Contacts of the helix formed by residues 593 - 608 (chain A) in PDB entry 5JZU
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 593 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A SER* 2.8 39.2 + - - +
590A LEU 3.7 2.5 - - - -
592A ARG* 1.3 87.2 - - - +
594A TRP* 1.3 64.3 + - - +
595A LYS* 3.1 5.0 + - - -
596A LEU* 3.3 32.1 + - + +
597A ILE* 3.4 11.2 + - - +
650A LEU* 3.9 26.1 - - + +
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Residues in contact with TRP 594 (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 LEU 3.1 16.6 + - - +
591A GLU 3.1 21.3 - - - +
592A ARG 3.5 3.1 - - - -
593A ASN* 1.3 77.7 - - - +
595A LYS* 1.3 88.8 + - + +
597A ILE* 3.2 4.1 + - - +
598A ARG* 2.9 57.3 + - + +
691A LEU* 3.9 15.0 - - + -
692A GLY 3.7 6.1 - - - -
693A LEU* 3.3 29.6 - - + +
713A GLU* 3.8 27.8 + - + -
714A GLY* 3.4 34.8 - - - -
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Residues in contact with LYS 595 (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 ARG 5.3 0.2 + - - -
593A ASN 3.1 1.4 + - - -
594A TRP* 1.3 119.5 - - + +
596A LEU* 1.3 60.1 + - - +
598A ARG* 3.3 25.3 + - - +
599A ASP* 2.9 38.7 + - - +
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Residues in contact with LEU 596 (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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593A ASN* 3.3 35.6 + - + +
595A LYS* 1.3 79.2 - - - +
597A ILE* 1.3 70.8 + - + +
599A ASP* 4.0 7.5 - - - +
600A GLU* 3.1 31.0 + - + +
646A LYS* 3.9 37.7 - - + +
647A THR* 3.8 20.2 - - - +
650A LEU* 5.0 6.7 - - + -
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Residues in contact with ILE 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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590A LEU* 3.9 26.0 - - + +
593A ASN 3.5 14.4 - - - +
594A TRP* 3.2 8.0 + - - +
595A LYS 3.2 0.4 - - - -
596A LEU* 1.3 81.9 - - + +
598A ARG* 1.3 65.2 + - - +
601A GLY 3.2 3.5 + - - -
647A THR* 3.7 18.4 - - + +
650A LEU* 4.1 14.4 - - + -
651A LEU* 6.3 0.4 - - + -
667A TYR* 2.6 40.7 + - + +
691A LEU* 3.8 19.3 - - + -
693A LEU* 4.0 9.0 - - + -
738A PHE* 3.8 32.3 - - + -
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Residues in contact with ARG 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 TRP* 2.9 37.6 + - + +
595A LYS* 3.5 36.0 - - - +
597A ILE* 1.3 76.4 - - - +
599A ASP* 1.3 79.4 + - - +
601A GLY* 3.0 4.7 + - - -
602A LEU* 2.8 43.4 + - + +
693A LEU* 3.5 42.1 + - + +
694A VAL* 4.0 15.0 - - + -
713A GLU* 5.0 3.2 + - - -
736A LEU* 4.5 2.1 - - + +
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Residues in contact with ASP 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A LYS* 2.9 25.0 + - - +
596A LEU* 4.0 6.9 - - - +
597A ILE 3.3 0.2 - - - -
598A ARG* 1.3 104.4 + - - +
600A GLU* 1.3 59.7 + - + +
602A LEU* 3.3 12.3 + - - +
603A ALA* 2.8 29.5 + - - +
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Residues in contact with GLU 600 (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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596A LEU* 3.1 16.6 + - + +
599A ASP* 1.3 78.1 - - + +
601A GLY* 1.3 61.1 + - - +
603A ALA* 3.4 7.4 + - - +
604A VAL* 3.1 28.3 + - - +
643A GLY 3.8 10.1 - - - +
644A ALA* 3.3 14.4 - - - -
645A PRO* 3.2 14.1 - - + +
646A LYS* 3.1 37.8 + - + +
647A THR* 2.7 37.1 + - - -
667A TYR* 4.0 9.9 - - - +
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Residues in contact with GLY 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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597A ILE 3.2 6.9 + - - -
598A ARG 3.0 6.9 + - - -
600A GLU* 1.3 75.4 - - - +
602A LEU* 1.3 63.8 + - - +
604A VAL* 3.2 7.6 + - - +
605A MET* 3.0 26.6 + - - +
612A PHE* 4.1 3.0 - - - -
667A TYR* 3.6 31.9 + - - -
736A LEU* 4.5 7.0 - - - -
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Residues in contact with LEU 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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598A ARG* 2.8 44.8 + - + +
599A ASP* 3.6 13.5 - - - +
601A GLY* 1.3 72.4 - - - +
603A ALA* 1.3 58.2 + - - +
605A MET* 3.2 19.6 + - + +
606A ASP* 2.9 40.4 + - - +
694A VAL* 4.2 8.7 - - + -
734A PHE* 3.8 30.7 - - + -
736A LEU* 4.3 2.6 - - + +
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Residues in contact with ALA 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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599A ASP 2.8 17.5 + - - +
600A GLU* 3.6 10.1 - - - +
601A GLY 3.2 0.4 - - - -
602A LEU* 1.3 78.4 - - - +
604A VAL* 1.3 57.0 + - + +
606A ASP* 3.4 2.4 + - - -
607A LYS* 2.9 59.7 + - + +
643A GLY 5.5 1.8 - - - +
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Residues in contact with VAL 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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600A GLU 3.1 15.3 + - - +
601A GLY 3.2 6.9 + - - +
603A ALA* 1.3 75.6 - - + +
605A MET* 1.3 60.9 + - - +
608A ALA* 2.8 55.3 + - + +
609A LYS 3.1 0.2 + - - -
611A LEU* 4.0 19.7 - - + -
612A PHE* 3.6 23.3 - - + -
628A PHE* 3.8 20.6 - - + -
643A GLY* 3.4 26.7 - - - +
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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 GLY 3.0 16.5 + - - +
602A LEU* 3.2 29.8 + - + +
604A VAL* 1.3 78.5 - - - +
606A ASP* 1.3 65.7 + - - +
609A LYS* 3.4 25.3 - - - +
612A PHE* 3.8 20.9 - - + -
669A ILE* 3.4 33.7 - - + -
671A HIS* 5.6 0.7 - - + -
734A PHE* 3.7 31.0 - - + -
736A LEU* 4.2 11.0 - - - -
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Residues in contact with ASP 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 LEU* 2.9 27.8 + - - +
603A ALA* 3.8 5.3 - - - +
605A MET* 1.3 85.9 - - - +
607A LYS* 1.3 75.9 + - + +
608A ALA 3.6 0.6 + - - -
609A LYS* 5.1 3.1 + - - +
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Residues in contact with LYS 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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603A ALA* 2.9 36.5 + - + +
606A ASP* 1.3 92.2 - - + +
608A ALA* 1.3 63.7 + - + +
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Residues in contact with ALA 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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604A VAL* 2.8 27.5 + - + +
607A LYS* 1.3 82.9 - - + +
609A LYS* 1.3 58.6 + - - +
610A GLY* 2.8 12.4 + - - -
611A LEU* 3.0 32.9 + - + +
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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