Contacts of the helix formed by residues 405 - 424 (chain K) in PDB entry 6Y5D
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 CYS 405 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404K CYS* 1.3 72.7 - - - +
406K ARG* 1.3 60.0 + - - +
407K LYS 3.3 2.5 - - - -
408K ASP* 3.7 11.7 - - + +
409K CYS* 2.7 33.8 + - - -
455K TRP* 2.6 26.4 + - - +
456K ASP 3.7 4.7 - - - -
457K ARG* 4.1 11.9 - - - -
460K LEU* 3.7 24.2 - - + -
463K CYS* 3.4 40.4 - - - -
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Residues in contact with ARG 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343K TRP* 3.5 17.1 - - - +
390K HIS* 3.7 31.0 + - + -
391K GLY* 4.8 0.2 - - - -
392K LYS 6.1 0.2 - - - -
404K CYS* 3.5 22.7 - - - -
405K CYS* 1.3 77.8 - - - +
407K LYS* 1.3 64.2 + - - +
410K LEU 3.0 7.8 + - - -
442K PHE* 2.9 32.1 - - + -
446K CYS* 3.6 18.3 - - - +
449K ASN 3.1 17.4 + - - -
450K PRO* 3.0 30.9 + - - +
451K GLN 3.3 4.0 + - - -
452K ASP* 2.7 28.3 + - - +
455K TRP* 3.2 45.7 - - + +
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Residues in contact with LYS 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387K LEU* 4.0 21.1 + - + +
388K ASN* 4.3 15.8 + - - +
390K HIS* 3.9 34.9 - - + +
397K CYS* 4.6 13.3 - - + +
403K LYS* 4.6 11.5 - - - +
404K CYS* 4.9 1.9 + - - +
405K CYS* 3.3 0.4 - - - +
406K ARG* 1.3 79.1 - - - +
408K ASP* 1.3 63.1 + - - +
410K LEU* 3.4 8.2 + - - +
411K LYS* 3.1 54.0 + - - +
442K PHE* 4.7 1.8 - - - -
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Residues in contact with ASP 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K ARG* 2.7 34.0 + - - -
169K LEU* 3.5 28.2 - - + +
403K LYS* 3.7 25.6 + - - -
405K CYS* 3.3 11.6 + - - +
407K LYS* 1.3 78.0 - - - +
409K CYS* 1.3 64.4 + - - +
411K LYS* 3.3 5.5 + - - +
412K LEU* 3.0 27.4 + - - +
460K LEU* 3.6 15.5 - - + -
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Residues in contact with CYS 409 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405K CYS* 2.7 31.4 + - - +
406K ARG 3.6 3.8 - - - +
408K ASP* 1.3 72.4 - - - +
410K LEU* 1.3 56.6 + - - +
412K LEU* 3.2 4.6 + - - +
413K MET* 2.8 35.4 + - - +
442K PHE* 4.4 0.9 - - + -
455K TRP* 3.7 8.3 - - + -
460K LEU* 3.8 7.2 - - - -
463K CYS* 3.6 19.7 - - - -
464K PHE* 3.4 37.4 - - - -
467K CYS* 3.7 17.7 - - - -
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Residues in contact with LEU 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387K LEU* 3.2 36.6 - - + -
406K ARG 3.0 5.5 + - - -
407K LYS* 3.7 9.2 - - - +
409K CYS* 1.3 74.7 - - - +
411K LYS* 1.3 63.0 + - + +
413K MET* 3.2 2.4 + - - -
414K LYS* 2.8 54.1 + - + +
438K VAL* 3.8 12.6 - - + -
439K LYS* 3.8 24.7 - - + -
442K PHE* 3.6 48.4 - - + -
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Residues in contact with LYS 411 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K LEU* 3.6 28.0 - - + +
172K LEU* 5.1 1.8 - - + -
173K LYS* 6.3 3.4 - - + -
220K ILE* 3.6 36.4 - - + +
407K LYS* 3.1 47.1 + - - +
408K ASP* 3.7 3.3 + - - +
410K LEU* 1.3 77.4 - - + +
412K LEU* 1.3 52.0 + - - +
414K LYS* 3.3 14.4 + - + +
