Contacts of the helix formed by residues 584 - 595 (chain A) in PDB entry 4JVS
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 ASP 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A LYS 3.6 3.3 - - - +
583A SER* 1.3 74.3 - - - +
585A SER* 1.3 59.8 - - - +
586A LEU 3.6 0.2 - - - -
587A TRP* 3.9 9.4 - - - +
588A GLN* 3.5 23.7 + - - +
617A ARG* 2.6 48.0 + - - +
621A GLN* 5.3 1.6 - - - +
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Residues in contact with SER 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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553A ASN* 4.3 8.1 + - - -
583A SER* 2.3 25.1 + - - -
584A ASP* 1.3 68.9 - - - +
586A LEU* 1.3 69.4 + - - +
587A TRP 3.3 0.2 - - - -
588A GLN* 3.3 25.5 - - - +
589A GLU* 3.5 12.4 - - - +
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Residues in contact with LEU 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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549A GLU* 5.4 5.4 - - - +
552A LEU* 3.6 38.4 - - + +
553A ASN* 3.4 31.9 - - - +
555A MET 5.6 0.4 - - - +
560A LEU* 3.7 20.1 - - + +
579A ARG 4.1 2.9 - - - +
580A ILE* 3.5 26.0 - - + +
583A SER* 3.3 30.5 + - - +
585A SER* 1.3 78.9 + - - +
587A TRP* 1.3 61.5 + - - +
589A GLU* 3.2 8.4 + - + +
590A VAL* 3.0 30.0 + - - +
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Residues in contact with TRP 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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580A ILE 3.7 6.4 + - - +
581A LEU* 4.0 19.3 - - + +
584A ASP 3.9 10.8 - - - +
585A SER 3.3 0.4 - - - -
586A LEU* 1.3 75.3 - - - +
588A GLN* 1.3 58.7 + - + +
590A VAL* 3.1 15.0 + - + -
591A ASP* 2.7 56.3 + - + +
594A LEU* 4.3 7.2 - - + -
613A ILE* 3.6 31.0 - - + -
614A CYS* 4.2 20.4 - - + -
617A ARG* 3.4 72.2 - - + +
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Residues in contact with GLN 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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584A ASP 3.5 14.3 + - - +
585A SER* 3.3 19.1 + - - +
587A TRP* 1.3 83.9 - - + +
589A GLU* 1.3 65.4 + - + +
591A ASP* 3.4 4.8 + - - +
592A ASP* 3.1 29.0 + - - +
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Residues in contact with GLU 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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555A MET 3.7 17.7 - - - +
556A SER* 4.4 1.4 - - - -
557A GLY* 3.4 31.8 + - - -
560A LEU* 3.9 9.4 - - + +
585A SER 3.5 16.2 - - - +
586A LEU* 3.2 8.9 + - + +
588A GLN* 1.3 79.4 - - + +
590A VAL* 1.3 63.8 + - - +
592A ASP* 3.4 12.3 - - - +
593A SER* 3.3 15.8 + - - -
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Residues in contact with VAL 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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557A GLY 4.6 5.4 - - - -
560A LEU* 3.6 29.2 - - + -
561A ALA* 4.7 7.5 - - - +
564A CYS* 4.4 14.4 - - + -
580A ILE* 3.7 20.2 - - + -
581A LEU* 4.8 0.2 - - + -
586A LEU 3.0 15.2 + - - +
587A TRP* 3.5 22.0 - - + +
589A GLU* 1.3 77.7 - - - +
591A ASP* 1.3 57.3 + - - +
593A SER* 3.5 2.3 + - - -
594A LEU* 3.0 46.1 + - + +
613A ILE* 4.6 1.8 - - + -
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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 TRP* 2.7 49.9 + - + +
588A GLN* 3.8 6.1 - - - +
590A VAL* 1.3 75.1 - - - +
592A ASP* 1.3 58.9 + - + +
594A LEU* 3.3 12.2 + - - +
595A ASN* 2.8 51.5 + - - +
614A CYS* 5.3 3.8 - - - -
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Residues in contact with ASP 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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557A GLY* 5.4 1.2 - - - -
588A GLN* 3.1 21.0 + - - +
589A GLU* 3.4 12.9 - - - +
591A ASP* 1.3 80.8 - - + +
593A SER* 1.3 64.5 + - - +
595A ASN* 3.8 11.5 - - + +
596A GLY* 3.7 12.5 + - - -
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Residues in contact with SER 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 GLY* 3.1 14.9 - - - -
558A ASP* 2.4 40.1 + - - +
561A ALA* 4.2 2.7 - - - -
589A GLU 3.3 13.8 + - - -
590A VAL 3.8 3.1 - - - -
591A ASP 3.2 0.8 - - - -
592A ASP* 1.3 81.5 + - - +
594A LEU* 1.3 63.8 + - - +
595A ASN 3.1 1.6 - - - -
596A GLY* 3.0 14.7 + - - -
598A ALA* 5.7 0.3 - - - +
599A PHE* 3.5 24.0 - - - -
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Residues in contact with LEU 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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561A ALA* 5.0 4.5 - - + +
565A PHE* 3.4 37.0 - - + -
587A TRP* 4.3 8.7 - - + -
590A VAL* 3.0 40.9 + - + +
591A ASP* 3.5 14.1 - - - +
593A SER* 1.3 75.8 - - - +
595A ASN* 1.3 61.2 + - - +
596A GLY 3.3 6.9 + - - +
599A PHE* 4.8 6.3 - - - +
610A ARG* 3.6 50.4 + - + +
613A ILE* 4.0 23.6 - - + -
614A CYS* 5.0 4.3 - - - -
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Residues in contact with ASN 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 ASP* 2.8 43.0 + - - +
592A ASP* 3.8 13.2 - - - +
593A SER 3.1 0.4 - - - -
594A LEU* 1.3 79.2 + - - +
596A GLY* 1.3 60.2 + - - +
610A ARG* 5.6 4.6 - - - +
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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