Contacts of the helix formed by residues 537 - 553 (chain B) in PDB entry 5J3V
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 537 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B LYS* 3.5 8.7 + - - +
497B GLN* 3.4 34.6 + - - +
498B GLU* 3.3 44.0 + - - +
533B TYR* 3.4 28.4 - - + -
534B GLN 4.7 3.2 - - - +
535B HIS 4.5 1.2 - - - +
536B LYS* 1.3 83.0 - - - +
538B LEU* 1.3 55.0 + - - +
539B LEU 3.1 1.8 - - - -
540B ILE* 3.1 11.1 + - + +
541B LEU* 2.7 34.5 + - - +
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Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B PHE* 3.9 42.0 - - + +
533B TYR* 3.8 23.0 - - + +
535B HIS* 3.8 50.3 - - + +
536B LYS 3.4 0.2 - - - -
537B ASN* 1.3 76.3 - - - +
539B LEU* 1.3 59.7 + - + +
541B LEU* 3.7 6.2 - - + +
542B TYR* 2.7 53.1 + - + +
572B LYS* 4.3 17.5 - - + +
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B HIS 4.6 13.7 - - - +
536B LYS* 3.8 13.6 + - - +
538B LEU* 1.3 83.4 - - + +
540B ILE* 1.3 59.7 + - - +
542B TYR* 3.7 9.2 - - + +
543B ASP 3.5 9.9 + - - -
582B ASP* 5.6 5.2 - - - +
585B PRO* 3.6 36.3 - - + +
20D LEU* 5.4 5.2 - - + -
21D ALA* 4.9 15.5 - - + +
22D THR* 3.3 38.8 + - + +
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Residues in contact with ILE 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B GLU* 3.9 40.6 - - + +
501B CYS* 3.9 8.2 - - + +
502B SER* 3.6 39.3 - - - +
505B ALA* 5.5 0.2 - - - +
536B LYS 4.5 11.0 - - - +
537B ASN* 3.1 8.6 + - + +
539B LEU* 1.3 74.2 - - - +
541B LEU* 1.3 61.8 + - - +
542B TYR 3.3 0.4 - - - -
543B ASP* 3.1 10.7 + - + +
544B ALA* 3.0 24.3 + - - +
22D THR* 3.7 21.8 - - + -
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Residues in contact with LEU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE* 5.0 0.2 - - + -
501B CYS* 3.7 20.8 - - - -
526B LEU* 3.8 34.5 - - + +
529B ALA* 3.4 38.4 - - + +
530B PHE* 3.6 27.6 - - + +
533B TYR* 3.5 14.6 - - + -
537B ASN 2.7 20.6 + - - +
538B LEU* 3.2 6.7 + - + +
540B ILE* 1.3 71.4 - - - +
542B TYR* 1.3 64.6 + - - +
544B ALA 3.1 0.9 + - - -
545B ILE* 3.0 28.0 + - + +
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Residues in contact with TYR 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B PHE* 3.5 38.7 - + - -
538B LEU* 2.7 40.7 + - + +
539B LEU* 3.7 8.7 - - + +
541B LEU* 1.3 72.7 - - - +
543B ASP* 1.3 56.8 + - - +
545B ILE* 4.7 1.6 - - + -
546B GLY* 2.9 26.3 + - - -
569B LEU* 4.1 4.5 - - + -
572B LYS* 3.6 25.5 - - - +
576B LEU* 5.8 0.3 - - - +
582B ASP 5.2 3.1 + - - -
585B PRO* 3.5 41.1 - - + +
586B LEU* 3.6 33.0 - - + +
588B GLU* 5.5 2.3 - - - +
589B CYS* 3.6 27.9 - - + +
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Residues in contact with ASP 543 (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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502B SER* 5.3 1.4 + - - +
505B ALA* 3.6 7.7 - - + +
539B LEU 3.5 3.3 + - - +
540B ILE* 3.1 15.5 + - - +
542B TYR* 1.3 79.2 - - - +
544B ALA* 1.3 55.7 + - - +
546B GLY* 5.1 0.7 - - - -
547B THR* 2.7 40.4 + - - -
588B GLU* 5.9 2.2 - - - -
22D THR* 3.8 25.2 - - - +
23D LYS* 3.6 21.7 + - - +
26D ARG* 2.7 43.2 + - - +
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Residues in contact with ALA 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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501B CYS* 3.7 34.1 - - - +
504B PHE* 5.1 4.7 - - + -
505B ALA* 4.3 6.0 - - + +
508B GLU* 2.9 28.2 - - - +
526B LEU* 4.2 19.7 - - + +
540B ILE 3.0 5.6 + - - +
541B LEU 3.1 8.0 + - - +
543B ASP* 1.3 77.8 - - - +
545B ILE* 1.3 61.5 + - - +
548B LEU* 3.1 12.5 + - - +
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Residues in contact with ILE 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LEU* 5.7 2.7 - - + -
526B LEU* 4.4 28.3 - - + +
527B VAL* 5.5 1.1 - - - +
530B PHE* 4.3 28.9 - - + -
541B LEU* 3.0 20.9 + - + +
542B TYR* 3.9 3.4 - - - +
