Contacts of the helix formed by residues 451 - 470 (chain A) in PDB entry 3CKI
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 SER 451 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A ASP* 2.6 28.8 + - - -
423A CYS* 3.6 11.4 - - - -
433A TYR* 3.3 41.4 - - - +
450A PHE* 1.3 76.9 - - - +
452A GLN* 1.3 60.0 + - - +
453A CYS* 3.0 5.4 + - - +
454A SER* 3.0 16.7 + - - -
455A LYS* 2.9 28.4 + - - +
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Residues in contact with GLN 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASN* 2.5 42.6 + - - -
422A GLU* 4.4 18.6 + - + +
423A CYS* 4.1 9.7 - - - +
433A TYR* 5.2 1.8 - - - -
450A PHE 5.8 0.2 + - - -
451A SER* 1.3 75.3 - - - +
453A CYS* 1.3 62.4 + - - +
455A LYS* 3.6 16.2 - - - +
456A GLN* 3.1 24.9 + - - +
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Residues in contact with CYS 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A HIS 5.7 0.2 - - - +
416A ASP* 3.9 5.8 - - - +
417A PRO* 4.1 14.1 - - + -
420A LEU* 3.8 21.5 - - - -
423A CYS* 2.0 50.7 - - + -
451A SER* 3.0 5.5 + - - +
452A GLN* 1.3 77.8 - - - +
454A SER* 1.3 61.1 + - - +
456A GLN* 4.0 5.3 - - - +
457A SER* 3.3 22.7 + - - -
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Residues in contact with SER 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A TRP* 4.8 0.4 - - - -
413A ALA* 4.1 8.5 - - - +
414A GLU 4.4 2.4 + - - +
416A ASP* 3.4 13.3 + - - -
435A MET* 3.0 27.2 - - - +
450A PHE* 3.7 26.5 - - - -
451A SER* 3.0 13.0 + - - -
453A CYS* 1.3 73.8 - - - +
455A LYS* 1.3 57.1 + - - +
457A SER* 3.3 5.9 + - - -
458A ILE* 2.7 41.5 + - - +
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Residues in contact with LYS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A THR* 3.9 15.2 - - - +
266A ALA* 3.5 26.5 + - - +
267A TRP* 3.8 33.4 - - + +
269A ASN* 3.4 26.1 + - - +
449A MET* 6.0 3.6 - - - +
450A PHE* 3.9 19.7 + - + +
451A SER 2.9 19.1 + - - +
452A GLN* 3.6 22.8 - - - +
453A CYS 3.3 0.2 - - - -
454A SER* 1.3 73.6 - - - +
456A GLN* 1.3 60.2 + - - +
458A ILE* 4.0 0.3 - - - +
459A TYR* 2.8 34.7 + - - +
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Residues in contact with GLN 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A TRP 5.1 1.1 - - - -
452A GLN 3.1 13.5 + - - +
453A CYS* 4.0 4.9 - - - +
455A LYS* 1.3 78.4 - - - +
457A SER* 1.3 67.0 + - - +
459A TYR* 3.6 6.1 - - - +
460A LYS* 2.9 51.5 + - - +
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Residues in contact with SER 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A PRO* 5.4 0.5 - - - +
412A GLY 2.6 28.0 + - - +
413A ALA* 3.7 7.9 - - - -
414A GLU* 4.4 6.6 + - - +
453A CYS 3.3 15.5 + - - -
454A SER* 3.3 5.6 + - - -
455A LYS 3.2 0.4 - - - -
456A GLN* 1.3 84.9 - - - +
458A ILE* 1.3 61.5 + - - +
460A LYS* 3.6 6.5 + - - +
461A THR* 3.4 21.5 + - - -
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Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A TYR* 5.2 0.4 - - + -
267A TRP* 3.5 43.3 - - + -
408A GLY* 4.1 2.5 - - - +
411A PHE* 3.6 38.1 - - + +
413A ALA* 3.8 22.9 - - + +
450A PHE* 3.8 22.7 - - + -
454A SER 2.7 22.3 + - - +
457A SER* 1.3 70.3 - - - +
459A TYR* 1.3 60.2 + - - +
461A THR* 3.1 2.4 + - - -
462A ILE* 2.8 47.4 + - + +
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Residues in contact with TYR 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TRP* 3.8 27.5 - - + +
268A ASP* 4.4 13.2 - - + -
272A PHE* 3.9 41.1 - + - -
455A LYS 2.8 22.8 + - - +
456A GLN* 3.6 5.8 - - - +
458A ILE* 1.3 73.8 - - - +
460A LYS* 1.3 76.2 + - + +
462A ILE* 3.9 4.5 - - - +
463A GLU* 2.5 64.0 + - + +
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Residues in contact with LYS 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A PRO* 3.6 19.2 - - + +
456A GLN* 2.9 54.8 + - - +
457A SER* 4.0 6.1 - - - +
459A TYR* 1.3 90.1 - - + +
461A THR* 1.3 65.4 + - - +
463A GLU* 3.4 4.4 + - - +
464A SER* 3.2 24.3 + - - -
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Residues in contact with THR 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A SER* 3.7 18.0 - - - +
