Contacts of the helix formed by residues 590 - 611 (chain A) in PDB entry 4K33
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 THR 590 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A GLN 4.4 5.4 - - - +
589A LEU* 1.3 77.5 - - - +
591A PHE* 1.3 65.9 + - - +
592A LYS* 3.2 12.5 + - - +
593A ASP* 2.9 46.4 + - - +
594A LEU* 3.2 16.7 + - - +
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Residues in contact with PHE 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A THR* 1.3 71.5 - - - +
592A LYS* 1.3 61.4 + - - +
594A LEU* 3.2 12.5 + - - +
595A VAL* 3.0 37.9 + - + +
688A PHE* 3.9 11.7 - + - -
718A ASN* 4.4 9.9 - - + -
720A THR* 3.5 36.3 - - + -
723A LEU* 3.5 33.9 - - + -
751A VAL* 4.1 11.0 - - + -
755A THR* 3.6 33.9 - - + -
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Residues in contact with LYS 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A THR* 3.1 10.8 + - - +
591A PHE* 1.3 86.0 - - + +
593A ASP* 1.3 59.1 + - - +
595A VAL* 3.4 1.0 + - - -
596A SER* 2.9 30.0 + - - -
752A LEU* 3.8 37.4 + - + +
755A THR* 5.3 20.0 - - + +
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Residues in contact with ASP 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A GLN 4.2 1.9 - - - +
589A LEU* 3.5 28.3 - - + +
590A THR* 2.9 44.5 + - - +
592A LYS* 1.3 76.6 - - - +
594A LEU* 1.3 58.5 + - - +
596A SER* 3.2 8.9 - - - -
597A CYS* 3.0 26.2 + - - +
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Residues in contact with LEU 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LEU* 3.7 21.1 - - + -
589A LEU* 3.8 15.9 - - + +
590A THR 3.2 13.8 + - - +
591A PHE* 3.6 7.9 - - - +
592A LYS 3.2 0.2 - - - -
593A ASP* 1.3 75.2 - - - +
595A VAL* 1.3 64.8 + - - +
597A CYS* 3.2 8.1 + - + +
598A ALA* 3.0 19.2 + - - +
687A ILE* 3.7 21.3 - - + +
688A PHE* 3.5 37.0 - - + -
690A LEU* 3.7 33.7 - - + -
718A ASN* 4.8 11.7 - - + +
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A PHE* 3.0 34.9 + - + +
592A LYS* 4.5 0.7 - - - -
594A LEU* 1.3 72.2 - - - +
596A SER* 1.3 55.6 + - - +
598A ALA* 3.2 4.8 + - - +
599A TYR* 2.7 32.6 + - - +
688A PHE* 3.6 7.0 - - + -
723A LEU* 3.5 27.6 - - + -
748A LEU* 4.0 24.9 - - + +
751A VAL* 3.9 18.2 - - + -
752A LEU* 3.6 24.5 - - + -
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Residues in contact with SER 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LYS* 2.9 16.1 + - - -
593A ASP* 3.2 13.7 - - - -
594A LEU 3.2 0.2 - - - -
595A VAL* 1.3 76.9 - - - +
597A CYS* 1.3 57.1 + - - +
599A TYR* 3.2 8.9 + - - +
600A GLN* 2.8 49.4 + - - +
752A LEU* 3.9 14.2 - - - +
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Residues in contact with CYS 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A LEU* 3.5 31.6 - - + -
567A LEU* 5.6 2.0 - - + -
593A ASP 3.0 12.3 + - - +
594A LEU* 3.2 13.0 + - + +
596A SER* 1.3 78.1 - - - +
598A ALA* 1.3 60.3 + - - +
600A GLN* 3.5 1.9 + - - +
601A VAL* 3.2 24.7 + - - +
631A MET* 3.4 40.8 - - + +
687A ILE* 3.5 16.6 - - + -
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Residues in contact with ALA 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A LEU 3.0 12.2 + - - +
595A VAL* 3.2 10.5 + - - +
597A CYS* 1.3 76.9 - - - +
599A TYR* 1.3 57.2 + - - +
601A VAL* 3.2 2.7 + - - -
602A ALA* 2.9 29.1 + - - +
680A PHE* 3.6 8.3 - - + -
684A LEU* 3.5 31.9 - - + -
687A ILE* 3.9 11.7 - - + -
688A PHE* 4.9 2.9 - - + -
748A LEU* 4.0 15.7 - - + -
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Residues in contact with TYR 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL 2.7 20.5 + - - +
596A SER* 3.5 9.0 - - - +
598A ALA* 1.3 73.8 - - - +
600A GLN* 1.3 69.6 + - + +
602A ALA* 3.4 3.0 + - - +
603A ARG* 3.0 65.4 + - + +
745A VAL* 3.5 38.3 - - + +
748A LEU* 4.0 16.7 - - + +
749A ASP* 3.6 37.2 + - + -
752A LEU* 4.3 16.8 - - + -
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Residues in contact with GLN 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LYS* 5.7 1.5 - - - -
537A ASN* 3.3 32.6 + - - +
596A SER* 2.8 40.1 + - - +
597A CYS* 4.5 0.8 - - - +
598A ALA 3.3 0.4 - - - -
599A TYR* 1.3 80.3 - - + +
601A VAL* 1.3 63.4 + - - +
603A ARG* 3.2 4.6 + - - +
604A GLY 3.1 16.8 + - - -
629A ASN 3.5 17.2 + - - -
630A VAL* 3.2 11.6 - - - +
631A MET* 2.8 44.0 + - + +
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Residues in contact with VAL 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ASN* 5.2 0.9 - - - -
597A CYS* 3.2 20.2 + - - +
598A ALA* 3.7 6.1 - - - +