544B ALA* 1.3 74.7 - - - +
546B GLY* 1.3 64.3 + - - +
548B LEU* 3.3 9.8 + - + +
549B ALA* 3.2 20.6 + - - +
556B LEU* 5.8 0.5 - - - +
565B LEU* 3.9 35.0 - - + -
569B LEU* 4.9 7.6 - - + -
589B CYS* 3.9 16.4 - - - -
593B VAL* 4.2 11.7 - - + -
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Residues in contact with GLY 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B TYR 2.9 16.5 + - - -
543B ASP* 4.0 0.7 - - - -
545B ILE* 1.3 77.5 - - - +
547B THR* 1.3 60.4 + - - +
549B ALA* 3.2 3.0 + - - -
550B ASP* 3.2 27.2 + - - +
588B GLU* 6.0 0.7 - - - -
589B CYS* 4.0 13.9 - - - -
592B SER* 3.4 22.8 - - - -
593B VAL* 5.2 0.2 - - - -
23D LYS* 5.9 0.2 - - - -
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Residues in contact with THR 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ALA* 3.5 24.0 - - - +
508B GLU* 3.6 17.9 - - + -
509B GLU* 3.6 22.7 - - + +
543B ASP* 2.7 35.3 + - - -
546B GLY* 1.3 73.8 - - - +
548B LEU* 1.3 66.7 + - - +
550B ASP* 3.1 17.8 + - + +
551B SER* 3.0 21.4 + - - +
23D LYS* 3.5 9.2 + - - +
26D ARG* 3.2 9.7 + - - -
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Residues in contact with LEU 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B GLU* 3.3 20.8 + - - +
515B LEU* 4.5 11.7 - - + -
519B LEU* 3.9 29.6 - - + -
522B ILE* 4.4 13.5 - - + -
523B LEU* 4.2 21.1 - - + -
526B LEU* 4.0 21.8 - - + -
544B ALA 3.1 18.4 + - - +
545B ILE* 3.4 9.4 - - + +
546B GLY 3.2 0.2 - - - -
547B THR* 1.3 77.5 - - - +
549B ALA* 1.3 60.8 - - - +
551B SER* 3.2 4.1 + - - -
552B VAL* 3.1 37.4 + - + +
556B LEU* 4.9 7.2 - - + -
565B LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 549 (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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545B ILE 3.2 9.8 + - - +
546B GLY 3.6 8.3 - - - +
547B THR 3.2 0.2 - - - -
548B LEU* 1.3 79.9 - - - +
550B ASP* 1.3 59.1 + - - +
551B SER 3.2 0.4 - - - -
552B VAL* 4.4 4.9 - - - -
553B GLY* 3.3 21.2 + - - -
556B LEU* 4.2 10.7 - - + +
592B SER* 3.3 27.7 - - - +
593B VAL* 3.9 8.7 - - + +
596B ALA* 3.5 22.6 - - + +
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Residues in contact with ASP 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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546B GLY 3.2 12.7 + - - +
547B THR* 3.1 12.9 + - + +
549B ALA* 1.3 77.9 - - - +
551B SER* 1.3 60.9 + - - +
553B GLY* 4.6 2.1 - - - -
592B SER* 3.1 33.4 + - - +
595B THR* 5.6 2.8 - - - +
17D ARG* 4.2 7.8 + - - -
23D LYS* 5.1 7.6 + - - -
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Residues in contact with SER 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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508B GLU* 2.8 31.4 + - - +
509B GLU* 4.1 5.4 + - - -
512B CYS* 3.6 36.8 - - - +
513B THR* 3.9 10.0 - - - +
515B LEU* 4.8 4.3 - - - -
547B THR* 3.0 16.7 + - - +
548B LEU* 3.2 7.1 + - - -
550B ASP* 1.3 82.5 - - - +
552B VAL* 1.3 65.5 + - - +
553B GLY 3.4 0.4 + - - -
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Residues in contact with VAL 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B CYS 4.1 12.6 - - - +
513B THR* 5.0 3.3 - - - +
515B LEU* 4.4 6.3 - - + -
516B VAL* 4.2 12.6 - - + -
519B LEU* 4.0 30.1 - - + -
548B LEU* 3.1 26.6 + - + +
549B ALA* 4.4 2.2 - - - -
551B SER* 1.3 79.1 - - - +
553B GLY* 1.3 64.1 + - - +
554B HIS* 3.3 0.7 + - - -
555B HIS* 2.8 40.4 + - + -
556B LEU* 4.0 30.3 - - + +
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Residues in contact with GLY 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ALA 3.3 15.6 + - - -
550B ASP 5.3 1.6 - - - -
551B SER 3.4 3.0 - - - +
552B VAL* 1.3 78.6 - - - +
554B HIS* 1.3 59.6 + - - -
555B HIS 3.1 4.6 + - - -
556B LEU* 3.4 8.5 + - - +
596B ALA* 3.2 28.7 - - - +
598B GLN* 5.4 0.4 - - - -
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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