356A PRO* 3.3 25.5 - - - +
364A VAL* 3.9 22.4 - - + -
411A PHE* 3.1 33.8 + - - +
412A GLY* 3.5 9.4 + - - -
457A SER 3.4 9.3 + - - -
458A ILE 3.1 3.9 + - - -
460A LYS* 1.3 79.1 - - - +
462A ILE* 1.3 58.7 + - + +
464A SER* 3.2 2.6 + - - -
465A LYS* 2.8 29.5 + - + +
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Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TRP* 3.9 25.1 - - + +
272A PHE* 3.7 24.2 - - + -
275A TYR* 3.9 29.2 - - + -
364A VAL* 6.2 0.4 - - - -
411A PHE* 3.9 29.8 - - + -
458A ILE* 2.8 36.9 + - + +
459A TYR 3.9 2.5 - - - +
461A THR* 1.3 70.3 - - + +
463A GLU* 1.3 61.7 + - - +
464A SER 2.9 4.5 - - - -
465A LYS* 4.5 0.9 - - - +
466A ALA* 2.8 36.9 + - + +
470A PHE* 4.4 8.7 - - + -
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A PHE* 4.6 14.8 - - + -
459A TYR* 2.5 59.2 + - + +
460A LYS* 3.8 5.3 - - - +
462A ILE* 1.3 79.5 - - - +
464A SER* 1.3 57.3 + - - +
466A ALA* 5.1 1.8 + - - +
467A GLN* 5.6 2.6 + - - +
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Residues in contact with SER 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A PRO* 3.0 34.0 + - - -
358A ALA* 5.5 0.9 - - - -
460A LYS 3.2 15.2 + - - -
461A THR 3.8 2.2 - - - -
462A ILE 2.9 1.0 - - - -
463A GLU* 1.3 80.6 - - - +
465A LYS* 1.3 67.2 + - - +
466A ALA 3.6 0.2 - - - -
467A GLN* 4.5 7.9 + - - +
468A GLU* 4.7 5.2 + - - +
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Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A SER 2.8 28.2 + - - +
356A PRO 4.2 2.7 - - - -
357A ARG 3.7 11.4 + - - -
358A ALA* 4.7 10.1 - - - +
360A SER* 3.3 26.2 + - - -
362A GLY 5.3 0.2 + - - -
364A VAL* 3.9 29.4 + - + +
365A CYS* 3.5 26.6 + - + +
367A LYS* 5.7 0.7 - - - +
461A THR 2.8 20.8 + - - +
462A ILE* 5.1 0.7 - - - -
464A SER* 1.3 85.4 - - - +
466A ALA* 1.3 63.7 + - - +
467A GLN 3.2 2.9 - - - -
468A GLU* 2.9 32.0 + - + +
469A CYS 3.2 10.9 + - - -
470A PHE* 4.7 2.2 - - + -
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Residues in contact with ALA 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 3.9 15.5 - - + +
275A TYR* 4.3 5.8 - - + +
462A ILE* 2.8 32.3 + - + +
463A GLU* 5.4 2.0 - - - -
464A SER 3.6 0.2 - - - -
465A LYS* 1.3 70.7 - - - +
467A GLN* 1.3 64.2 + - - +
470A PHE* 3.0 57.5 + - + +
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Residues in contact with GLN 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASP* 3.8 26.7 + - - +
222A LYS* 3.7 37.4 + - - +
463A GLU 5.6 2.8 + - - +
464A SER 4.5 7.5 + - - +
465A LYS 3.2 1.0 - - - -
466A ALA* 1.3 81.4 - - - +
468A GLU* 1.3 62.3 + - - +
469A CYS 3.7 0.2 + - - -
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Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 5.8 0.8 + - - -
358A ALA 5.2 1.0 - - - +
365A CYS* 3.6 25.1 - - + +
366A PRO 4.7 6.4 - - - +
367A LYS* 3.8 27.7 + - - +
464A SER 4.7 3.1 + - - +
465A LYS* 2.9 29.9 + - + +
467A GLN* 1.3 81.7 - - - +
469A CYS* 1.3 59.5 + - + +
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Residues in contact with CYS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 5.5 0.9 - - - +
224A THR 4.7 0.3 - - - +
226A LYS 5.6 0.5 + - - -
332A VAL 5.8 0.4 - - - -
333A CYS* 3.8 30.7 + - - +
365A CYS* 2.0 59.9 - - + -
366A PRO* 4.6 7.6 - - + -
465A LYS 3.2 5.9 + - - -
468A GLU* 1.3 79.0 - - + +
470A PHE* 1.3 71.6 + - - +
471A GLN* 3.7 10.7 + - - +
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Residues in contact with PHE 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 3.3 42.2 + - - +
223A ASN 3.8 7.0 - - - -
224A THR 3.4 21.8 - - - +
225A CYS* 3.8 23.3 - - + +
275A TYR* 4.0 17.7 - + + -
276A GLY 5.0 0.7 - - - -
333A CYS* 3.9 9.2 - - - -
364A VAL* 4.3 16.8 - - + -
411A PHE* 3.8 30.5 - + - -
462A ILE* 4.4 13.9 - - + -
465A LYS 4.4 0.9 - - - -
466A ALA* 3.0 40.2 + - + +
469A CYS* 1.3 91.1 - - - +
471A GLN* 1.3 59.5 + - - +
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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
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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