - - - +
505C LEU* 1.3 58.6 + - - +
507C ASN* 3.2 2.3 + - - +
508C LEU* 2.9 36.3 + - + +
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Residues in contact with LEU 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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472C LEU* 3.5 44.9 - - + +
475C ILE* 3.9 15.5 - - + -
476C ALA* 3.9 20.0 - - + +
479C LEU* 3.8 28.5 - - + -
501C ALA 2.9 15.6 + - - +
502C GLY* 3.2 7.8 + - - +
504C ALA* 1.3 75.7 - - - +
506C THR* 1.3 56.5 + - - +
508C LEU* 3.8 1.1 - - + +
509C THR* 2.8 36.9 + - - +
519C LEU* 4.3 21.1 - - + -
525C CYS* 4.9 2.2 - - - -
529C LEU* 5.1 4.9 - - + -
547C VAL* 4.4 8.1 - - + -
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Residues in contact with THR 506 (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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502C GLY 2.8 22.0 + - - -
503C MET* 3.4 10.1 - - - -
504C ALA 3.2 0.2 - - - -
505C LEU* 1.3 77.4 - - - +
507C ASN* 1.3 59.2 + - - +
509C THR* 3.1 9.3 + - - -
510C PHE* 3.2 4.9 + - - +
543C VAL 4.1 0.5 + - - -
546C SER* 3.7 13.2 - - - +
547C VAL* 3.3 22.9 + - - +
549C ARG* 3.6 22.7 - - - +
550C ASN* 2.8 26.1 + - - +
385D GLY 3.6 2.8 - - - +
387D TYR* 3.6 31.9 - - + +
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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
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457C SER* 2.7 45.3 + - - +
458C PHE* 3.6 37.3 - - - -
463C ARG* 3.5 15.7 - - - -
503C MET 3.0 16.1 + - - -
504C ALA 3.2 2.7 + - - +
506C THR* 1.3 75.8 - - - +
508C LEU* 1.3 60.4 + - - +
509C THR 3.6 0.3 + - - -
510C PHE* 3.8 7.4 + - - +
386D TYR* 3.6 26.6 - - + +
387D TYR 2.9 26.8 + - - -
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Residues in contact with LEU 508 (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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457C SER* 4.8 2.5 - - - -
463C ARG* 4.0 31.4 - - + +
466C MET* 2.9 39.3 - - + -
467C ASN* 3.7 21.9 + - - +
472C LEU* 3.9 37.2 - - + +
475C ILE* 4.0 7.6 - - + -
504C ALA 2.9 22.4 + - - +
505C LEU* 4.2 0.7 - - - +
507C ASN* 1.3 76.3 - - - +
509C THR* 1.3 62.7 + - - +
510C PHE 4.9 0.7 - - - -
512C ASP* 3.5 6.6 - - - +
515C ASN* 2.8 31.6 + - - +
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Residues in contact with THR 509 (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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472C LEU* 4.1 11.0 - - + -
505C LEU 2.8 24.0 + - - +
506C THR* 3.1 10.7 + - - -
508C LEU* 1.3 79.6 - - - +
510C PHE* 1.3 66.2 + - - +
511C GLY 3.0 1.4 + - - -
512C ASP 2.9 15.0 + - - +
515C ASN* 4.2 14.6 - - - +
516C LYS* 3.3 20.7 - - - -
519C LEU* 4.0 15.0 - - + -
547C VAL* 5.0 2.4 + - + -
550C ASN* 3.2 19.1 + - - +
551C LEU* 4.0 22.0 - - + -
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Residues in contact with PHE 510 (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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709A ASN 5.9 3.1 - - - -
710A LEU* 6.1 4.9 - - + -
506C THR 3.2 10.5 + - - +
507C ASN 4.1 3.4 - - - +
508C LEU 3.5 1.5 - - - +
509C THR* 1.3 73.8 + - - +
511C GLY* 1.3 63.5 + - - +
512C ASP* 2.9 10.4 + - - +
550C ASN* 3.5 15.0 - - - +
384D GLU* 3.5 36.6 - - + -
385D GLY* 3.5 33.0 - - - +
386D TYR* 3.4 52.8 - + + -
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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
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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