Contacts of the helix formed by residues 434 - 449 (chain L) 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 SER 434 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218L VAL* 6.0 2.5 - - - -
417L LEU* 3.3 17.6 - - - +
421L LYS* 5.1 3.1 - - - +
432L LYS 5.0 0.9 - - - -
433L PHE* 1.3 75.5 - - - +
435L SER* 1.3 64.5 + - - +
436L TYR* 3.2 23.4 + - - +
437L HIS* 3.0 33.6 + - - +
438L VAL 3.4 1.2 + - - -
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Residues in contact with SER 435 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L VAL* 3.0 45.8 + - - +
219L LYS* 5.4 1.3 - - - -
414L LYS* 4.0 21.4 - - - +
417L LEU* 4.3 2.1 - - - +
418L GLU* 4.7 8.3 - - - +
421L LYS* 6.0 0.2 - - - +
434L SER* 1.3 74.4 - - - +
436L TYR* 1.3 53.8 + - - +
437L HIS 3.2 0.2 - - - -
438L VAL* 3.2 12.4 + - - +
439L LYS* 2.7 39.4 + - - +
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Residues in contact with TYR 436 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376L ARG* 5.8 7.6 - - - -
379L PHE* 5.7 0.9 - - - -
383L GLU* 3.3 38.6 + - - -
434L SER* 3.0 12.4 + - - +
435L SER* 1.3 80.8 + - - +
437L HIS* 1.3 58.6 + + - +
439L LYS* 4.1 13.7 - - + +
440L THR* 2.6 55.6 + - - -
443L PHE* 6.1 0.9 - + - -
482L ASN* 3.1 30.6 + - - -
483L TYR* 4.9 1.0 + - - +
484L PHE* 4.2 7.7 - + - -
490L LEU* 3.7 24.2 - - + -
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Residues in contact with HIS 437 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417L LEU* 5.4 0.2 - - + -
432L LYS 3.2 25.4 - - - -
433L PHE* 3.6 5.8 - - + -
434L SER* 3.0 34.3 + - - +
436L TYR* 1.3 76.6 - + - +
438L VAL* 1.3 67.2 + - - +
440L THR* 3.4 0.8 + - - -
441L ALA* 3.0 22.2 + - - +
471L PHE* 3.7 6.9 - - + -
480L LEU* 3.3 14.6 - - + +
490L LEU* 3.6 40.2 + - + +
491L PHE* 3.5 31.9 - + + -
496L ILE* 4.2 8.9 - - + +
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Residues in contact with VAL 438 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410L LEU* 3.7 13.2 - - + -
413L MET* 3.3 43.0 - - + +
414L LYS* 3.7 9.4 - - + +
417L LEU* 3.5 39.9 - - + -
434L SER 3.9 0.7 - - - +
435L SER* 3.2 10.9 + - - +
437L HIS* 1.3 77.5 - - - +
439L LYS* 1.3 56.3 + - - +
441L ALA 3.3 0.9 + - - -
442L PHE* 2.9 27.5 + - - +
471L PHE* 3.7 22.0 - - + -
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Residues in contact with LYS 439 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380L SER* 5.2 2.6 + - - +
383L GLU* 2.8 47.3 + - + +
384L LYS* 5.3 0.4 - - - +
387L LEU* 4.8 9.8 - - + +
410L LEU* 3.7 33.0 - - + -
414L LYS* 5.8 4.7 - - + +
435L SER* 2.7 21.5 + - - +
436L TYR* 3.9 16.9 - - - +
438L VAL* 1.3 70.8 - - - +
440L THR* 1.3 61.1 + - - +
442L PHE* 3.2 2.1 - - + +
443L PHE* 2.9 53.8 + - + -
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Residues in contact with THR 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436L TYR* 2.6 39.7 + - - -
437L HIS 3.6 4.7 - - - -
439L LYS* 1.3 74.7 - - - +
441L ALA* 1.3 66.6 + - - +
443L PHE* 3.3 11.6 + - - +
444L HIS* 3.1 27.6 + - + -
480L LEU* 3.9 7.9 - - + -
481L GLU 2.9 33.7 - - - +
483L TYR* 3.8 14.1 + - + +
490L LEU* 3.3 21.7 - - + +
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Residues in contact with ALA 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413L MET* 4.3 5.2 - - + -
437L HIS 3.0 17.4 + - - +
438L VAL 3.6 4.3 - - - +
440L THR* 1.3 75.7 - - - +
442L PHE* 1.3 57.5 + - - +
444L HIS* 3.2 5.7 + - - +
445L VAL* 3.0 31.9 + - - +
470L TYR* 3.4 19.5 - - + -
471L PHE* 3.6 26.0 - - + -
480L LEU* 3.7 15.9 - - + +
