Contacts of the helix formed by residues 518 - 538 (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 THR 518 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C ALA 3.8 15.3 - - - +
516C GLU* 2.8 16.4 + - - +
517C PHE* 1.4 75.3 - - - +
519C PRO* 1.3 77.7 - - + +
520C ALA* 3.7 7.2 + - - +
521C VAL* 3.2 24.8 + - + +
522C HIS* 2.9 20.4 + - - +
630D ARG* 3.7 1.6 - - - +
716D HIS* 5.7 0.4 - - - -
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Residues in contact with PRO 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C THR* 1.3 86.3 - - - +
520C ALA* 1.4 56.9 + - - +
522C HIS* 3.3 4.0 - - + +
523C ALA* 3.0 27.9 + - - +
626D GLU* 5.0 1.3 - - - +
630D ARG* 3.8 35.2 - - + +
633D VAL* 4.0 18.5 - - + +
634D VAL* 4.2 2.1 - - + +
651D PRO* 4.9 5.4 - - + -
655D MET* 3.9 41.7 - - + -
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Residues in contact with ALA 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ASN* 3.8 11.6 + - - +
518C THR* 3.2 7.0 + - - +
519C PRO* 1.4 75.5 - - - +
521C VAL* 1.4 61.2 + - + +
523C ALA* 3.4 7.3 + - - +
524C SER* 3.1 29.8 + - - -
633D VAL* 4.9 0.2 - - - -
651D PRO* 4.4 25.6 - - + +
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Residues in contact with VAL 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ASN* 4.0 33.7 - - + +
412C ALA* 6.4 0.9 - - + -
413C ALA* 4.0 18.2 - - + +
513C LEU* 6.3 0.4 - - + -
516C GLU* 3.5 26.9 - - + +
517C PHE* 4.6 3.6 - - - -
518C THR* 3.2 18.2 + - + +
520C ALA* 1.4 74.7 - - + +
522C HIS* 1.4 55.2 + - - +
524C SER* 3.2 2.1 + - - -
525C LEU* 2.8 54.4 + - + +
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Residues in contact with HIS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C LEU* 4.2 14.9 - - + +
517C PHE* 3.5 27.0 - + + -
518C THR 2.9 12.5 + - - +
519C PRO 3.3 10.5 - - - +
521C VAL* 1.4 76.8 - - - +
523C ALA* 1.4 56.7 + - - +
525C LEU* 3.9 1.6 - - - +
526C ASP* 2.9 25.6 + - - +
630D ARG* 3.2 38.7 + - + +
634D VAL* 3.7 26.6 - - + +
635D TYR* 5.4 1.8 + - - -
709D VAL* 4.8 12.7 - - + +
712D CYS* 4.0 33.5 - - + -
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Residues in contact with ALA 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 4.5 2.1 + - - +
406C ASP* 5.9 0.4 - - - +
519C PRO 3.0 12.9 + - - +
520C ALA* 3.7 9.0 - - - +
521C VAL 3.3 0.2 - - - -
522C HIS* 1.4 74.6 - - - +
524C SER* 1.4 63.6 + - - +
526C ASP* 3.3 3.6 + - - +
527C LYS* 3.0 30.4 + - + +
633D VAL* 4.3 12.8 - - + +
634D VAL* 3.9 32.5 - - + +
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Residues in contact with SER 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C LEU* 4.6 1.6 - - - +
406C ASP* 2.8 37.7 + - - -
409C ASN* 2.9 44.1 + - - -
410C VAL* 3.9 4.9 - - - +
520C ALA 3.1 10.4 + - - -
521C VAL 3.2 2.0 + - - -
523C ALA* 1.4 76.3 - - - +
525C LEU* 1.4 57.3 + - - +
527C LYS* 3.2 5.2 + - - +
528C PHE* 2.9 28.1 + - - +
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Residues in contact with LEU 525 (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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410C VAL* 4.4 22.9 - - + +
