Contacts of the helix formed by residues 495 - 513 (chain C) in PDB entry 1K0Y
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 495 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B TRP* 3.7 20.4 - - + +
493C VAL 3.2 4.2 - - - +
494C ASP* 1.3 93.4 - - - +
496C VAL* 1.4 62.6 + - + +
497C ASN 3.2 1.0 + - - -
498C PHE* 3.2 29.3 + - + +
499C LYS* 4.3 3.8 + - - +
537C THR* 4.4 7.6 - - + +
540C TYR* 4.0 13.7 - - + -
801D CNO 3.7 41.1 - - + +
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Residues in contact with VAL 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP* 4.8 0.4 - - - +
301B GLU* 3.8 34.8 - - + +
494C ASP* 3.1 20.0 + - - +
495C PRO* 1.4 75.3 - - + +
497C ASN* 1.4 76.6 + - - +
499C LYS* 3.1 28.7 + - + +
500C LEU* 3.6 8.1 + - - +
801D CNO 6.5 0.7 - - + -
802D CNO 4.1 30.8 - - + +
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Residues in contact with ASN 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP* 2.9 29.4 + - - +
432C MET* 4.6 1.2 - - - +
438C THR* 4.7 3.1 + - - -
439C THR* 3.4 23.8 + - + +
442C TYR* 3.4 19.1 + - - -
493C VAL* 3.8 12.3 - - + -
494C ASP* 2.9 26.4 + - - +
496C VAL* 1.4 79.0 - - - +
498C PHE* 1.4 64.0 + - - +
499C LYS 3.2 0.2 - - - -
500C LEU* 3.2 15.5 + - - +
501C LEU* 3.1 19.6 + - - +
543C HEM 3.5 19.2 - - + +
802D CNO 5.2 0.5 - - - +
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Residues in contact with PHE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C HIS* 4.0 17.9 - + + -
493C VAL* 4.0 16.4 - - + -
494C ASP 4.1 1.1 - - - -
495C PRO* 3.2 19.0 + - + +
496C VAL 3.2 1.4 - - - -
497C ASN* 1.4 76.7 - - - +
499C LYS* 1.4 57.6 + - + +
501C LEU* 3.5 2.5 + - - +
502C SER* 2.9 34.6 + - - -
533C SER* 3.6 32.3 - - - +
536C LEU* 3.9 23.6 - - + -
537C THR* 3.6 26.9 - - + -
540C TYR* 3.6 20.0 - - - -
543C HEM 3.4 46.0 - + + +
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Residues in contact with LYS 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 6.4 2.0 - - - +
495C PRO 5.1 3.1 - - - +
496C VAL* 3.1 18.3 + - + +
498C PHE* 1.4 77.4 - - + +
500C LEU* 1.4 60.2 + - + +
502C SER* 3.6 5.6 + - - -
503C HIS* 3.0 29.5 + - - +
530C ALA* 5.8 3.6 - - - +
533C SER* 6.4 1.3 - - - -
802D CNO 3.5 78.2 + - + +
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Residues in contact with LEU 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C MET* 4.4 8.3 - - + -
436C PHE* 3.8 42.6 - - + -
439C THR* 3.8 22.4 - - + -
496C VAL* 3.8 11.0 - - + +
497C ASN* 3.2 15.8 + - - +
499C LYS* 1.4 75.0 - - + +
501C LEU* 1.4 64.9 + - - +
503C HIS* 3.5 4.4 + - - +
504C CYS* 3.2 27.0 + - - -
802D CNO 3.9 63.0 - - + -
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Residues in contact with LEU 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ALA* 4.2 25.4 - - + +
429C LEU* 4.1 23.1 - - + -
432C MET* 3.8 25.9 - - + -
462C VAL* 4.6 13.9 - - + -
497C ASN 3.1 13.0 + - - +
498C PHE* 4.0 3.1 - - - +
500C LEU* 1.4 74.2 - - - +