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Residues in contact with PHE 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343L TRP* 5.5 0.9 - + - -
387L LEU* 4.1 9.9 - - + -
390L HIS* 6.1 2.5 - - + -
406L ARG* 2.8 42.6 - - + -
407L LYS* 4.2 1.3 - - + -
409L CYS* 4.2 5.4 - - + -
410L LEU* 3.8 41.1 - - + -
413L MET* 3.9 19.9 - - - +
438L VAL 2.9 18.5 + - - +
439L LYS 3.2 6.7 - - - +
441L ALA* 1.3 74.4 - - - +
443L PHE* 1.3 78.9 + + - +
445L VAL* 3.1 6.9 + - - +
446L CYS* 2.9 53.8 + - - -
455L TRP* 4.4 2.7 - + - -
467L CYS* 4.5 6.3 - - - -
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Residues in contact with PHE 443 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343L TRP* 3.8 8.1 - + + -
383L GLU* 3.7 44.9 - - + -
386L ILE* 3.4 34.5 - - + -
387L LEU* 4.0 16.4 - - + -
436L TYR* 6.1 0.9 - + - -
439L LYS* 2.9 45.3 + - + +
440L THR* 3.3 3.1 + - - +
442L PHE* 1.3 86.8 - + - +
444L HIS* 1.3 56.6 + - - +
446L CYS* 3.3 5.5 + - - +
447L THR* 2.9 30.8 + - - -
483L TYR* 3.5 43.2 - + + -
484L PHE* 5.0 1.6 - + - -
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Residues in contact with HIS 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339L ARG* 5.6 10.3 - - + +
440L THR* 3.1 24.7 + - + +
441L ALA* 3.2 8.2 + - - +
443L PHE* 1.3 78.5 - - - +
445L VAL* 1.3 57.2 + - - +
447L THR* 3.1 9.2 + - - +
448L GLN* 2.9 33.9 + - + +
470L TYR* 3.5 32.8 + + + +
480L LEU* 4.4 3.8 - - + -
481L GLU* 2.7 48.7 + - + +
482L ASN 4.7 0.9 - - - -
483L TYR* 3.7 25.8 - + - -
486L PRO* 6.3 0.4 - - + -
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Residues in contact with VAL 445 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413L MET* 5.6 0.2 - - + -
441L ALA 3.0 17.3 + - - +
442L PHE* 3.1 8.3 + - - +
444L HIS* 1.3 73.6 - - - +
446L CYS* 1.3 60.6 + - - +
448L GLN* 3.2 9.3 + - - +
449L ASN* 2.9 50.0 + - - +
455L TRP* 3.8 18.4 - - + -
466L ASN* 4.6 4.9 - - + -
467L CYS* 3.8 29.8 - - - +
470L TYR* 3.3 34.5 - - + -
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Residues in contact with CYS 446 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343L TRP* 3.4 33.2 - - + -
406L ARG* 3.6 23.3 - - - +
442L PHE* 2.9 51.9 + - - -
443L PHE 3.5 4.5 - - - +
445L VAL* 1.3 75.5 - - - +
447L THR* 1.3 58.5 + - - +
449L ASN 2.9 27.4 - - - +
450L PRO* 3.2 6.8 - - - +
455L TRP* 3.8 11.7 - - - -
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Residues in contact with THR 447 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339L ARG* 3.2 25.5 + - + +
342L ASN* 5.2 12.3 - - + +
343L TRP* 3.7 13.7 - - + +
443L PHE 2.9 11.5 + - - -
444L HIS* 3.3 14.1 - - - +
446L CYS* 1.3 78.3 - - - +
448L GLN* 1.3 61.3 + - + +
449L ASN 3.4 0.5 + - - -
450L PRO* 3.7 13.0 - - - +
483L TYR* 2.5 31.2 + - + -
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Residues in contact with GLN 448 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444L HIS* 2.9 18.8 + - + +
445L VAL* 3.2 14.7 + - - +
447L THR* 1.3 78.1 - - + +
449L ASN* 1.3 69.7 + - - +
450L PRO* 3.3 7.9 - - - +
454L GLN* 4.7 1.9 + - - -
470L TYR* 3.7 36.0 - - - +
473L GLN* 5.5 1.0 + - - -
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Residues in contact with ASN 449 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406L ARG* 3.2 4.7 + - - -
445L VAL* 2.9 39.1 + - - +
446L CYS 2.9 6.9 + - - +
448L GLN* 1.3 87.9 + - - +
450L PRO* 1.3 59.3 - - - +
451L GLN 3.4 0.7 + - - -
454L GLN* 3.3 34.1 + - + +
455L TRP* 2.7 42.5 + - + +
466L ASN* 5.5 11.0 + - - +
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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