Contacts of the helix formed by residues 597 - 611 (chain A) in PDB entry 2ZJ4
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 597 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLN* 6.3 0.4 - - - +
544A ARG* 4.2 26.1 + - + +
545A GLY* 4.4 21.5 - - - -
546A TYR* 5.4 2.2 - - + +
593A MET 4.8 1.2 + - - -
595A ASP* 2.8 23.9 + - - +
596A HIS* 1.3 80.4 - - + +
598A TYR* 1.3 63.2 + - - +
599A ALA 3.4 2.5 - - - -
600A LYS* 3.2 15.0 + - + +
601A CYS* 2.9 32.8 + - - -
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Residues in contact with TYR 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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592A ILE* 3.8 15.9 - - + -
593A MET 3.5 21.3 - - - +
594A ARG* 3.8 16.4 - - + -
595A ASP* 3.2 16.3 + - - +
596A HIS 3.3 2.2 - - - -
597A THR* 1.3 78.2 + - - +
599A ALA* 1.3 58.7 + - + +
601A CYS* 3.2 6.7 + - - +
602A GLN* 2.8 61.5 + - + +
623A ASP* 2.7 42.8 + - - -
625A GLU* 3.8 12.8 - - + +
626A THR* 3.4 0.6 - - + +
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Residues in contact with ALA 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A HIS 5.1 1.5 + - - +
597A THR 3.4 0.2 - - - -
598A TYR* 1.3 85.0 - - + +
600A LYS* 1.3 59.2 + - + +
602A GLN* 3.3 7.5 + - - +
603A ASN* 3.0 34.6 + - - +
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Residues in contact with LYS 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ARG* 3.7 47.2 + - - +
596A HIS 5.8 1.3 - - - +
597A THR* 3.2 15.5 + - + +
599A ALA* 1.3 77.4 - - + +
601A CYS* 1.3 63.1 + - - +
603A ASN* 3.3 17.7 + - - +
604A ALA* 3.1 19.6 + - - +
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Residues in contact with CYS 601 (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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544A ARG* 3.6 29.6 - - - +
571A ALA* 5.6 2.7 - - - -
590A MET* 4.7 3.6 - - + +
591A ILE 4.1 15.0 - - - +
592A ILE* 3.9 29.3 - - + +
593A MET 5.0 2.5 - - - -
597A THR* 2.9 26.3 + - - -
598A TYR* 3.5 8.7 - - - +
600A LYS* 1.3 75.2 - - - +
602A GLN* 1.3 65.0 + - - +
604A ALA* 3.2 9.1 + - - +
605A LEU* 3.0 23.4 + - - +
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Residues in contact with GLN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ILE* 4.3 6.7 - - + -
598A TYR* 2.8 46.9 + - + +
599A ALA* 3.3 10.7 + - - +
601A CYS* 1.3 71.1 - - - +
603A ASN* 1.3 62.7 + - - +
605A LEU* 3.3 22.9 + - - +
606A GLN* 3.1 42.1 + - - +
625A GLU* 4.5 4.8 - - - +
626A THR* 3.2 40.8 - - - +
629A ASN* 5.8 1.8 - - - +
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Residues in contact with ASN 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A ALA* 3.0 22.3 + - - +
600A LYS* 3.4 19.3 - - - +
601A CYS 3.2 0.2 - - - -
602A GLN* 1.3 74.2 - - - +
604A ALA* 1.3 66.4 + - - +
606A GLN* 3.4 21.3 + - - +
607A GLN* 3.0 28.5 + - + +
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Residues in contact with ALA 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ARG* 6.4 0.2 - - - +
571A ALA* 4.3 22.0 - - + +
574A LEU* 3.9 18.3 - - + +
590A MET* 4.0 17.7 - - + -
600A LYS 3.1 13.4 + - - +
601A CYS* 3.2 9.4 + - - +
603A ASN* 1.3 73.5 - - - +
605A LEU* 1.3 57.8 + - - +
607A GLN* 3.2 6.3 + - - +
608A VAL* 3.0 30.8 + - - +
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Residues in contact with LEU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A MET* 3.7 17.2 - - + -
592A ILE* 3.9 18.2 - - + -
601A CYS 3.0 11.9 + - - +
602A GLN* 3.5 27.4 - - - +
604A ALA* 1.3 73.8 - - - +
606A GLN* 1.3 65.0 - - + +
608A VAL* 3.3 2.4 + - - +
609A VAL* 3.0 29.5 + - + +
615A PRO* 3.5 29.6 - - + -
617A VAL* 3.8 18.2 - - + -
626A THR* 5.1 2.5 - - - -
630A THR* 3.9 23.1 - - + +
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Residues in contact with GLN 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A GLN* 3.1 32.5 + - - +
603A ASN* 3.6 24.4 + - - +
605A LEU* 1.3 78.4 - - + +
607A GLN* 1.3 60.5 + - + +
609A VAL* 3.4 6.7 + - - +
610A ALA* 2.8 30.9 + - - +
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Residues in contact with GLN 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LEU* 4.8 8.3 - - + -
575A LYS* 4.2 28.8 - - + +
579A LEU* 3.9 23.5 - - + +
603A ASN* 3.0 21.6 + - + +
604A ALA* 3.6 7.0 - - - +
606A GLN* 1.3 77.0 + - + +
608A VAL* 1.3 64.4 + - - +
610A ALA* 3.5 15.5 + - - +
611A ARG* 3.3 45.1 + - - +
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Residues in contact with VAL 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A MET* 3.9 14.4 - - + -
574A LEU* 3.7 20.0 - - + -
579A LEU* 4.4 4.0 - - + -
582A VAL* 3.7 22.6 - - + +
588A VAL* 4.3 9.9 - - + -
590A MET* 3.7 18.8 - - - -
604A ALA 3.0 18.0 + - - +
605A LEU 3.6 6.7 - - - +
607A GLN* 1.3 73.1 - - - +
609A VAL* 1.3 61.1 + - - +
611A ARG 3.3 6.6 + - - -
612A GLN 3.6 0.2 + - - -
613A GLY* 3.0 32.6 + - - -
615A PRO* 4.2 23.8 - - + -
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Residues in contact with VAL 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 3.0 28.1 + - + +
606A GLN* 3.9 6.5 - - - +
608A VAL* 1.3 70.1 - - - +
610A ALA* 1.3 65.8 + - - +
611A ARG 3.1 1.6 - - - -
612A GLN* 3.0 15.2 + - - +
613A GLY 3.8 9.4 - - - +
615A PRO* 4.1 26.2 - - + -
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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
----------------------------------------------------------
606A GLN 2.8 21.0 + - - +
607A GLN* 3.8 22.0 - - - +
608A VAL 3.4 0.4 - - - -
609A VAL* 1.3 74.1 - - - +
611A ARG* 1.3 68.8 + - - +
612A GLN* 3.3 5.6 + - - +
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Residues in contact with ARG 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A LEU* 4.1 25.5 - - + +
582A VAL* 3.7 18.1 - - + +
583A ASP* 3.7 14.7 - - - +
607A GLN* 3.3 38.3 + - - +
608A VAL 3.3 5.6 + - - +
609A VAL 3.0 1.0 + - - -
610A ALA* 1.3 86.2 - - - +
612A GLN* 1.3 69.8 + - - +
613A GLY 3.3 3.9 + - - -
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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