415K TYR* 2.8 36.2 + - - +
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Residues in contact with LEU 412 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K LEU* 3.8 46.0 - - + +
168K VAL* 4.0 18.4 - - + -
169K LEU* 4.0 19.5 - - + -
172K LEU* 5.6 0.2 - - + -
408K ASP 3.0 19.5 + - - +
409K CYS 3.5 1.3 - - - +
411K LYS* 1.3 74.4 - - - +
413K MET* 1.3 55.0 + - - +
415K TYR* 3.6 4.7 - - - +
416K LEU* 2.7 34.7 + - - +
460K LEU* 3.7 26.7 - - + -
464K PHE* 3.3 27.5 - - + -
519K PHE* 3.8 8.1 - - + -
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Residues in contact with MET 413 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409K CYS 2.8 24.2 + - - +
410K LEU* 3.5 3.1 - - - +
412K LEU* 1.3 72.3 - - - +
414K LYS* 1.3 65.9 + - - +
416K LEU* 3.3 7.0 + - - +
417K LEU* 3.0 23.4 + - - +
438K VAL* 3.3 41.5 - - + +
441K ALA* 4.5 3.8 - - + -
442K PHE* 3.9 33.2 - - + +
445K VAL* 5.3 0.7 - - + -
464K PHE* 3.4 18.6 - - + -
467K CYS* 3.6 39.9 - - + +
468K VAL* 5.0 3.8 - - + -
471K PHE* 4.2 16.8 - - + -
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Residues in contact with LYS 414 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217K HIS 4.0 12.7 + - - -
218K VAL* 3.1 27.8 + - - +
220K ILE* 4.0 16.8 - - + +
387K LEU* 5.7 5.9 - - - +
410K LEU* 2.8 54.6 + - + +
411K LYS* 3.6 11.5 - - + +
413K MET* 1.3 71.9 - - - +
415K TYR* 1.3 52.9 + - - +
417K LEU* 3.2 2.8 + - - +
418K GLU* 2.8 52.7 + - - +
435K SER* 4.0 18.6 - - - +
438K VAL* 4.0 13.0 - - + -
439K LYS* 5.7 5.9 - - + +
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Residues in contact with TYR 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K VAL* 3.3 29.4 - - + -
171K LYS* 3.8 11.0 + - - -
172K LEU* 3.5 32.7 - - + +
220K ILE* 3.6 9.1 - - + +
221K SER* 3.8 14.6 - - - -
411K LYS 2.8 17.6 + - - +
412K LEU* 3.6 5.4 - - + +
413K MET 3.2 0.2 - - - -
414K LYS* 1.3 74.4 - - - +
416K LEU* 1.3 55.2 + - - +
418K GLU* 4.3 2.0 - - - -
419K GLN* 2.7 72.4 + - + +
519K PHE* 2.7 58.0 + + - -
522K PHE* 4.0 4.7 + - - -
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Residues in contact with LEU 416 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412K LEU 2.7 20.4 + - - +
413K MET* 3.3 6.9 + - - +
415K TYR* 1.3 73.2 - - - +
417K LEU* 1.3 63.0 + - - +
419K GLN* 3.8 1.6 - - - +
420K LEU* 3.0 51.1 + - + +
464K PHE* 4.1 2.2 - - + -
468K VAL* 4.1 15.5 - - + -
508K ILE* 4.0 27.6 - - + -
511K GLU* 4.3 7.0 - - + -
516K PHE* 3.8 38.4 - - + -
518K VAL* 4.3 9.2 - - + -
519K PHE* 3.7 15.6 - - + -
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Residues in contact with LEU 417 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K MET 3.0 13.7 + - - +
414K LYS 3.7 5.8 - - - +
416K LEU* 1.3 78.4 - - - +
418K GLU* 1.3 55.3 + - + +
420K LEU* 3.2 4.2 + - - -
421K LYS* 2.7 53.1 + - + +
430K LEU* 5.1 0.7 - - + -
433K PHE* 3.9 13.7 - - + -
434K SER* 3.3 43.3 - - - +
435K SER* 4.2 2.2 - - - +
437K HIS* 5.5 0.2 - - + -
438K VAL* 3.6 18.4 - - + -
471K PHE* 5.0 6.5 - - + -
504K LEU* 3.6 39.3 - - + -
508K ILE* 6.2 1.1 - - + -
