Contacts of the helix formed by residues 589 - 602 (chain A) in PDB entry 5XA0
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 VAL 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A ASP* 1.3 75.6 - - - +
590A LEU* 1.3 56.3 + - - +
591A ALA* 3.3 2.9 - - - -
592A GLU* 2.3 45.3 - - + +
593A ASP 3.7 0.3 + - - -
629A ARG* 2.9 38.1 - - + -
630A PHE* 4.9 1.1 - - - +
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Residues in contact with LEU 590 (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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553A CYS* 5.9 7.9 - - + +
554A ARG* 6.0 4.0 - - - -
557A TYR* 5.0 19.2 - - + +
588A ASP* 3.3 13.9 - - + +
589A VAL* 1.3 72.5 - - - +
591A ALA* 1.3 69.6 + - - +
592A GLU 2.9 1.6 - - - -
593A ASP* 2.8 25.2 + - - +
594A THR* 3.6 3.1 + - - -
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Residues in contact with ALA 591 (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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581A MET* 5.1 15.9 - - + +
584A GLN* 5.4 10.5 - - + -
585A ILE* 6.1 2.5 - - - -
588A ASP 5.0 2.6 + - - +
589A VAL 3.3 0.8 - - - -
590A LEU* 1.3 76.7 - - - +
592A GLU* 1.3 63.1 + - - +
594A THR* 3.0 12.7 + - - -
595A ILE* 2.8 23.6 + - - +
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Residues in contact with GLU 592 (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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589A VAL* 2.3 39.0 + - + +
591A ALA* 1.3 75.7 - - - +
593A ASP* 1.3 50.9 + - - +
595A ILE* 2.9 11.0 + - - +
596A THR* 2.6 38.2 + - - -
629A ARG* 5.3 4.3 - - + -
630A PHE* 5.3 7.0 - - - +
633A TYR* 4.4 17.5 - - + +
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Residues in contact with ASP 593 (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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557A TYR* 6.0 5.2 - - + -
589A VAL 3.7 0.4 + - - -
590A LEU* 2.8 16.4 + - - +
592A GLU* 1.3 74.0 - - - +
594A THR* 1.3 56.5 + - - +
596A THR* 3.1 10.5 + - - -
597A ALA* 2.9 27.5 + - - +
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Residues in contact with THR 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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557A TYR* 6.3 2.9 - - - -
560A LEU* 5.3 13.2 - - - -
561A ARG* 5.9 4.9 - - - -
590A LEU 3.6 2.3 + - - -
591A ALA* 3.0 15.8 + - - -
592A GLU 3.0 0.4 + - - -
593A ASP* 1.3 74.0 - - - +
595A ILE* 1.3 66.4 + - - +
596A THR 3.0 2.2 + - - -
597A ALA* 3.0 16.4 + - - +
598A LEU* 3.1 12.7 + - - +
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Residues in contact with ILE 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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591A ALA 2.8 16.1 + - - +
592A GLU* 3.4 11.0 - - - +
594A THR* 1.3 71.7 - - - +
596A THR* 1.4 56.5 + - - +
598A LEU* 3.0 10.2 + - - +
599A LEU* 3.0 31.1 + - - +
633A TYR* 5.5 5.8 - - + -
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Residues in contact with THR 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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592A GLU 2.6 16.8 + - - -
593A ASP* 3.2 16.6 - - - -
594A THR 3.0 0.2 - - - -
595A ILE* 1.4 71.3 - - - +
597A ALA* 1.3 63.7 + - - +
598A LEU 3.5 0.2 + - - -
599A LEU* 3.9 9.1 + - - +
600A HIS* 4.0 12.3 + - - +
633A TYR* 4.6 16.6 - - - +
636A ASP* 6.1 3.8 - - - -
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Residues in contact with ALA 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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561A ARG* 5.3 12.8 - - + -
564A GLN 6.0 1.6 - - - +
593A ASP 2.9 12.7 + - - +
594A THR* 3.0 9.6 + - - +
596A THR* 1.3 75.8 - - - +
598A LEU* 1.4 57.2 + - - +
600A HIS* 4.5 1.8 - - - +
601A ASN* 3.4 29.1 + - - +
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Residues in contact with LEU 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 THR 3.1 10.5 + - - +
595A ILE* 3.0 12.8 + - - +
597A ALA* 1.4 76.3 - - - +
599A LEU* 1.3 59.6 + - - +
600A HIS 3.5 0.2 - - - -
601A ASN* 5.0 1.3 - - - -
602A ASN* 2.8 41.2 + - + +
606A LEU* 5.6 0.5 - - - +
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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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595A ILE 3.0 14.8 + - - +
596A THR* 4.5 4.9 - - - +
597A ALA 3.5 0.2 - - - -
598A LEU* 1.3 77.0 - - - +
600A HIS* 1.3 60.2 + - - +
602A ASN 3.0 18.1 - - - +
603A ARG* 4.3 6.4 - - - +
637A LEU* 2.7 46.8 - - + +
639A VAL* 4.8 5.9 - - - +
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Residues in contact with HIS 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 THR 4.0 11.2 + - - +
597A ALA* 3.9 3.2 + - - +
598A LEU 3.5 0.2 - - - -
599A LEU* 1.3 78.6 - - - +
601A ASN* 1.3 65.0 + - - +
602A ASN 4.9 0.5 - - - -
603A ARG* 5.4 2.6 - - - +
637A LEU* 5.1 6.0 - - - +
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Residues in contact with ASN 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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565A GLN 6.1 1.6 - - - +
597A ALA 3.4 17.9 + - - +
598A LEU* 4.9 1.3 - - - +
600A HIS* 1.3 80.3 - - - +
602A ASN* 1.4 58.9 + - + +
603A ARG* 4.3 0.8 + - - +
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Residues in contact with ASN 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 LEU* 2.8 34.3 + - + +
599A LEU* 3.0 14.3 - - - +
601A ASN* 1.4 77.8 - - + +
603A ARG* 1.3 62.2 + - - +
606A LEU* 4.4 19.9 - - + +
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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