Contacts of the helix formed by residues 600 - 613 (chain A) in PDB entry 4EZJ
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 GLN 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A LYS* 5.3 3.6 + - - -
422A ASP* 3.3 29.6 + - - +
597A LYS* 3.2 23.7 + - + +
598A TRP 3.2 2.6 + - - -
599A GLY* 1.4 80.3 + - - +
601A GLN* 1.4 62.0 + - - +
602A GLU* 4.1 14.4 + - + +
603A ILE* 2.9 44.9 + - + -
604A VAL* 3.3 7.1 + - - +
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Residues in contact with GLN 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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421A LYS* 3.8 28.3 + - - +
422A ASP* 3.1 27.6 + - - +
600A GLN* 1.4 70.7 + - - +
602A GLU* 1.3 63.1 + - - +
604A VAL* 3.3 10.4 + - + +
605A ALA* 3.0 38.5 + - - +
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Residues in contact with GLU 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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600A GLN* 3.3 15.4 + - + +
601A GLN* 1.3 86.6 + - - +
603A ILE* 1.4 63.9 + - + +
605A ALA* 3.6 5.0 - - - +
606A LYS* 3.2 40.1 + - - +
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Residues in contact with ILE 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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576A TRP* 3.7 35.4 - - + +
595A SER 5.6 0.2 - - - +
596A VAL* 3.7 8.3 - - + -
597A LYS* 3.4 48.2 - - + +
600A GLN* 2.9 33.1 + - + +
602A GLU* 1.4 78.8 - - + +
604A VAL* 1.4 52.3 + - - +
606A LYS* 2.9 14.8 + - + +
607A THR* 2.8 35.2 + - - -
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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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422A ASP 5.8 0.4 - - - +
424A PRO* 4.9 9.4 - - + -
596A VAL* 4.8 0.2 - - - -
597A LYS 3.9 5.8 - - - +
598A TRP* 3.5 52.9 - - + +
600A GLN 3.3 14.3 + - - +
601A GLN* 3.7 10.1 - - + +
603A ILE* 1.4 73.5 - - - +
605A ALA* 1.3 55.7 - - - +
607A THR* 3.3 10.7 + - - -
608A TYR* 3.0 49.9 + - + +
637A ASP* 4.5 1.3 - - - +
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Residues in contact with ALA 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A GLN* 3.0 28.8 + - - +
602A GLU* 3.6 7.6 - - - +
604A VAL* 1.3 77.6 - - - +
606A LYS* 1.4 56.2 + - - +
608A TYR* 3.3 11.8 + - - +
609A GLN* 3.0 40.5 + - - +
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Residues in contact with LYS 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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576A TRP* 3.8 29.2 - - + +
579A ARG* 4.3 22.0 + - - +
580A TYR* 5.4 1.0 + - - -
602A GLU* 3.2 30.5 + - - +
603A ILE* 2.9 13.5 + - + +
605A ALA* 1.4 71.9 - - - +
607A THR* 1.3 59.9 + - - +
609A GLN* 3.2 25.2 + - - +
610A LEU* 2.9 29.5 + - - +
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Residues in contact with THR 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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576A TRP* 3.8 11.9 - - + -
593A PHE* 3.7 33.0 - - + -
596A VAL* 3.3 23.3 - - + +
598A TRP* 4.0 18.8 - - + -
603A ILE 2.8 14.2 + - - -
604A VAL* 3.3 11.7 - - - -
606A LYS* 1.3 75.6 - - - +
608A TYR* 1.3 59.2 + - + +
610A LEU* 3.3 8.9 + - + +
611A LEU* 3.0 37.6 + - + +
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Residues in contact with TYR 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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425A LYS* 5.9 2.6 - - - +
598A TRP* 4.9 2.9 - + - -
604A VAL* 3.0 32.1 + - + +
605A ALA* 3.4 12.3 - - - +
607A THR* 1.3 79.5 - - - +
609A GLN* 1.4 54.7 + - - +
611A LEU* 3.5 11.2 + - + +
612A ALA* 3.1 27.2 + - - +
637A ASP* 2.6 39.6 + - - -
638A GLU* 4.9 1.9 + - - +
639A ASN* 3.1 36.8 + - + -
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Residues in contact with GLN 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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580A TYR* 4.9 10.7 + - - +
605A ALA* 3.0 32.4 + - - +
606A LYS* 3.2 27.3 + - - +
608A TYR* 1.4 73.2 - - - +
610A LEU* 1.3 64.3 + - - +
612A ALA* 3.4 18.0 + - - +
613A ARG* 4.2 8.1 + - - +
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Residues in contact with LEU 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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576A TRP* 5.3 4.7 - - + -
579A ARG* 3.7 47.6 - - + +
580A TYR* 3.7 36.9 + - + -
583A LEU* 3.6 46.2 - - + +
592A LEU* 3.9 14.1 - - + -
593A PHE* 5.0 7.0 - - + -
606A LYS 2.9 12.2 + - - +
607A THR* 3.3 11.7 - - - +
609A GLN* 1.3 74.3 - - - +
611A LEU* 1.3 62.1 + - + +
612A ALA 3.5 0.7 + - - -
613A ARG* 3.5 20.4 + - - +
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Residues in contact with LEU 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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583A LEU* 5.1 2.5 - - + -
589A TYR* 5.0 2.2 - - + -
593A PHE* 3.5 38.6 - - + -
607A THR* 3.0 27.5 + - + +
608A TYR* 3.5 16.6 + - + +
609A GLN 3.3 0.2 - - - -
610A LEU* 1.3 76.1 - - + +
612A ALA* 1.3 63.0 + - - +
614A ARG* 3.0 61.9 + - + +
639A ASN* 4.7 12.1 - - + +
640A VAL* 4.2 17.7 - - + +
643A ILE* 3.9 14.8 - - + -
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Residues in contact with ALA 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 TYR 3.1 13.5 + - - +
609A GLN* 3.6 13.2 - - - +
610A LEU 3.4 1.0 - - - -
611A LEU* 1.3 74.5 - - - +
613A ARG* 1.3 56.8 + - + +
614A ARG* 3.5 8.3 + - - +
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Residues in contact with ARG 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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580A TYR* 3.4 37.7 - - + -
583A LEU* 3.5 25.6 - - + +
609A GLN 4.4 7.2 - - - +
610A LEU 3.9 9.4 - - - +
611A LEU 3.3 1.8 - - - -
612A ALA* 1.3 75.1 - - + +
614A ARG* 1.3 56.6 + - - +
615A GLU* 3.4 10.8 + - + +
616A VAL* 6.0 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