Contacts of the helix formed by residues 585 - 596 (chain A) in PDB entry 2XKK
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 ARG 585 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A ASP 4.5 0.9 - - - +
579A LYS* 4.1 17.5 - - - +
582A ALA* 2.5 37.3 + - + +
584A LYS* 1.3 72.6 - - + +
586A ALA* 1.3 50.9 + - - +
587A ALA* 2.7 19.9 + - - +
588A ASP* 3.1 20.7 + - + +
589A ARG* 3.8 7.3 + - - -
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Residues in contact with ALA 586 (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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582A ALA 3.6 0.2 + - - -
583A LYS 5.1 6.1 - - - +
584A LYS 3.6 2.8 + - - -
585A ARG* 1.3 74.0 - - - +
587A ALA* 1.3 60.2 + - - +
588A ASP 3.4 0.2 - - - -
589A ARG* 3.1 48.8 + - - +
590A LYS 3.3 5.5 + - - -
1179A GLY* 3.8 20.3 - - - +
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Residues in contact with ALA 587 (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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584A LYS 5.0 2.0 + - - +
585A ARG* 2.7 8.6 + - - +
586A ALA* 1.3 75.2 - - - +
588A ASP* 1.3 66.9 + - - +
590A LYS* 3.4 25.0 + - - +
591A GLN* 3.9 4.5 + - - +
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Residues in contact with ASP 588 (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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579A LYS* 4.1 24.3 + - + +
585A ARG* 3.1 12.6 + - + +
587A ALA* 1.3 79.6 - - - +
589A ARG* 1.3 67.2 + - - +
591A GLN* 3.2 21.1 + - - +
592A TRP* 2.8 24.7 + - - +
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Residues in contact with ARG 589 (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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423A ASN* 6.0 0.8 - - - +
579A LYS* 3.0 25.9 + - + +
580A LEU* 2.9 26.7 + - + +
581A LEU* 4.9 2.6 - - - +
582A ALA 2.8 34.2 + - - +
583A LYS* 4.7 3.0 - - - +
585A ARG 3.8 1.6 + - - -
586A ALA* 3.1 35.8 + - - +
588A ASP* 1.3 79.0 - - - +
590A LYS* 1.3 67.8 + - - +
592A TRP* 3.2 27.1 + - + +
593A LEU* 3.0 27.3 + - + +
1022A TYR* 3.9 17.2 + - + -
1178A VAL* 5.0 6.3 - - + +
1179A GLY* 4.1 17.1 - - - +
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Residues in contact with LYS 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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586A ALA 3.3 4.2 + - - +
587A ALA* 3.5 15.3 - - - +
588A ASP 3.2 0.6 - - - -
589A ARG* 1.3 78.9 - - - +
591A GLN* 1.3 69.0 + - - +
593A LEU* 3.1 23.0 + - - +
594A GLU* 3.3 5.9 + - - +
1179A GLY* 3.5 25.5 - - - +
1180A MET* 4.1 25.7 - - + +
1240A ARG* 5.2 10.5 - - - +
1344A VAL* 6.3 1.0 - - - +
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Residues in contact with GLN 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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579A LYS* 3.8 16.3 + - - -
587A ALA 3.9 3.7 + - - +
588A ASP* 3.2 25.7 + - - +
590A LYS* 1.3 77.9 - - - +
592A TRP* 1.3 60.8 + - - +
594A GLU* 2.5 37.6 + - - +
595A GLN* 3.0 22.9 + - + +
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Residues in contact with TRP 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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576A LEU* 5.8 2.5 - - + +
579A LYS* 3.6 28.3 - - + +
580A LEU* 3.5 33.7 - - + -
588A ASP 2.8 15.1 + - - +
589A ARG* 3.3 26.7 - - + +
591A GLN* 1.3 77.1 - - - +
593A LEU* 1.3 75.3 + - + +
595A GLN* 3.1 8.6 + - + +
596A LYS* 2.5 54.6 + - + +
1019A GLU* 3.9 25.4 + - + +
1022A TYR* 3.9 13.5 - + + -
1023A LEU* 3.6 47.6 - - + -
1026A ALA* 4.5 2.5 - - + -
1178A VAL* 5.4 0.4 - - + -
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Residues in contact with LEU 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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589A ARG 3.0 16.8 + - - +
590A LYS* 3.3 13.9 - - - +
591A GLN 2.7 4.0 + - - -
592A TRP* 1.3 98.3 - - + +
594A GLU* 1.3 57.8 + - - +
595A GLN 2.9 4.3 - - - -
596A LYS 2.9 31.0 + - - +
1023A LEU* 3.8 12.3 - - + -
1026A ALA* 3.5 22.0 - - + -
1027A MET* 4.1 21.5 - - - +
1030A ILE* 3.6 28.9 - - + -
1178A VAL* 4.0 12.8 - - + +
1179A GLY* 4.6 1.8 - - - -
1180A MET* 4.6 2.5 - - + -
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Residues in contact with GLU 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 LYS* 3.3 6.6 + - + +
591A GLN* 2.5 19.6 + - - +
593A LEU* 1.3 75.3 - - - +
595A GLN* 1.3 63.8 + - + +
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Residues in contact with GLN 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 GLN* 3.0 27.4 + - + +
592A TRP* 3.3 10.8 - - + +
593A LEU 2.9 0.6 - - - -
594A GLU* 1.3 89.1 + - + +
596A LYS* 1.3 59.2 + - + +
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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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592A TRP* 2.5 41.9 + - + +
593A LEU 3.1 15.3 - - - -
595A GLN* 1.3 76.7 - - + +
1019A GLU* 4.9 5.4 - - - +
1023A LEU* 3.9 35.3 - - + +
1027A MET* 5.4 4.4 - - - +
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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