413C ALA* 4.2 20.0 - - + -
414C TRP* 5.3 6.7 - - + -
506C LEU* 3.6 16.6 - - + -
509C LEU* 3.8 29.8 - - + -
513C LEU* 5.8 1.1 - - + -
517C PHE* 4.0 19.3 - - + -
521C VAL* 2.8 42.4 + - + +
522C HIS 3.9 1.3 - - - +
524C SER* 1.4 71.7 - - - +
526C ASP* 1.4 57.4 + - - +
528C PHE* 3.2 11.3 + - + +
529C LEU* 2.9 35.2 + - + +
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Residues in contact with ASP 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 2.8 35.2 + - - +
502C SER* 5.4 5.0 - - - -
503C HIS* 6.0 0.2 - - - -
506C LEU* 3.2 26.9 - - + +
522C HIS 2.9 18.7 + - - +
523C ALA 3.7 4.3 - - - +
525C LEU* 1.4 77.4 - - - +
527C LYS* 1.4 61.4 + - - +
529C LEU* 3.4 5.3 + - - +
530C ALA* 3.1 19.1 + - - +
634D VAL* 4.1 6.3 - - + -
635D TYR* 2.8 27.1 + - - -
802D CNO 4.2 5.7 + - - +
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Residues in contact with LYS 527 (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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141A ARG* 2.9 66.5 + - + +
401C VAL 2.8 29.9 + - - +
402C LEU* 3.8 9.0 - - + -
403C SER* 4.4 3.0 + - - +
406C ASP* 2.7 35.1 + - - +
523C ALA* 3.0 20.0 + - + +
524C SER 3.5 7.4 - - - +
526C ASP* 1.4 73.2 - - - +
528C PHE* 1.4 62.6 + - - +
530C ALA* 3.3 4.6 + - - +
531C SER* 3.0 25.8 + - - -
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Residues in contact with PHE 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C LEU* 3.9 25.3 - - + +
410C VAL* 3.7 26.5 - - + -
414C TRP* 5.7 5.6 - + - -
466C LEU* 4.2 10.8 - - + -
469C ALA* 4.1 6.5 - - + -
470C VAL* 3.6 34.1 - - + -
473C VAL* 4.0 19.5 - - + -
476C MET* 4.2 9.9 - - + -
524C SER 2.9 14.2 + - - +
525C LEU* 3.2 14.1 + - + +
527C LYS* 1.4 75.5 - - - +
529C LEU* 1.4 73.8 + - + +
531C SER* 3.1 6.4 + - - -
532C VAL* 2.9 52.1 + - + +
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Residues in contact with LEU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C TRP* 6.4 2.0 - - + -
466C LEU* 4.7 13.7 - - + -
502C SER* 3.4 46.2 + - - +
505C LEU* 4.1 27.6 - - + -
506C LEU* 3.9 25.6 - - + +
509C LEU* 5.8 3.1 - - + -
525C LEU* 2.9 18.4 + - + +
526C ASP* 3.9 4.5 - - - +
528C PHE* 1.4 92.9 - - + +
530C ALA* 1.4 56.9 + - - +
532C VAL* 3.5 5.7 + - + +
533C SER* 2.8 33.4 + - - -
543C HEM 5.4 3.5 - - + +
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Residues in contact with ALA 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 4.2 13.0 - - - +
499C LYS* 5.8 3.4 - - - +
502C SER* 5.5 0.8 - - - -
526C ASP 3.1 17.9 + - - +
527C LYS* 3.3 5.4 + - - +
529C LEU* 1.4 74.3 - - - +
531C SER* 1.4 50.9 + - - +
533C SER* 3.4 7.8 + - - -
534C THR* 2.8 40.2 + - - +
802D CNO 4.4 24.5 - - + +
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Residues in contact with SER 531 (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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401C VAL* 5.8 2.8 + - - -
402C LEU* 4.3 13.0 + - - +
476C MET* 3.8 21.8 - - - -
527C LYS 3.0 16.4 + - - -
528C PHE* 3.4 9.2 - - - -
530C ALA* 1.4 72.8 - - - +
532C VAL* 1.4 64.7 + - - +
534C THR* 3.2 7.6 + - - -
535C VAL* 3.0 29.5 + - - +
