Contacts of the helix formed by residues 520 - 543 (chain B) in PDB entry 5Y41
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 GLU 520 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B LEU* 5.1 0.7 - - + -
431B PRO* 3.3 29.5 - - + +
434B ASP* 2.8 18.9 + - - +
518B LEU* 4.5 1.3 - - - -
519B LYS* 1.3 77.0 - - - +
521B PRO* 1.4 64.8 - - - +
522B LYS* 3.3 2.9 - - - -
523B ARG* 3.0 52.3 + - + +
524B VAL* 3.2 14.9 + - - +
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Residues in contact with PRO 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B GLU* 6.6 0.4 - - + -
515B ARG 5.7 0.7 - - - +
518B LEU* 3.4 40.8 - - + +
519B LYS 3.4 5.4 - - - +
520B GLU* 1.4 87.2 - - - +
522B LYS* 1.3 62.5 + - + +
524B VAL* 3.4 3.5 + - - +
525B GLU* 2.9 28.8 + - - +
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLU 3.3 1.0 - - - -
521B PRO* 1.3 82.3 - - + +
523B ARG* 1.3 58.2 + - - +
525B GLU* 3.3 7.6 + - - +
526B GLU* 2.9 29.1 + - - +
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Residues in contact with ARG 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLY 5.1 1.3 - - - -
429B ASP* 3.7 37.2 + - - +
430B LEU* 3.2 27.5 - - + +
520B GLU* 3.0 41.4 + - + +
522B LYS* 1.3 76.7 - - - +
524B VAL* 1.3 65.3 + - - +
526B GLU* 3.3 8.4 + - + +
527B LEU* 3.0 24.1 + - + +
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 4.0 17.7 - - + -
434B ASP* 4.9 2.0 - - - +
438B LEU* 3.9 24.2 - - + -
512B VAL* 3.5 13.0 - - + +
513B THR* 3.7 40.4 - - - +
514B GLU* 4.5 1.3 - - - +
518B LEU* 4.1 22.7 - - + -
520B GLU 3.2 13.0 + - - +
521B PRO 3.6 7.2 - - - +
523B ARG* 1.3 74.4 - - - +
525B GLU* 1.3 57.9 + - - +
527B LEU* 3.2 2.7 + - - -
528B GLN* 2.8 27.9 + - + +
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Residues in contact with GLU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B GLU* 4.0 15.3 - - + +
521B PRO 2.9 17.4 + - - +
522B LYS* 3.6 8.5 - - - +
523B ARG 3.2 0.2 - - - -
524B VAL* 1.3 79.3 - - - +
526B GLU* 1.3 58.0 + - - +
528B GLN* 2.6 30.2 - - - +
529B ASN* 3.0 34.7 + - - +
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Residues in contact with GLU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B LYS 2.9 17.5 + - - +
523B ARG* 3.3 9.6 + - + +
525B GLU* 1.3 75.8 + - - +
527B LEU* 1.3 59.6 + - - +
529B ASN* 3.3 7.2 + - + +
530B LYS* 2.8 67.0 + - + +
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 4.8 9.0 - - + -
424B ILE* 4.2 5.2 - - + -
425B PRO 3.4 28.3 - - - +
426B GLY* 4.1 7.0 - - - +
427B PHE* 4.1 17.3 - - - +
430B LEU* 5.2 8.1 - - + -
512B VAL* 3.9 28.5 - - + -
523B ARG* 3.0 16.9 + - + +
524B VAL* 3.7 4.3 - - - +
526B GLU* 1.3 74.1 + - - +
528B GLN* 1.3 65.5 + - - +
530B LYS* 3.2 19.1 + - + +
531B ILE* 3.0 41.8 + - + +
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Residues in contact with GLN 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B LEU* 3.6 18.1 + - + +
512B VAL* 3.4 21.0 + - - +
513B THR* 3.4 24.7 + - - +
514B GLU* 2.8 31.4 + - - +
524B VAL 2.8 13.2 + - - +
525B GLU* 2.6 37.5 - - - +
527B LEU* 1.3 75.8 - - - +
529B ASN* 1.3 57.4 + - - +
531B ILE* 3.1 6.6 + - - +
