Contacts of the helix formed by residues 543 - 560 (chain B) in PDB entry 5YDJ
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 ASN 543 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B ASP* 5.4 1.0 + - - -
540B GLU* 3.0 55.9 + - + +
541B PRO 3.4 0.8 - - - -
542B ASP* 1.3 73.8 - - - +
544B PRO* 1.4 66.5 - - - +
545B ASN* 3.0 28.2 + - - +
546B SER* 3.7 18.9 - - - -
547B ASN* 3.0 32.8 + - - -
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Residues in contact with PRO 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B THR* 3.6 24.1 - - + +
507B VAL 3.1 39.4 + - - +
508B THR* 4.7 15.3 - - + +
540B GLU* 5.1 1.8 - - - +
542B ASP 3.4 9.6 - - - +
543B ASN* 1.4 91.2 - - - +
545B ASN* 1.3 60.6 + - - +
548B ARG* 3.3 8.1 + - - +
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Residues in contact with ASN 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B THR* 3.1 17.5 - - - +
543B ASN* 3.0 15.2 + - - +
544B PRO* 1.3 77.7 - - - +
546B SER* 1.3 62.9 + - - +
548B ARG* 3.0 37.9 + - - +
549B ASP* 3.2 21.1 + - - +
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Residues in contact with SER 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B ASP* 3.0 40.9 + - - +
540B GLU 4.6 0.9 - - - -
543B ASN* 3.4 24.4 + - - -
545B ASN* 1.3 78.8 - - - +
547B ASN* 1.3 59.1 + - - +
549B ASP* 3.5 6.7 + - - +
550B ALA* 3.1 27.4 + - - +
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Residues in contact with ASN 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B VAL* 3.2 23.3 - - - +
509B ARG* 2.7 43.5 + - - +
512B PHE* 3.3 42.2 - - + +
536B THR* 5.4 1.3 - - - -
541B PRO 2.8 26.0 + - - -
542B ASP* 3.7 7.5 - - - +
543B ASN 3.0 20.9 + - - +
546B SER* 1.3 74.4 - - - +
548B ARG* 1.3 63.3 + - - +
550B ALA* 3.6 8.9 - - - +
551B LEU* 3.6 5.5 + - - +
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Residues in contact with ARG 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B TYR* 2.7 43.3 + - + +
499B LEU* 3.8 23.1 - - + +
505B VAL 3.1 26.5 + - - -
506B THR* 4.1 3.8 - - - +
507B VAL* 3.9 17.4 - - + +
544B PRO 3.3 12.1 + - - +
545B ASN* 3.0 45.3 + - - +
546B SER 3.3 0.4 - - - -
547B ASN* 1.3 76.1 - - - +
549B ASP* 1.3 66.4 + - - +
550B ALA 3.2 0.2 - - - -
551B LEU* 3.1 21.0 + - - +
552B ASP 3.5 4.2 + - - -
595B TRP* 3.6 37.9 + - - +
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Residues in contact with ASP 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B GLU* 4.2 3.6 - - - +
488B TYR* 3.3 23.6 + - - +
545B ASN 3.2 12.4 + - - +
546B SER* 3.9 7.2 - - - +
548B ARG* 1.3 80.7 + - - +
550B ALA* 1.3 62.5 + - - +
552B ASP* 3.3 5.9 + - - +
553B LYS* 3.1 53.7 + - - +
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Residues in contact with ALA 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B PHE* 3.7 8.3 - - + -
535B TYR* 3.2 37.5 - - - +
536B THR* 5.0 2.2 - - - -
537B ASP 5.8 0.4 - - - +
546B SER 3.1 17.7 + - - +
547B ASN* 3.6 11.2 - - - +
548B ARG 3.2 0.4 - - - -
549B ASP* 1.3 77.4 - - - +
551B LEU* 1.3 55.4 + - - +
553B LYS* 3.5 7.1 + - - +
554B MET* 3.2 28.6 + - - +
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Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B ILE* 3.2 30.8 - - + +
495B LEU* 6.0 0.7 - - + -
498B LEU* 4.9 4.5 - - + -
499B LEU* 5.4 4.5 - - + -
507B VAL* 4.0 35.2 - - + -
512B PHE* 3.6 17.0 - - + +
515B ALA* 3.4 34.5 - - + -
516B VAL 4.5 0.9 - - - +
519B LEU* 3.8 9.0 - - + -
547B ASN 3.7 10.3 - - - +
548B ARG 3.1 8.4 + - - +
550B ALA* 1.3 75.0 - - - +
552B ASP* 1.3 65.0 + - - +
554B MET* 3.3 34.3 - - - +
555B VAL* 3.4 5.0 - - - +
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Residues in contact with ASP 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B THR 3.6 0.5 - - - +
485B GLU* 3.2 22.4 - - - +
487B GLY* 3.1 14.1 + - - -
488B TYR* 3.0 54.1 + - + -
491B ILE* 3.5 12.6 - - - +
548B ARG 3.5 2.8 + - - -
549B ASP* 3.3 8.9 + - - +
