Contacts of the helix formed by residues 585 - 592 (chain A) in PDB entry 4Z7I
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 585 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A LYS* 5.1 16.3 + - + +
482A ASP* 4.3 11.7 - - - +
485A LEU* 3.9 7.5 - - - +
584A ILE* 1.3 84.6 - - - +
586A SER* 1.3 73.7 + - - +
587A ASP* 4.1 24.3 + - - +
588A ASP* 3.3 34.1 + - - +
589A LEU* 3.6 4.9 + - - +
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Residues in contact with SER 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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482A ASP* 3.1 24.7 + - - -
484A TRP* 3.2 30.0 + - - -
485A LEU* 3.6 8.4 - - - +
531A SER* 3.4 11.7 + - - -
585A GLN* 1.3 77.3 - - - +
587A ASP* 1.3 68.0 + - - +
589A LEU* 3.4 12.5 + - - +
590A TRP* 3.0 28.7 + - - -
611A THR* 4.8 1.6 - - - +
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Residues in contact with ASP 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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585A GLN* 3.2 21.6 + - - +
586A SER* 1.3 83.3 + - - +
588A ASP* 1.3 52.9 + - - +
590A TRP* 3.0 16.3 + - - +
591A ASP* 2.7 46.0 + - - +
608A LYS* 3.5 34.8 + - - -
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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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575A TYR* 4.1 4.2 - - - -
579A HIS* 4.0 13.0 + - + +
583A SER 4.8 2.1 - - - +
584A ILE* 3.3 25.0 - - + +
585A GLN* 3.3 35.8 + - - +
587A ASP* 1.3 75.1 - - - +
589A LEU* 1.3 62.6 + - - +
591A ASP* 3.5 17.4 - - - +
592A SER* 3.3 22.7 + - - -
1G NAG 3.8 20.2 + - - +
2G NAG 4.3 9.1 - - - +
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Residues in contact with LEU 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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484A TRP* 4.8 0.2 - - + -
485A LEU* 3.7 28.0 - - + -
489A PHE* 3.7 23.3 - - + -
556A LEU* 4.4 8.3 - - + -
571A ALA 5.5 0.2 - - - +
572A VAL* 6.1 0.9 - - - -
575A TYR* 3.5 51.0 - - + +
585A GLN 3.6 5.5 + - - +
586A SER 3.4 10.2 + - - +
587A ASP 3.2 0.6 - - - -
588A ASP* 1.3 77.0 - - - +
590A TRP* 1.3 87.0 + - + +
592A SER* 3.4 5.7 + - - -
593A PHE* 3.2 37.6 + - + +
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Residues in contact with TRP 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 TRP* 3.8 31.2 - + - -
555A LEU* 5.6 0.7 - - + -
556A LEU* 5.2 4.5 - - + -
559A LEU* 3.5 26.5 - - + -
586A SER* 3.0 25.4 + - - -
587A ASP* 3.0 21.0 + - + +
589A LEU* 1.3 94.4 - - + +
591A ASP* 1.3 61.7 + - - +
593A PHE* 3.0 17.0 + + - +
594A ASN* 2.6 26.8 + - - +
604A LYS* 3.5 28.9 - - + +
607A MET* 3.5 45.0 + - + +
608A LYS* 5.3 7.3 - - + +
611A THR* 3.8 19.9 + - + +
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Residues in contact with ASP 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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587A ASP* 2.7 29.1 + - - +
588A ASP* 3.5 23.1 - - - +
589A LEU 3.3 0.2 - - - -
590A TRP* 1.3 69.8 - - - +
592A SER* 1.3 57.3 + - - +
593A PHE 3.0 9.0 + - - -
594A ASN* 3.2 18.3 + - - +
595A GLU* 3.5 16.4 + - - +
1G NAG 4.5 7.3 - - - -
2G NAG 4.2 41.5 + - - +
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Residues in contact with SER 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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571A ALA* 3.3 22.8 - - - +
574A LEU* 4.3 15.4 - - - +
575A TYR* 3.2 36.4 - - - +
578A ASN* 5.3 5.8 - - - -
579A HIS* 5.3 6.3 - - - -
588A ASP 3.3 15.1 + - - -
589A LEU 3.4 5.2 + - - -
591A ASP* 1.3 76.4 - - - +
593A PHE* 1.3 56.8 + - - +
594A ASN 3.4 0.4 - - - -
595A GLU* 3.8 19.3 - - - +
1G NAG 5.6 3.1 - - - -
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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