Contacts of the helix formed by residues 544 - 565 (chain C) in PDB entry 5Y3R
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 ILE 544 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542C ASP 3.2 4.9 + - - -
543C SER* 1.3 73.5 - - - +
545C LEU* 1.3 63.3 + - - +
546C ALA* 2.9 11.4 - - + +
547C ASP* 3.2 47.1 - - - +
548C GLU* 2.6 23.6 - - - +
632C GLU* 4.2 10.5 - - - +
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Residues in contact with LEU 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C VAL* 4.7 11.0 - - + -
537C SER 4.3 4.7 - - - +
538C ASP* 3.0 36.0 - - - +
539C GLN* 3.9 10.1 - - - +
540C MET 3.2 30.1 - - - +
541C MET 4.7 4.7 - - - +
542C ASP 4.1 11.1 + - - +
543C SER 3.2 1.6 + - - +
544C ILE* 1.3 74.8 - - - +
546C ALA* 1.3 66.3 + - - +
548C GLU* 2.9 27.6 - - - +
549C ALA* 3.0 19.5 + - - +
630C CYS* 5.6 0.7 - - - -
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Residues in contact with ALA 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C ILE* 2.9 8.1 - - + +
545C LEU* 1.3 75.1 - - - +
547C ASP* 1.3 69.8 + - - +
549C ALA* 2.6 19.0 + - - +
550C PHE 2.7 10.4 + - - -
630C CYS* 4.0 18.5 - - + -
632C GLU* 3.3 26.5 - - - +
633C ILE* 3.4 24.8 - - + +
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Residues in contact with ASP 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C ILE* 3.2 35.0 - - + +
546C ALA* 1.3 72.0 - - - +
548C GLU* 1.3 69.0 + - + +
550C PHE* 2.9 18.3 + - - -
551C PHE* 2.9 37.5 + - + -
632C GLU* 4.4 2.6 - - - +
633C ILE* 3.6 18.2 - - - +
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Residues in contact with GLU 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C VAL* 3.8 21.1 - - - +
465C PHE* 4.7 29.5 - - + +
537C SER 4.7 5.1 - - - +
538C ASP* 5.7 0.5 - - - -
543C SER 2.9 15.4 - - - +
544C ILE 2.6 23.5 - - - +
545C LEU* 2.9 28.4 - - - +
547C ASP* 1.3 76.0 - - + +
549C ALA* 1.3 59.7 + - - +
551C PHE* 3.5 2.7 + - - +
552C SER* 2.3 33.4 + - - +
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Residues in contact with ALA 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C ASP* 5.1 18.6 - - + +
545C LEU* 3.0 7.4 + - + +
546C ALA* 2.6 15.2 + - - +
548C GLU* 1.3 75.8 - - - +
550C PHE* 1.3 64.1 + - - +
552C SER* 3.0 9.9 - - - -
553C VAL* 2.8 31.0 + - + +
627C VAL* 5.2 12.8 - - + -
628C GLU* 4.7 11.4 - - - +
630C CYS* 5.6 2.5 - - - -
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Residues in contact with PHE 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C ALA 2.7 8.3 + - - -
547C ASP* 2.9 11.8 + - - +
549C ALA* 1.3 71.0 - - - +
551C PHE* 1.3 113.5 + + - +
553C VAL* 2.8 26.6 + - - +
554C ASN* 2.9 44.1 + - - -
628C GLU* 5.1 2.7 - - - -
633C ILE* 3.4 53.3 - - + +
636C GLU* 5.0 13.5 - - + -
637C LYS* 4.8 14.8 - - + -
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Residues in contact with PHE 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C ARG* 5.2 13.9 - - - -
477C ASN* 5.4 15.5 - - + +
480C SER* 4.2 7.2 - - - +
547C ASP* 2.9 47.9 + - + +
548C GLU* 4.3 2.2 - - - +
550C PHE* 1.3 108.2 - + - +
552C SER* 1.3 65.3 + - - +
554C ASN* 4.4 4.0 - - + +
555C SER* 2.9 36.1 + - - +
1491C ILE* 5.6 8.5 - - + -
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Residues in contact with SER 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C SER* 3.4 19.4 + - - -
484C HIS* 2.9 18.1 + - - -
548C GLU 2.3 28.1 + - - -
549C ALA* 3.0 15.9 - - - -
551C PHE* 1.3 75.0 - - - +
553C VAL* 1.3 52.0 + - - +
556C SER* 2.7 24.8 + - - -
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Residues in contact with VAL 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C ALA* 2.8 26.0 + - + +
550C PHE* 2.8 9.3 + - - +
552C SER* 1.3 70.2 - - - +
554C ASN* 1.3 62.1 + - - +
556C SER* 2.1 41.2 + - - +
557C SER* 2.7 6.4 + - - +
623C PHE* 5.9 1.6 - - + -
624C ILE* 3.6 32.3 - - + -
627C VAL* 5.8 0.2 - - + -
628C GLU* 4.8 6.7 - - + -
637C LYS* 3.4 29.8 - - + +
641C PHE* 3.4 17.3 - - + -
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Residues in contact with ASN 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C PHE* 2.9 54.2 + - - +
551C PHE* 4.3 4.5 - - + +
553C VAL* 1.3 80.8 - - - +
555C SER* 1.3 59.8 + - - +
557C SER* 2.9 9.7 - - - -
558C GLU* 2.9 31.8 + - - +
637C LYS* 4.5 5.9 - - - +
641C PHE* 2.9 34.0 - - + +
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Residues in contact with SER 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C ASN* 3.1 19.9 + - - -