551B LEU* 1.3 79.0 - - - +
553B LYS* 1.3 87.2 + - - +
556B GLY* 2.8 27.0 + - - -
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Residues in contact with LYS 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B THR* 3.4 13.8 + - - +
485B GLU* 3.0 22.0 + - - -
535B TYR* 3.8 14.1 - - + -
549B ASP* 3.1 39.2 + - - +
550B ALA* 3.9 2.9 - - - +
551B LEU 3.2 0.2 - - - -
552B ASP* 1.3 97.0 + - - +
554B MET* 1.3 58.2 + - - +
556B GLY* 4.7 0.9 - - - -
557B ASP* 2.7 39.8 + - - +
679B ARG* 3.5 46.9 - - - +
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Residues in contact with MET 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B PHE* 4.6 3.6 - - - -
516B VAL* 3.8 34.8 - - + -
519B LEU* 4.1 13.2 - - + -
520B ASN* 3.1 32.4 + - - +
531B ILE* 3.8 13.2 - - + -
535B TYR* 3.7 31.3 - - + -
550B ALA 3.2 12.0 + - - +
551B LEU* 3.3 30.3 - - - +
553B LYS* 1.3 78.2 - - - +
555B VAL* 1.3 64.7 + - + +
558B TYR* 3.3 26.4 + - - +
686B TRP* 3.7 9.4 - - + -
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Residues in contact with VAL 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ILE* 3.9 17.3 - - + -
447B CYS* 3.7 18.8 - - - -
487B GLY* 4.3 11.4 - - - +
491B ILE* 3.9 13.0 - - + -
519B LEU* 3.7 30.1 - - + +
551B LEU 3.4 17.6 + - - +
552B ASP 4.2 0.4 - - - +
553B LYS 3.2 0.4 - - - -
554B MET* 1.3 78.8 - - + +
556B GLY* 1.3 64.3 + - - +
557B ASP 3.3 0.2 - - - -
559B HIS* 3.2 48.1 + - + +
560B PHE* 4.0 1.5 - - + -
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Residues in contact with GLY 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486B GLU* 3.7 23.2 - - - +
487B GLY* 3.8 4.6 - - - -
552B ASP 2.8 23.7 + - - -
553B LYS* 3.7 1.6 - - - -
555B VAL* 1.3 75.1 - - - +
557B ASP* 1.3 59.0 + - - +
560B PHE* 3.4 11.1 + - - +
561B THR* 2.9 29.3 + - - -
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Residues in contact with ASP 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B TYR* 2.7 28.5 + - - +
553B LYS* 2.7 25.8 + - - +
556B GLY* 1.3 75.6 - - - +
558B TYR* 1.3 65.8 + - - +
559B HIS 3.4 0.7 + - - -
560B PHE 3.6 0.3 + - - -
561B THR* 3.6 10.1 + - - -
562B CYS* 3.0 45.7 + - - +
679B ARG* 2.8 49.0 + - - -
682B GLN* 3.4 7.5 - - - +
686B TRP* 3.9 1.3 - - - +
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Residues in contact with TYR 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B PRO* 3.7 29.0 - - + +
520B ASN* 4.8 13.0 - - - -
554B MET 3.3 19.3 + - - +
555B VAL 4.4 0.7 - - - +
557B ASP* 1.3 79.9 - - - +
559B HIS* 1.3 93.8 + + + +
562B CYS* 5.0 1.9 - - - +
563B ASN* 2.9 20.3 + - - +
686B TRP* 3.4 56.5 - + + +
690B LEU* 6.0 0.4 - - + -
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Residues in contact with HIS 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ALA* 3.8 5.0 - - - +
392B PRO* 4.0 11.7 - - + +
393B TRP* 3.2 29.4 + - + -
446B ILE* 4.0 13.5 + - - +
447B CYS* 3.4 36.4 + - + +
519B LEU 5.4 2.6 + - - -
520B ASN* 5.8 0.2 + - - -
555B VAL* 3.2 43.4 + - + +
558B TYR* 1.3 105.0 - + - +
560B PHE* 1.3 76.4 + - + +
563B ASN* 3.1 16.8 + - - +
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Residues in contact with PHE 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B SEB 4.7 1.1 - - - -
386B SER* 3.7 20.4 - - - +
387B GLY* 6.2 0.9 - - - -
388B SER* 5.3 0.2 - - - -
393B TRP* 3.8 30.3 - + - -
447B CYS* 4.2 8.3 - - - -
449B PHE* 6.0 0.4 - + - -
486B GLU* 3.9 35.9 - - + +
490B PHE* 3.4 41.1 - + - -
555B VAL* 4.0 6.1 - - + -
556B GLY* 3.4 9.6 + - - +
557B ASP 3.6 1.0 + - - -
559B HIS* 1.3 95.1 - - + +
561B THR* 1.3 69.1 + - - +
562B CYS 3.2 2.6 + - - -
563B ASN* 3.2 6.3 + - - +
564B VAL* 3.2 27.8 + - - +
600B HIS* 3.5 22.4 - + - -
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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
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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