Contacts of the helix formed by residues 595 - 608 (chain A) in PDB entry 1JEQ
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 LYS 595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A VAL* 5.4 1.6 - - - -
594A LEU* 1.3 91.8 - - + +
596A LYS* 1.3 64.8 + - - +
597A GLN* 4.5 4.7 - - + +
598A GLU* 3.1 33.5 + - + +
599A LEU* 3.5 24.6 + - - +
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Residues in contact with LYS 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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574A GLY 3.0 28.5 + - - -
575A LYS* 4.9 2.0 - - - +
576A PHE 3.6 18.7 + - - +
578A VAL* 3.9 22.2 - - + +
581A LEU* 3.5 21.1 - - + -
595A LYS* 1.3 69.7 - - - +
597A GLN* 1.3 69.2 + - - +
598A GLU 2.9 1.9 + - - -
599A LEU* 3.0 5.1 + - - +
600A LEU* 2.7 40.1 + - + +
144B LYS* 5.3 6.1 - - - +
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Residues in contact with GLN 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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595A LYS* 4.5 5.9 - - + +
596A LYS* 1.3 78.5 - - - +
598A GLU* 1.3 57.4 + - + +
600A LEU* 3.2 19.4 + - - +
601A GLU* 2.7 74.8 + - - +
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Residues in contact with GLU 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 SER 4.4 6.8 - - - +
593A GLY* 2.7 18.1 - - - +
594A LEU* 2.7 33.6 + - - +
595A LYS* 3.1 38.6 + - + +
596A LYS 2.9 0.6 + - - -
597A GLN* 1.3 76.2 - - + +
599A LEU* 1.3 65.3 + - - +
601A GLU* 2.8 28.0 + - - +
602A ALA* 2.9 14.0 + - - +
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Residues in contact with LEU 599 (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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578A VAL* 4.0 8.7 - - + +
581A LEU* 3.4 37.5 - - + -
582A LYS* 3.7 28.0 - - + +
585A CYS* 3.7 15.5 - - + -
592A SER* 3.1 36.6 - - - -
593A GLY 3.7 11.9 - - - +
594A LEU 5.8 1.6 - - - -
595A LYS 3.6 14.1 - - - +
596A LYS 3.0 6.5 + - - +
598A GLU* 1.3 79.8 - - - +
600A LEU* 1.3 61.2 + - - +
602A ALA* 3.7 4.4 - - - +
603A LEU* 3.1 30.7 + - - +
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Residues in contact with LEU 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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573A LEU* 4.1 19.2 - - + +
574A GLY* 3.5 32.1 - - - +
581A LEU* 4.5 13.4 - - + +
596A LYS* 2.7 48.0 + - + +
597A GLN* 3.3 24.9 - - - +
598A GLU 2.9 0.6 + - - -
599A LEU* 1.3 72.8 - - - +
601A GLU* 1.3 64.5 + - - +
603A LEU* 4.3 1.7 - - - +
604A THR* 3.0 30.7 + - - +
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Residues in contact with GLU 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 GLN* 2.7 62.5 + - - +
598A GLU* 2.8 16.0 + - - +
600A LEU* 1.3 72.5 - - - +
602A ALA* 1.3 65.9 + - - +
604A THR* 3.4 4.1 + - - -
605A LYS* 3.0 22.7 + - - +
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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
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585A CYS* 4.4 6.1 - - - -
590A LEU* 4.2 14.8 - - + +
591A LYS 4.0 19.3 - - - +
592A SER* 5.1 1.6 - - - -
598A GLU 2.9 14.8 + - - +
599A LEU* 3.7 8.7 - - - +
601A GLU* 1.3 74.4 - - - +
603A LEU* 1.3 52.2 + - - +
605A LYS* 2.7 31.0 + - - +
606A HIS* 2.7 16.5 + - - +
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Residues in contact with LEU 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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564A LEU* 4.9 6.3 - - + -
568A ILE* 4.3 2.8 - - + +
573A LEU* 4.5 20.2 - - + -
581A LEU* 4.0 28.0 - - + +
584A ALA* 3.3 37.9 - - + +
585A CYS* 3.5 22.0 - - - -
588A TYR* 5.0 2.9 - - + -
590A LEU* 4.1 17.5 - - + +
599A LEU 3.1 8.9 + - - +
600A LEU 4.3 1.8 - - - +
602A ALA* 1.3 77.5 - - - +
604A THR* 1.3 60.7 + - - +
606A HIS* 3.5 3.5 + - - -
607A PHE* 3.0 44.3 + - + -
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Residues in contact with THR 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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568A ILE* 3.9 28.1 - - + +
573A LEU* 3.6 15.6 - - - +
600A LEU* 3.0 21.5 + - - +
601A GLU* 3.7 4.7 - - - -
602A ALA 2.9 1.2 + - - -
603A LEU* 1.3 78.1 - - - +
605A LYS* 1.3 59.6 + - - +
607A PHE* 3.3 2.8 + - - +
608A GLN* 3.0 37.1 + - + +
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Residues in contact with LYS 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 GLU 3.0 13.4 + - - +
602A ALA* 2.7 16.5 + - - +
604A THR* 1.3 71.8 - - - +
606A HIS* 1.3 65.1 + - - +
607A PHE 2.9 1.6 + - - -
609A ASP* 3.0 59.9 + - + +
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Residues in contact with HIS 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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561A GLU* 5.9 1.1 - - - -
588A TYR* 3.6 33.0 + + + +
590A LEU* 3.3 43.7 - - + -
602A ALA 2.7 9.7 + - - +
603A LEU 3.7 9.0 - - - +
604A THR 3.3 0.2 - - - -
605A LYS* 1.3 74.2 - - - +
607A PHE* 1.3 75.3 + + + +
609A ASP 5.3 1.2 - - - -
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Residues in contact with PHE 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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561A GLU* 3.7 37.9 - - + -
564A LEU* 3.9 17.9 - - + -
565A LYS* 4.5 18.4 - - + -
568A ILE* 4.4 12.8 - - + -
588A TYR* 3.6 34.1 - + - -
603A LEU* 3.0 31.2 - - + +
604A THR 3.3 5.2 + - - +
605A LYS 2.9 1.6 + - - -
606A HIS* 1.3 101.4 - - + +
608A GLN* 1.3 65.5 + - - +
609A ASP 4.8 1.6 - - - -
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Residues in contact with GLN 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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568A ILE* 5.6 7.6 - - + -
604A THR* 3.0 24.1 + - + +
607A PHE* 1.3 80.1 - - + +
609A ASP* 1.3 70.8 + - + +
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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