480C SER* 4.6 1.1 - - - -
481C THR* 3.1 25.0 - - - +
484C HIS* 3.1 15.7 - - - -
551C PHE* 2.9 15.9 + - - +
554C ASN* 1.3 75.7 - - - +
556C SER* 1.3 53.1 - - - +
558C GLU* 3.8 8.0 - - - +
559C SER* 2.2 38.6 + - - -
562C HIS* 5.2 0.2 + - - -
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Residues in contact with SER 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C HIS* 2.9 30.8 + - - -
487C LEU* 5.4 0.7 - - - -
552C SER 2.7 13.1 + - - -
553C VAL* 2.1 37.5 + - - +
555C SER* 1.3 69.0 - - - +
557C SER* 1.3 67.9 + - - +
559C SER* 2.9 5.9 - - - -
560C LEU 2.9 13.9 + - - -
616C LYS* 3.3 19.9 - - - +
620C PHE* 5.0 14.8 - - - -
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Residues in contact with SER 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C VAL* 2.7 18.8 + - - +
554C ASN 2.9 8.5 - - - -
556C SER* 1.3 75.4 + - - +
558C GLU* 1.3 56.5 + - - +
560C LEU* 2.4 28.8 + - - -
616C LYS* 3.1 14.3 + - - +
641C PHE* 3.0 34.8 - - - -
645C TRP* 2.8 33.0 - - - -
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Residues in contact with GLU 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C ASN 2.9 14.1 + - - +
555C SER* 4.1 6.5 - - - +
557C SER* 1.3 76.9 - - - +
559C SER* 1.3 57.2 + - - +
561C ASN* 2.9 24.5 + - + +
562C HIS* 2.8 52.5 + - + +
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Residues in contact with SER 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C THR* 3.2 22.9 - - - +
484C HIS* 3.5 11.9 + - - +
485C GLN* 5.7 1.6 - - - -
488C ILE* 6.2 2.7 - - - -
555C SER 2.2 26.0 + - - -
556C SER* 2.9 17.7 - - - -
557C SER 2.8 0.2 + - - -
558C GLU* 1.3 75.4 - - - +
560C LEU* 1.3 52.1 + - - -
562C HIS* 2.5 44.1 + - - +
563C LEU* 3.1 4.7 + - - +
1803C GLU* 4.1 3.1 - - - +
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Residues in contact with LEU 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C ILE* 6.2 0.2 - - + -
556C SER 2.9 4.9 + - - -
557C SER 2.4 11.7 + - - -
559C SER* 1.3 71.8 - - - +
561C ASN* 1.3 62.5 + - - +
563C LEU* 3.1 11.1 + - + +
564C LEU* 2.9 32.2 + - + +
612C LEU 4.1 9.9 - - - +
613C HIS* 3.8 21.3 - - - +
616C LYS* 3.1 49.6 - - + +
617C PRO* 3.5 26.5 - - + -
645C TRP* 3.9 10.1 - - + -
655C LEU* 3.8 13.2 - - + -
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Residues in contact with ASN 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C SER 2.9 5.5 + - - -
558C GLU* 2.9 27.1 - - + +
560C LEU* 1.3 76.3 - - - +
562C HIS* 1.3 50.7 + - + +
564C LEU* 3.0 8.1 - - - +
565C TYR* 2.5 74.7 + - + -
644C PRO* 5.5 5.2 - - - +
645C TRP* 3.0 48.5 - - - +
648C SER* 4.5 3.4 + - - -
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Residues in contact with HIS 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C THR* 5.5 6.5 - - + +
555C SER 5.2 0.2 + - - -
558C GLU* 2.8 53.2 + - + +
559C SER* 2.5 31.2 + - - +
561C ASN* 1.3 72.6 - - + +
563C LEU* 1.3 55.3 + - - -
565C TYR* 3.1 11.4 - - - +
566C ASP* 2.7 31.0 + - - +
1803C GLU* 3.0 20.9 - - - +
1806C ARG* 4.3 2.4 + - - +
1807C LYS* 3.1 35.9 + - + +
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Residues in contact with LEU 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C ILE* 4.7 7.2 - - + -
559C SER 3.1 5.9 + - - +
560C LEU* 4.0 11.9 - - + +
562C HIS* 1.3 76.9 - - - +
564C LEU* 1.3 57.4 + - - +
566C ASP* 2.6 29.8 + - - +
567C GLU 3.2 5.2 + - - -
568C PHE 4.5 1.5 + - - +
609C ALA* 3.7 24.9 - - + +
612C LEU* 3.5 31.4 - - + +
613C HIS* 4.0 14.1 - - + +
1800C SER* 3.3 50.0 - - - +
1803C GLU* 3.0 16.7 + - - +
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Residues in contact with LEU 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560C LEU* 2.9 30.8 + - + +
561C ASN* 3.0 24.9 - - - +
563C LEU* 1.3 79.7 - - - +
565C TYR* 1.3 99.8 + - + +
566C ASP 3.1 0.7 + - - -
567C GLU 3.9 3.9 + - - +
568C PHE* 4.4 5.6 + - + +
569C VAL* 3.7 25.6 + - - +
613C HIS* 4.9 8.1 - - - +
645C TRP* 3.5 24.5 - - + -
648C SER* 5.2 7.2 - - - -
653C LEU* 4.4 26.2 - - + -
655C LEU* 5.2 0.7 - - + -
656C GLN* 5.5 2.5 - - - +
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Residues in contact with TYR 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C ASN* 2.5 56.2 + - + +
562C HIS* 3.1 12.1 - - - +
564C LEU* 1.3 92.0 - - + +
566C ASP* 1.3 62.9 + - - +
569C VAL* 5.7 1.1 - - + -
644C PRO* 5.5 0.7 - - - +
648C SER* 2.9 27.7 + - - -
651C TYR* 5.9 6.3 - + - -
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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