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Residues in contact with VAL 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C LEU* 4.1 20.6 - - + -
469C ALA* 4.2 7.0 - - + -
476C MET* 3.8 19.3 - - - -
480C LEU* 4.2 11.2 - - + -
528C PHE* 2.9 47.4 + - + +
529C LEU* 3.8 6.7 - - + +
531C SER* 1.4 73.7 - - - +
533C SER* 1.4 58.6 + - - +
535C VAL* 3.2 6.8 + - - +
536C LEU* 2.9 45.9 + - + +
543C HEM 4.3 9.6 - - + -
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Residues in contact with SER 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C PHE* 3.6 35.2 + - - +
499C LYS* 5.6 1.5 - - - -
502C SER* 3.5 15.2 + - - -
529C LEU 2.8 22.3 + - - -
530C ALA* 3.5 8.9 - - - -
532C VAL* 1.4 77.6 - - - +
534C THR* 1.4 58.5 + - - +
536C LEU* 3.4 2.3 + - - +
537C THR* 3.0 32.8 + - - +
543C HEM 5.3 4.0 - - - +
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Residues in contact with THR 534 (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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134A THR* 6.2 4.0 - - + -
530C ALA* 2.8 27.2 + - - +
531C SER* 3.2 9.8 + - - -
533C SER* 1.4 71.8 - - - +
535C VAL* 1.4 63.3 + - + +
537C THR* 3.3 8.8 + - - -
538C SER* 3.1 25.0 + - - -
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Residues in contact with VAL 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C MET* 4.0 22.2 - - + +
477C PRO* 3.8 35.7 - - + +
480C LEU* 4.0 21.3 - - + -
484C SER* 3.1 19.1 + - - +
531C SER* 3.0 16.6 + - - +
532C VAL* 3.2 7.2 + - - +
534C THR* 1.4 77.1 - - + +
536C LEU* 1.4 61.2 + - - +
537C THR 3.1 0.3 + - - -
538C SER* 2.7 29.4 + - - +
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Residues in contact with LEU 536 (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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480C LEU* 4.3 14.8 - - + -
483C LEU* 3.7 33.0 - - + +
484C SER* 3.8 28.3 - - - +
487C HIS* 4.0 9.5 - - + +
498C PHE* 3.9 19.7 - - + -
532C VAL* 2.9 26.1 + - + +
533C SER 4.0 2.2 - - - +
534C THR 3.4 0.2 - - - -
535C VAL* 1.4 73.8 - - - +
537C THR* 1.4 58.9 + - - +
538C SER 3.6 0.2 - - - -
539C LYS 5.2 0.2 + - - -
540C TYR* 3.5 15.1 - - - -
543C HEM 3.5 52.9 - - + -
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Residues in contact with THR 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C PRO* 4.4 12.7 - - + +
498C PHE* 3.6 35.9 - - + -
533C SER 3.0 17.8 + - - +
534C THR* 3.4 8.4 + - - -
535C VAL 3.1 1.0 - - - -
536C LEU* 1.4 74.7 - - - +
538C SER* 1.4 63.3 + - - +
539C LYS 3.2 5.0 + - - -
540C TYR* 3.3 34.4 + - + +
801D CNO 3.6 25.2 - - - +
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Residues in contact with SER 538 (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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1A VAL* 4.1 30.1 + - - +
484C SER* 4.3 2.1 + - - -
534C THR* 3.1 14.2 + - - -
535C VAL* 2.7 26.1 + - - +
536C LEU 3.6 0.2 - - - -
537C THR* 1.4 76.2 - - - +
539C LYS* 1.4 74.6 + - - +
540C TYR 3.5 0.2 - - - -
541C ARG 4.6 4.5 - - - +
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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