600A GLN* 1.3 76.1 - - - +
602A ALA* 1.3 59.2 + - - +
604A GLY 3.1 2.0 + - - +
605A MET* 2.9 28.9 + - + +
618A LEU* 4.0 16.6 - - + -
623A VAL* 3.9 31.0 - - + -
631A MET* 4.0 8.5 - - + -
633A ILE* 3.6 16.7 - - + +
680A PHE* 4.0 11.9 - - + -
683A LEU* 3.6 27.1 - - + -
687A ILE* 5.5 0.2 - - + -
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Residues in contact with ALA 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ALA 2.9 16.8 + - - +
599A TYR* 3.6 5.6 - - - +
600A GLN 3.3 0.2 - - - -
601A VAL* 1.3 75.7 - - - +
603A ARG* 1.3 56.5 + - - +
605A MET* 3.8 5.1 - - - +
606A GLU* 2.8 29.6 + - - +
680A PHE* 3.6 22.3 - - + -
741A PHE* 4.2 5.6 - - + +
744A LEU* 4.4 6.5 - - + -
745A VAL* 3.4 21.3 - - + +
748A LEU* 4.1 12.3 - - + -
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Residues in contact with ARG 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A HIS* 3.8 16.7 + - + -
537A ASN* 3.5 13.0 - - - +
599A TYR* 3.0 59.1 + - + +
600A GLN* 3.4 9.9 - - - +
601A VAL 3.1 0.2 - - - -
602A ALA* 1.3 78.1 - - - +
604A GLY* 1.3 56.8 - - - +
606A GLU* 3.4 16.7 + - - +
607A TYR* 3.1 24.9 + - - +
745A VAL* 3.8 18.9 - - + +
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Residues in contact with GLY 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A HIS* 4.1 9.0 - - - -
537A ASN* 3.9 17.8 - - - +
538A ILE* 3.6 7.1 - - - +
600A GLN 3.1 4.8 + - - -
601A VAL 3.1 6.3 + - - -
603A ARG* 1.3 76.7 - - - +
605A MET* 1.3 60.8 + - - +
607A TYR* 3.2 3.3 + - - +
608A LEU* 2.8 27.7 + - - +
633A ILE* 3.6 16.2 - - - -
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Residues in contact with MET 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A VAL* 2.9 21.2 + - + +
602A ALA* 3.8 0.7 - - - +
604A GLY* 1.3 73.0 - - - +
606A GLU* 1.3 60.4 + - - +
608A LEU* 3.1 18.7 + - + +
609A ALA* 2.9 31.7 + - - +
613A CYS 5.9 0.4 - - - +
615A HIS* 4.1 12.1 - - + -
618A LEU* 3.7 32.5 - - + -
633A ILE* 3.5 19.3 - - + +
676A ASP* 3.8 26.0 - - + +
741A PHE* 3.5 49.3 - - + -
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Residues in contact with GLU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A ALA 2.8 18.7 + - - +
603A ARG* 3.5 19.4 + - - +
605A MET* 1.3 77.9 - - - +
607A TYR* 1.3 62.4 + - - +
609A ALA* 3.5 3.8 + - - +
610A SER* 3.1 22.1 + - - -
741A PHE* 3.8 14.9 - - + +
742A LYS* 3.4 45.3 - - + +
745A VAL* 3.8 21.9 - - + +
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Residues in contact with TYR 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A ILE* 3.0 18.8 + - + -
533A GLY* 3.1 32.6 - - - -
534A LYS 3.6 10.9 + - - -
535A HIS* 3.4 37.7 - + + +
538A ILE* 3.6 19.1 - - + -
603A ARG 3.1 9.5 + - - +
604A GLY 3.5 5.8 - - - +
605A MET 3.2 0.2 - - - -
606A GLU* 1.3 76.9 - - - +
608A LEU* 1.3 63.6 + - - +
610A SER* 2.6 27.3 + - - -
611A GLN* 3.0 44.4 + - + +
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Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A ILE* 3.7 43.3 - - + -
538A ILE* 3.8 11.2 - - + -
604A GLY 2.8 16.1 + - - +
605A MET* 3.1 20.2 + - + +
607A TYR* 1.3 77.9 - - - +
609A ALA* 1.3 58.1 + - - +
611A GLN* 3.0 19.9 + - + +
613A CYS* 3.2 40.0 + - + +
615A HIS* 3.9 28.0 - - + +
633A ILE* 5.1 1.6 - - + -
636A PHE* 3.9 18.8 - - + -
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Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A MET* 2.9 16.5 + - + +
606A GLU* 3.9 5.2 - - - +
608A LEU* 1.3 75.4 - - - +
610A SER* 1.3 58.0 + - - +
611A GLN 3.0 0.2 - - - -
612A LYS* 2.8 23.4 + - - +
613A CYS 4.0 1.3 + - - -
673A HIS* 3.5 44.5 + - + +
741A PHE* 4.7 10.8 - - + -
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Residues in contact with SER 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A GLU* 3.1 13.3 + - - -
607A TYR* 2.6 31.4 + - - -
609A ALA* 1.3 75.8 - - - +
611A GLN* 1.3 67.1 + - - +
612A LYS* 3.1 7.5 + - - +
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Residues in contact with GLN 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A MET* 4.1 12.6 + - - +
532A ILE* 2.3 45.4 + - + +
533A GLY* 4.1 1.8 - - - +
607A TYR* 3.1 46.6 + - + +
608A LEU* 3.0 11.9 + - - +
610A SER* 1.3 84.3 + - - +
612A LYS* 1.3 70.7 + - - +
613A CYS* 3.5 8.2 + - + +
641A ASP* 5.2 0.9 - - - +
643A HIS* 5.7 0.2 - - - +
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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
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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