502C SER* 1.4 59.9 + - - +
504C CYS* 3.0 2.5 + - - +
505C LEU* 2.8 36.6 + - + +
543C HEM 3.8 51.6 - - + -
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Residues in contact with SER 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C PHE 2.9 21.7 + - - -
499C LYS* 3.8 6.9 - - - -
500C LEU 3.4 0.2 - - - -
501C LEU* 1.4 74.9 - - - +
503C HIS* 1.4 61.2 + - - +
505C LEU* 3.2 8.6 + - - +
506C LEU* 3.0 21.8 + - - +
526C ASP* 5.4 5.4 - - - -
529C LEU* 3.4 38.8 + - - +
530C ALA* 5.5 0.6 - - - -
533C SER* 3.5 16.3 + - - -
543C HEM 5.3 5.4 - - - +
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Residues in contact with HIS 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C PHE* 4.0 21.1 - + - -
499C LYS 3.0 18.3 + - - +
500C LEU* 3.6 4.7 - - - +
501C LEU 3.3 0.2 - - - -
502C SER* 1.4 74.3 - - - +
504C CYS* 1.4 58.2 + - - +
506C LEU* 3.2 13.2 + - - +
507C VAL* 2.9 49.6 + - + +
526C ASP* 6.0 0.2 - - - -
708D ASN* 3.5 45.3 + - + +
711D VAL* 4.4 2.0 - - + -
712D CYS* 4.3 7.2 - - - -
727D GLN* 4.1 5.2 - - - -
731D GLN* 2.7 30.2 + - - -
802D CNO 3.8 18.8 - + + -
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Residues in contact with CYS 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ALA* 3.4 21.5 - - - +
431C ARG* 3.9 9.9 - - + -
432C MET* 3.5 31.6 - - + +
436C PHE* 3.8 17.5 - - - -
500C LEU 3.2 13.7 + - - +
501C LEU* 3.0 9.2 + - - +
503C HIS* 1.4 75.6 - - - +
505C LEU* 1.4 55.2 + - - +
507C VAL* 3.5 8.1 + - - +
508C THR* 2.8 36.2 + - - -
727D GLN* 3.9 13.5 - - - +
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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
----------------------------------------------------------
414C TRP* 5.3 9.6 - - + -
424C TYR* 4.6 9.2 - - + +
425C GLY* 4.8 8.1 - - - -
428C ALA* 3.5 22.2 - - + +
462C VAL* 5.1 3.6 - - + -
466C LEU* 3.9 30.1 - - + -
501C LEU* 2.8 31.2 + - + +
502C SER* 3.4 10.5 - - - +
504C CYS* 1.4 75.7 - - - +
506C LEU* 1.4 59.5 + - - +
508C THR* 3.2 5.5 + - + -
509C LEU* 2.9 42.6 + - + +
529C LEU* 4.1 22.4 - - + -
543C HEM 4.6 7.2 - - + -
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Residues in contact with LEU 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C SER 3.0 12.6 + - - +
503C HIS* 3.3 15.5 - - - +
505C LEU* 1.4 75.5 - - - +
507C VAL* 1.4 56.4 + - - +
509C LEU* 3.2 8.1 + - + +
510C ALA* 2.8 30.0 + - - +
517C PHE* 4.0 16.9 - - + -
522C HIS* 4.2 23.8 - - + +
525C LEU* 3.6 31.9 - - + -
526C ASP* 3.2 37.2 - - + +
529C LEU* 3.9 14.4 - - + -
635D TYR* 5.2 2.0 - - - +
712D CYS* 4.4 9.6 - - - -
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Residues in contact with VAL 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ARG* 3.9 12.1 - - - +
503C HIS* 2.9 47.0 + - + +
504C CYS* 3.8 6.1 - - - +
506C LEU* 1.4 74.5 - - - +
508C THR* 1.4 57.6 + - - +
510C ALA* 3.3 7.7 + - - +
511C ALA* 2.9 27.9 + - - +
711D VAL* 3.9 10.3 - - + -
712D CYS* 4.1 11.2 - - - -
715D ALA* 3.6 19.0 - - + +
722D PHE* 4.2 5.4 - - + -