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Residues in contact with GLU 418 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218K VAL 4.0 1.6 - - - +
219K LYS* 3.1 25.2 - - + +
220K ILE* 2.8 28.0 + - - +
221K SER* 2.7 42.5 + - - +
414K LYS* 2.8 40.0 + - - +
415K TYR 3.8 2.2 - - - +
417K LEU* 1.3 75.6 - - + +
419K GLN* 1.3 58.8 + - - +
421K LYS* 3.3 13.6 + - + +
422K GLU* 2.8 30.2 + - - +
435K SER* 4.7 7.0 - - - +
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Residues in contact with GLN 419 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221K SER* 4.2 10.4 + - - -
415K TYR* 2.7 68.7 + - + +
416K LEU 3.8 0.2 - - - +
418K GLU* 1.3 72.9 - - - +
420K LEU* 1.3 57.5 + - - +
422K GLU* 3.3 1.7 + - - +
423K ARG* 2.8 28.8 + - - +
518K VAL* 2.7 49.2 + - + +
519K PHE 4.4 0.2 + - - -
522K PHE* 2.8 50.3 + - - +
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Residues in contact with LEU 420 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416K LEU* 3.0 34.0 + - + +
417K LEU 3.8 2.5 - - - +
419K GLN* 1.3 73.0 - - - +
421K LYS* 1.3 61.2 + - - +
423K ARG* 3.9 6.5 - - - +
424K PHE* 2.8 45.1 + - + -
430K LEU* 3.4 15.7 - - + +
504K LEU* 3.8 12.3 - - + -
507K GLN* 4.0 20.4 - - + -
508K ILE* 3.6 34.1 - - + +
511K GLU* 3.9 27.6 - - + +
518K VAL* 4.5 7.0 - - + -
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Residues in contact with LYS 421 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K LYS* 5.6 10.8 - - - +
417K LEU* 2.7 44.8 + - + +
418K GLU* 3.6 11.4 - - + +
420K LEU* 1.3 74.2 - - - +
422K GLU* 1.3 52.3 + - - +
425K LYS* 2.7 39.5 + - - +
430K LEU* 2.9 43.1 + - + +
431K ASP* 3.3 16.0 + - - +
433K PHE 2.6 29.5 + - - +
434K SER* 5.1 2.5 - - - +
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Residues in contact with GLU 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K GLU 2.8 18.2 + - - +
419K GLN* 3.6 5.2 - - - +
421K LYS* 1.3 73.4 - - - +
423K ARG* 1.3 65.6 + - - +
424K PHE 3.2 0.7 + - - -
425K LYS* 2.8 59.5 + - - +
426K ASP* 4.7 0.7 - - - +
522K PHE* 3.5 27.1 - - + -
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Residues in contact with ARG 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419K GLN 2.8 20.8 + - - +
420K LEU* 3.4 9.3 - - - +
422K GLU* 1.3 75.5 - - - +
424K PHE* 1.3 98.2 + - + +
425K LYS 3.8 0.5 + - - -
426K ASP* 4.4 8.1 - - - +
507K GLN* 4.3 3.8 + - - -
510K TYR* 5.3 6.5 - - - -
511K GLU* 3.0 27.3 + - - -
517K PRO* 5.2 1.6 - - - +
518K VAL* 3.3 19.0 - - + +
521K GLU* 2.9 33.3 + - - -
522K PHE* 4.0 12.6 - - + -
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Residues in contact with PHE 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420K LEU* 2.8 33.8 + - + +
421K LYS* 3.4 3.1 - - - -
423K ARG* 1.3 108.9 - - + +
425K LYS* 1.3 56.8 + - - +
426K ASP* 2.9 5.8 - - - +
427K LYS* 2.9 48.1 + - + +
428K LYS* 3.1 9.7 + - - -
429K HIS* 4.2 2.5 + - + -
430K LEU* 4.2 11.1 + - + -
503K PHE* 3.5 34.3 - + + -
507K GLN* 2.9 42.2 - - + -
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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