Contacts of the helix formed by residues 601 - 615 (chain A) in PDB entry 2CKH
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 ASP 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A LEU* 4.1 10.6 - - - +
596A GLN* 3.4 6.2 + - - +
598A ASN* 2.9 22.5 + - - +
600A SER* 1.3 74.3 - - - +
602A CYS* 1.3 57.9 + - - +
603A GLY 3.7 0.4 - - - -
604A MET* 3.2 10.4 - - + +
605A PHE* 2.9 41.2 + - + -
623A GLN* 2.9 28.1 + - - -
626A MET* 3.4 17.9 - - + +
627A PRO* 5.0 1.0 - - - +
630A ARG* 3.0 32.7 + - - -
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Residues in contact with CYS 602 (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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534A TRP* 3.7 27.8 - - - +
551A SER* 4.0 6.7 + - - +
552A MET* 3.8 9.2 - - + -
596A GLN* 3.2 16.3 - - - +
600A SER 3.0 3.8 + - - -
601A ASP* 1.3 71.6 - - - +
603A GLY* 1.3 65.7 + - - +
604A MET 2.7 14.9 + - - -
605A PHE* 2.7 15.2 + - - +
606A ALA* 2.8 12.4 + - - +
91B GLY 3.4 5.8 - - - -
92B GLY* 1.7 71.1 - - - +
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Residues in contact with GLY 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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466A LEU* 4.0 15.7 - - - +
471A ILE* 4.2 5.5 - - - +
534A TRP* 3.4 31.6 - - - -
600A SER 4.4 1.8 + - - -
602A CYS* 1.3 84.7 - - - +
604A MET* 1.3 59.3 + - - +
606A ALA* 3.7 6.0 - - - +
607A CYS* 3.3 28.2 + - - -
91B GLY 4.7 0.2 + - - -
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Residues in contact with MET 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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460A LEU* 4.7 2.9 - - + -
466A LEU* 3.7 31.1 - - + +
601A ASP* 3.2 23.9 - - - +
602A CYS 2.7 0.8 + - - -
603A GLY* 1.3 76.5 - - - +
605A PHE* 1.3 66.5 + - - +
607A CYS* 3.0 5.8 + - - +
608A LYS* 3.0 25.2 + - + +
626A MET* 3.4 25.4 - - - -
629A PHE* 3.5 13.0 - - + +
630A ARG* 3.5 47.8 - - + +
633A MET* 3.3 33.2 - - + -
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Residues in contact with PHE 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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551A SER* 3.6 9.6 - - - +
594A PRO* 3.5 35.7 - - + -
595A GLN 3.1 20.2 - - - -
596A GLN* 3.3 32.8 - - - -
601A ASP* 2.9 24.5 + - + +
602A CYS 2.7 12.0 + - - +
604A MET* 1.3 70.3 - - - +
606A ALA* 1.3 54.2 + - - +
609A TYR* 2.5 72.9 + + + +
621A PHE* 4.3 5.3 - + - -
622A THR* 5.3 0.4 - - - -
623A GLN* 3.8 21.3 - - - -
626A MET* 3.4 26.4 - - + +
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Residues in contact with ALA 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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471A ILE* 5.7 2.9 - - + -
475A MET* 4.2 6.4 - - + +
527A PRO* 6.6 0.7 - - + -
534A TRP* 4.7 7.6 - - + +
535A CYS* 4.5 23.6 - - - +
536A LEU* 3.8 11.0 - - + +
602A CYS 2.8 14.2 + - - +
603A GLY* 3.7 11.4 - - - +
605A PHE* 1.3 75.2 - - - +
607A CYS* 1.3 66.6 + - - +
609A TYR* 3.2 14.3 - - - +
610A ALA* 3.2 19.8 + - - +
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Residues in contact with CYS 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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466A LEU* 5.2 1.1 - - - -
471A ILE* 3.6 25.4 - - - -
474A TYR* 3.8 40.8 - - + -
475A MET* 3.8 15.5 - - - -
603A GLY 3.3 14.2 + - - +
604A MET 3.0 8.5 + - - +
606A ALA* 1.3 76.8 - - - +
608A LYS* 1.3 60.5 + - - +
610A ALA* 2.9 22.2 + - - +
611A ASP* 3.0 10.0 + - - +
633A MET* 3.8 19.1 - - + -
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Residues in contact with LYS 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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474A TYR* 3.1 21.9 + - + +
604A MET* 3.0 16.9 + - + +
607A CYS* 1.3 73.5 - - - +
609A TYR* 1.3 67.0 + - - +
611A ASP* 3.1 37.3 + - - +
612A CYS* 3.4 6.9 + - - -