532B VAL* 2.9 35.9 + - + +
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Residues in contact with ASN 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLU* 3.0 27.5 + - - +
526B GLU* 3.7 8.0 + - + +
528B GLN* 1.3 78.6 + - - +
530B LYS* 1.3 57.4 + - - +
532B VAL* 3.3 11.9 + - - +
533B ASN* 2.5 60.3 + - - +
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Residues in contact with LYS 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 3.8 19.0 - - + +
526B GLU* 2.8 45.1 + - + +
527B LEU* 3.2 19.9 + - + +
529B ASN* 1.3 77.0 - - - +
531B ILE* 1.3 63.3 + - - +
533B ASN* 3.3 10.6 + - - +
534B CYS* 3.1 24.9 + - - -
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Residues in contact with ILE 531 (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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364B LEU* 4.1 18.2 - - + -
368B LEU* 3.9 20.4 - - + -
424B ILE* 4.5 6.3 - - + -
505B CYS* 3.4 28.4 - - + +
508B ALA* 3.9 20.4 - - + -
509B LEU* 3.8 10.3 - - + -
512B VAL* 4.1 18.6 - - + -
527B LEU* 3.0 35.5 + - + +
528B GLN* 3.5 5.8 - - - +
530B LYS* 1.3 74.1 - - - +
532B VAL* 1.3 65.0 + - - +
534B CYS* 3.3 5.4 - - - +
535B LEU* 3.1 21.7 + - - +
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Residues in contact with VAL 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B LEU* 3.8 27.8 - - + -
528B GLN* 2.9 25.2 + - + +
529B ASN* 3.7 15.7 - - - +
531B ILE* 1.3 75.3 - - - +
533B ASN* 1.3 61.0 + - - +
535B LEU* 3.2 8.8 + - + +
536B LYS* 2.9 53.5 + - + +
552B LEU* 6.1 0.2 - - + -
556B LEU* 5.3 14.6 - - + -
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Residues in contact with ASN 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ASN* 2.5 47.7 + - - +
530B LYS* 3.6 8.7 - - - +
532B VAL* 1.3 78.7 - - - +
534B CYS* 1.3 59.2 + - - +
536B LYS* 3.7 17.4 + - - +
537B ASP* 3.0 41.1 + - - +
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Residues in contact with CYS 534 (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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541A PHE* 4.9 1.8 - - - -
364B LEU* 3.5 35.7 - - - -
365B ILE* 3.9 21.1 - - + +
368B LEU* 4.8 1.1 - - - -
505B CYS* 3.8 15.5 - - - -
530B LYS 3.1 18.7 + - - -
531B ILE* 3.3 10.1 - - - +
533B ASN* 1.3 73.3 - - - +
535B LEU* 1.3 59.6 + - - +
537B ASP* 3.4 6.3 + - - +
538B HIS* 2.8 31.9 + - - +
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Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ALA* 3.7 41.5 - - + +
505B CYS* 3.8 12.8 - - + -
506B ILE* 3.7 27.1 - - + -
509B LEU* 4.2 9.2 - - + -
531B ILE 3.1 9.0 + - - +
532B VAL* 3.4 10.3 - - + +
534B CYS* 1.3 80.7 - - - +
536B LYS* 1.3 53.1 + - - +
538B HIS* 3.2 5.9 + - + +
539B VAL* 2.9 42.2 + - + +
552B LEU* 3.8 16.6 - - + -
555B LEU* 4.0 13.2 - - + -
556B LEU* 3.8 17.9 - - + -
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Residues in contact with LYS 536 (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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532B VAL* 2.9 39.3 + - + +
533B ASN* 3.7 16.5 + - - +
535B LEU* 1.3 76.2 - - - +
537B ASP* 1.3 64.2 + - - +
539B VAL* 3.4 3.1 + - - +
