Contacts of the helix formed by residues 584 - 594 (chain A) in PDB entry 3JUE
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 SER 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A ALA* 2.9 12.7 + - - +
582A PRO 3.6 2.3 + - - -
583A PRO* 1.3 72.1 - - - +
585A LEU* 1.3 57.9 + - - +
586A PRO* 3.7 10.5 - - - +
587A THR* 2.9 32.9 + - - -
588A MET* 2.9 30.3 + - - +
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Residues in contact with LEU 585 (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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472A LEU* 4.0 8.7 - - + -
475A GLU* 3.5 35.2 - - + +
476A LEU* 3.8 16.4 - - + +
583A PRO* 3.8 6.6 + - + +
584A SER* 1.3 71.2 - - - +
586A PRO* 1.4 66.1 - - + +
588A MET* 3.7 15.5 - - - +
589A ALA* 3.0 28.9 + - - +
621A LEU* 3.9 19.3 - - + +
622A ALA* 3.8 32.1 - - + +
625A PHE* 3.9 20.1 - - + -
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Residues in contact with PRO 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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475A GLU* 4.5 11.4 - - + +
476A LEU* 4.4 0.4 - - + -
480A ILE* 4.1 36.1 - - + -
484A ILE* 3.7 5.2 - - + +
584A SER* 3.5 11.2 - - - +
585A LEU* 1.4 93.9 - - + +
587A THR* 1.3 56.7 + - - +
589A ALA* 3.4 7.6 + - + +
590A ASP* 3.0 27.9 + - - +
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Residues in contact with THR 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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574A LEU* 3.8 31.0 - - + -
578A ALA* 3.6 20.0 - - + -
584A SER* 2.9 26.5 + - - -
586A PRO* 1.3 74.4 - - - +
588A MET* 1.3 61.0 + - - +
590A ASP* 3.2 7.3 + - + +
591A ALA* 2.9 27.9 + - - +
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Residues in contact with MET 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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575A LEU* 3.7 12.0 - - + +
578A ALA* 3.9 21.8 - - + +
579A SER* 3.5 27.8 - - - +
583A PRO* 4.6 1.1 - - - -
584A SER 2.9 17.8 + - - +
585A LEU* 3.4 19.9 + - - +
587A THR* 1.3 75.0 - - - +
589A ALA* 1.3 56.9 + - - +
591A ALA* 3.4 2.9 + - - +
592A LEU* 3.0 33.4 + - - +
622A ALA* 3.8 28.5 - - + +
625A PHE* 3.8 21.3 - - + -
626A LEU* 3.5 33.0 - - + -
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Residues in contact with ALA 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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476A LEU* 4.3 1.8 - - + -
481A ILE* 3.9 20.6 - - + -
484A ILE* 3.8 15.2 - - + +
485A TYR* 4.9 3.7 + - + -
585A LEU 3.0 17.9 + - - +
586A PRO* 3.5 7.6 - - + +
588A MET* 1.3 76.2 - - - +
590A ASP* 1.3 58.0 + - - +
592A LEU* 3.4 3.7 + - - +
593A ALA* 3.0 30.3 + - - +
625A PHE* 3.7 20.4 - - + -
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Residues in contact with ASP 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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484A ILE* 3.5 28.3 - - + +
521A THR* 5.2 0.9 + - - -
524A PRO* 3.4 25.3 - - + +
586A PRO 3.0 16.2 + - - +
587A THR* 3.2 10.1 + - + +
589A ALA* 1.3 74.0 - - - +
591A ALA* 1.3 65.2 + - - +
592A LEU 3.4 0.2 + - - -
593A ALA* 3.4 1.6 + - - +
594A HIS* 2.7 60.9 + - - -
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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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524A PRO* 4.1 11.6 - - - +
571A PRO* 3.4 24.8 - - - +
574A LEU* 4.2 10.5 - - + +
575A LEU* 3.8 21.8 - - + +
587A THR 2.9 16.2 + - - +
588A MET 3.8 4.0 - - - +
590A ASP* 1.3 76.1 - - - +
592A LEU* 1.3 61.6 + - - +
594A HIS* 3.1 11.7 + - - +
595A GLY 3.4 0.3 + - - -
596A ALA* 3.0 20.7 + - - +
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Residues in contact with LEU 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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485A TYR* 5.0 1.3 - - - +
517A LYS* 5.0 2.4 - - - -
575A LEU* 4.2 19.3 - - + -
588A MET 3.0 20.8 + - - +
589A ALA* 3.8 3.6 - - - +
591A ALA* 1.3 73.6 - - - +
593A ALA* 1.3 60.3 + - - +
595A GLY* 2.9 20.6 + - - -
596A ALA* 3.5 22.4 + - - +
598A VAL* 4.1 22.9 - - + -
625A PHE* 4.0 24.0 - - + -
626A LEU* 5.1 4.7 - - + -
629A ASN* 4.1 28.5 - - + +
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Residues in contact with ALA 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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484A ILE* 3.7 20.6 - - + -
485A TYR* 3.4 39.3 + - + +
517A LYS* 3.3 19.4 - - - +
520A LEU* 3.3 20.4 - - + +
589A ALA 3.0 16.5 + - - +
590A ASP 3.7 2.0 - - - +
591A ALA 3.4 0.2 - - - -
592A LEU* 1.3 75.8 - - - +
594A HIS* 1.3 58.9 + - + +
595A GLY 3.4 2.4 + - - -
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Residues in contact with HIS 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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484A ILE* 4.9 2.4 + - - +
520A LEU* 3.9 21.2 - - + +
521A THR* 2.9 37.0 + - - -
522A LYS 3.6 11.9 + - - -
523A LEU 3.6 13.9 - - - -
524A PRO* 3.4 26.6 - - + +
571A PRO* 3.6 15.6 - - + +
590A ASP* 2.7 46.3 + - - +
591A ALA 3.1 7.5 + - - +
593A ALA* 1.3 80.0 - - + +
595A GLY* 1.3 59.0 + - - +
596A ALA 3.4 2.5 - - - -
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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