621A PHE* 3.3 33.2 - - + -
626A MET* 4.5 3.6 - - + -
629A PHE* 3.4 54.0 - - + +
632A ARG* 3.3 28.7 - - - +
633A MET* 4.4 12.3 - - + -
636A GLU* 4.2 5.0 + - - +
643A LEU 4.9 0.6 + - - -
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Residues in contact with TYR 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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536A LEU* 4.5 7.6 - - + -
549A TYR* 4.3 23.3 - + + -
550A ASP 4.5 2.2 - - - -
551A SER* 3.3 27.3 - - - -
593A ILE* 3.6 27.4 - - + +
594A PRO* 2.7 42.7 + - + -
605A PHE* 2.5 52.4 + + + +
606A ALA* 3.2 12.6 - - - +
608A LYS* 1.3 74.0 - - - +
610A ALA* 1.3 63.5 + - - +
611A ASP 3.2 0.3 + - - -
612A CYS* 3.2 10.6 + - - +
613A ILE* 3.3 22.0 + - + +
619A ILE* 4.3 16.9 - - + +
621A PHE* 3.6 10.2 - + - -
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Residues in contact with ALA 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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475A MET* 4.2 8.5 - - + -
478A LEU* 3.2 14.4 - - + +
525A LEU* 3.9 17.7 - - + -
536A LEU* 3.6 24.4 - - + +
606A ALA 3.2 2.9 + - - +
607A CYS 2.9 10.6 + - - +
609A TYR* 1.3 79.1 - - - +
611A ASP* 1.3 51.4 + - - +
613A ILE* 3.5 7.5 - - - +
614A THR* 2.6 41.2 + - - +
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Residues in contact with ASP 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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474A TYR* 2.5 27.8 + - - +
478A LEU* 3.2 15.4 - - + +
481A ARG* 3.5 0.7 + - - -
607A CYS 3.0 6.5 + - - +
608A LYS* 3.1 36.7 + - - +
609A TYR 3.1 0.6 - - - -
610A ALA* 1.3 77.0 - - - +
612A CYS* 1.3 62.4 + - - +
614A THR* 2.8 13.2 + - - -
615A LYS* 2.5 50.1 + - - +
642A LEU* 5.0 1.7 - - - +
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Residues in contact with CYS 612 (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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608A LYS* 3.4 2.2 + - - -
609A TYR 3.2 6.5 + - - +
611A ASP* 1.3 75.1 - - - +
613A ILE* 1.3 67.1 + - - +
615A LYS* 3.0 11.1 + - - -
617A ARG* 3.0 29.5 + - - +
618A PRO 3.3 30.1 - - - +
619A ILE* 4.0 8.3 - - + -
620A ASN* 4.0 8.5 - - - -
621A PHE* 3.3 37.2 - - - -
629A PHE* 6.5 0.4 - - - -
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Residues in contact with ILE 613 (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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523A ILE* 4.1 22.1 - - + +
525A LEU* 5.2 1.3 - - + -
536A LEU* 4.5 1.8 - - + -
538A VAL* 3.8 31.2 - - + -
540A ASP* 5.6 2.5 - - - +
549A TYR* 3.7 43.5 - - + +
609A TYR* 3.4 22.0 - - + +
610A ALA* 3.2 10.9 + - - +
612A CYS* 1.3 77.7 - - - +
614A THR* 1.3 60.0 + - + +
616A ASP* 3.0 22.0 + - - +
617A ARG 4.6 2.7 - - - -
619A ILE* 5.0 9.6 - - + -
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Residues in contact with THR 614 (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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478A LEU* 3.0 21.1 - - + +
481A ARG* 2.6 30.9 + - - -
482A SER* 5.2 3.3 - - - -
487A LEU* 3.6 10.0 - - - +
488A PRO* 3.4 23.8 - - - +
490A VAL* 3.9 25.4 - - + -
523A ILE* 4.5 7.0 - - + -
525A LEU* 4.0 21.3 - - + -
610A ALA 2.6 24.7 + - - +
611A ASP 2.8 4.5 + - - -
613A ILE* 1.3 74.2 - - + +
615A LYS* 1.3 55.3 + - - +
616A ASP 3.2 0.9 - - - -
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Residues in contact with LYS 615 (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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481A ARG* 3.0 48.3 - - - +
487A LEU* 3.8 19.7 - - + +
611A ASP* 2.5 50.2 + - - +
612A CYS* 3.0 6.0 + - - +
614A THR* 1.3 77.1 - - - +
616A ASP* 1.3 54.0 - - - +
617A ARG* 2.3 41.9 + - + +
642A LEU* 4.1 17.3 + - - +
643A LEU 4.8 7.9 + - - -
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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