540B THR* 3.0 30.8 + - - +
552B LEU* 3.7 36.1 - - + -
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Residues in contact with ASP 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A PHE* 3.6 20.1 - - + -
533B ASN* 3.0 26.2 + - - +
534B CYS* 3.9 5.1 - - - +
536B LYS* 1.3 74.4 - - - +
538B HIS* 1.3 60.9 + - - +
540B THR* 3.5 5.5 + - - -
541B PHE* 2.8 32.2 + - - +
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Residues in contact with HIS 538 (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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541A PHE* 3.8 8.6 - - + -
602A PGE 3.3 31.7 + - - -
365B ILE* 3.7 16.4 - - + -
499B ASP* 2.8 40.0 + - - -
501B SER* 3.4 19.4 + - - -
502B ALA* 4.1 12.6 + - + +
534B CYS 2.8 19.1 + - - +
535B LEU* 3.2 7.4 + - + +
537B ASP* 1.3 76.6 - - - +
539B VAL* 1.3 66.8 + - - +
541B PHE* 3.3 2.1 + - - +
542B ASN* 2.9 42.8 + - - +
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Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ALA* 5.0 2.9 - - + -
535B LEU* 2.9 40.3 + - + +
536B LYS* 3.8 5.6 - - - +
538B HIS* 1.3 77.7 - - - +
540B THR* 1.3 62.3 + - - +
542B ASN* 3.4 5.9 + - - +
543B ASN* 3.1 22.3 + - - +
548B ARG* 3.9 42.2 + - + +
551B TYR* 4.0 27.4 - - + -
552B LEU* 4.5 11.9 - - + -
555B LEU* 4.5 2.5 - - + -
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Residues in contact with THR 540 (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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536B LYS* 3.0 18.7 + - - +
537B ASP* 3.8 6.1 - - - -
539B VAL* 1.3 74.2 - - - +
541B PHE* 1.3 64.0 + - - +
543B ASN 3.0 9.4 + - - -
545B GLY* 2.9 49.9 + - - +
546B LEU 3.6 10.4 - - - +
547B ASN* 2.9 31.7 + - - +
548B ARG 4.8 0.9 + - - -
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Residues in contact with PHE 541 (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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365A ILE* 6.0 2.9 - - + -
537A ASP* 4.0 29.4 - - + -
538A HIS 4.9 0.2 - - - -
541A PHE* 3.5 37.7 - + + -
602A PGE 3.5 32.3 - - - -
537B ASP 2.8 22.5 + - - +
538B HIS 3.7 2.7 - - - +
540B THR* 1.3 72.6 - - - +
542B ASN* 1.3 76.6 - - - +
544B GLY* 3.0 19.4 + - - -
545B GLY* 4.0 4.2 + - - +
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Residues in contact with ASN 542 (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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363A SER* 5.4 12.0 + - - -
365A ILE* 5.9 4.0 - - - +
602A PGE 4.9 1.4 + - - -
499B ASP* 3.0 11.6 - - - +
538B HIS* 2.9 48.5 + - - +
539B VAL* 3.8 6.7 - - - +
541B PHE* 1.3 97.9 - - - +
543B ASN* 1.3 57.1 + - - +
544B GLY 3.3 2.6 + - - -
548B ARG* 6.0 4.3 - - - +
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Residues in contact with ASN 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B VAL 3.1 11.9 + - - +
540B THR 3.0 2.6 + - - -
542B ASN* 1.3 77.8 - - - +
544B GLY* 1.3 61.4 + - - +
545B GLY 3.2 3.1 + - - -
546B LEU* 3.4 46.1 + - - +
547B ASN 4.1 1.6 + - - -
548B ARG* 3.5 35.0 + - - +
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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