727D GLN* 3.5 27.6 - - - +
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Residues in contact with THR 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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424C TYR* 3.5 39.7 - - + +
427C GLU* 3.7 25.6 - - - +
428C ALA* 3.4 10.9 + - - -
431C ARG* 3.4 17.0 - - - +
504C CYS 2.8 22.9 + - - -
505C LEU* 3.2 9.4 + - + -
507C VAL* 1.4 73.8 - - - +
509C LEU* 1.4 64.0 + - + +
511C ALA* 3.3 1.8 + - - +
512C HIS* 3.0 34.4 + - + -
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Residues in contact with LEU 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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413C ALA* 5.7 1.1 - - + -
414C TRP* 4.3 21.3 - - + -
417C VAL* 3.8 28.0 - - + -
424C TYR* 4.2 17.5 - - + -
505C LEU* 2.9 29.3 + - + +
506C LEU* 3.2 9.6 + - + +
508C THR* 1.4 74.0 - - + +
510C ALA* 1.4 59.4 + - - +
512C HIS* 3.1 2.0 + - - -
513C LEU* 2.9 47.7 + - + +
517C PHE* 4.5 10.8 - - + -
525C LEU* 3.8 32.5 - - + -
529C LEU* 5.8 2.5 - - + -
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Residues in contact with ALA 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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506C LEU 2.8 17.6 + - - +
507C VAL* 3.6 7.0 - - - +
509C LEU* 1.4 77.2 - - - +
511C ALA* 1.4 60.3 + - - +
512C HIS 3.3 0.9 + - - -
513C LEU 3.9 7.1 + - - -
514C PRO* 4.2 1.7 - - - +
517C PHE* 3.6 35.8 - - + -
712D CYS* 3.6 20.4 - - - +
715D ALA* 3.9 1.7 - - + +
716D HIS* 3.5 27.6 - - - +
719D GLY* 5.5 0.2 - - - -
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Residues in contact with ALA 511 (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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427C GLU* 4.5 0.2 - - - +
431C ARG* 4.2 18.6 - - - +
507C VAL 2.9 17.2 + - - +
508C THR 3.7 6.3 - - - +
509C LEU 3.3 0.4 - - - -
510C ALA* 1.4 75.0 - - - +
512C HIS* 1.4 65.9 + - + +
514C PRO* 5.0 3.3 - - - +
715D ALA* 3.5 18.8 + - + +
719D GLY* 3.5 35.7 - - - +
720D LYS* 4.1 2.4 + - - +
722D PHE 5.2 0.7 - - - +
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Residues in contact with HIS 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C GLU* 4.3 10.1 - - - -
424C TYR* 3.3 52.2 + + + +
427C GLU* 2.7 36.0 + - - -
508C THR* 3.0 28.4 + - + +
509C LEU* 3.1 3.4 + - - +
511C ALA* 1.4 84.0 + - + +
513C LEU* 1.4 63.7 + - + +
514C PRO* 3.3 13.7 - - - +
720D LYS* 6.2 4.5 - - + -
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Residues in contact with LEU 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ALA* 3.9 28.3 - - + +
416C LYS* 3.8 38.4 - - + +
417C VAL* 4.4 15.5 - - + +
424C TYR* 4.9 5.6 - - + +
509C LEU* 2.9 34.5 + - + +
510C ALA 4.2 3.6 - - - -
512C HIS* 1.4 82.7 - - + +
514C PRO* 1.3 67.6 - - - +
515C ALA 3.4 2.7 - - - -
516C GLU* 3.3 25.5 + - + +
517C PHE* 3.0 26.7 + - + +
521C VAL* 6.3 0.4 - - + -
525C LEU* 5.8 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