Contacts of the helix formed by residues 577 - 588 (chain A) in PDB entry 1JEQ
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 THR 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A LYS 3.7 1.1 + - - +
576A PHE* 1.3 78.5 - - - +
578A VAL* 1.3 65.9 + - - +
579A PRO* 3.2 17.2 - - - +
580A MET* 3.1 34.5 + - - +
581A LEU* 3.1 9.8 + - - +
144B LYS* 3.3 36.8 - - + +
145B SER* 5.1 3.8 - - - +
147B LEU* 4.0 21.1 - - + -
148B ASP* 4.3 6.9 - - - +
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Residues in contact with VAL 578 (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 PHE 3.9 0.2 + - - -
577A THR* 1.3 71.2 - - - +
579A PRO* 1.3 78.9 - - + +
581A LEU* 3.1 10.6 + - + +
582A LYS* 2.9 33.2 + - + +
594A LEU 5.8 3.4 - - - +
595A LYS 5.4 1.1 - - - -
596A LYS* 3.9 35.9 - - + +
599A LEU* 4.0 6.0 - - + +
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Residues in contact with PRO 579 (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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577A THR* 3.2 17.7 - - - +
578A VAL* 1.3 103.7 - - + +
580A MET* 1.3 62.5 + - - +
582A LYS* 3.2 10.8 + - + +
583A GLU* 3.1 32.0 + - + +
586A ARG* 6.1 0.7 - - - +
148B ASP* 3.8 29.4 - - + +
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Residues in contact with MET 580 (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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559A TYR* 3.3 32.7 - - + +
576A PHE* 3.4 42.4 - - + -
577A THR* 3.1 40.4 + - - +
579A PRO* 1.3 78.3 - - - +
581A LEU* 1.3 61.6 + - - +
583A GLU 3.7 0.2 + - - -
584A ALA* 3.1 24.3 + - - +
147B LEU* 4.7 4.9 - - - -
148B ASP* 4.0 15.5 - - - +
151B ILE* 3.7 26.2 - - + -
210B MET* 4.0 17.3 - - + -
214B SER* 5.0 1.3 - - - +
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Residues in contact with LEU 581 (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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573A LEU* 4.6 8.1 - - + +
576A PHE* 3.8 28.7 - - + +
577A THR 3.1 13.8 + - - +
578A VAL* 3.1 14.0 + - - +
580A MET* 1.3 75.1 - - - +
582A LYS* 1.3 64.4 + - - +
584A ALA* 3.4 5.3 - - - +
585A CYS* 3.0 27.5 + - - -
596A LYS* 3.5 35.4 - - + +
599A LEU* 3.4 32.8 - - + +
600A LEU* 4.5 11.2 - - + +
603A LEU* 4.0 19.8 - - + +
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Residues in contact with LYS 582 (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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578A VAL* 2.9 23.4 + - + +
579A PRO* 3.6 11.7 - - + +
581A LEU* 1.3 71.5 - - - +
583A GLU* 1.3 54.6 - - - +
584A ALA 2.9 1.1 - - - -
585A CYS* 2.6 12.5 + - - +
586A ARG* 2.6 67.4 + - + +
592A SER* 6.2 0.2 - - - -
593A GLY 5.1 9.6 - - - +
594A LEU* 6.0 4.0 - - - +
599A LEU* 3.9 17.3 - - + -
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Residues in contact with GLU 583 (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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559A TYR* 3.8 26.1 - - + +
579A PRO* 3.1 19.4 + - + +
582A LYS* 1.3 78.2 - - - +
584A ALA* 1.3 56.8 + - - +
586A ARG* 3.3 42.7 + - - +
587A ALA* 2.9 30.1 + - - +
148B ASP* 5.3 4.3 - - - +
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Residues in contact with ALA 584 (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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559A TYR* 4.4 21.1 - - + -
564A LEU* 4.7 11.0 - - + -
576A PHE* 5.1 1.3 - - + -
580A MET 3.1 16.5 + - - +
581A LEU 3.4 1.1 - - - +
582A LYS 2.8 1.2 + - - -
583A GLU* 1.3 79.9 - - - +
585A CYS* 1.3 61.3 + - - +
587A ALA* 3.2 6.5 + - - +
588A TYR* 3.1 27.6 - - - -
603A LEU* 3.3 31.4 - - + -
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Residues in contact with CYS 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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581A LEU 3.0 13.8 + - - +
582A LYS* 2.6 13.0 + - - +
584A ALA* 1.3 71.1 - - - +
586A ARG* 1.3 58.5 + - + +
589A GLY* 2.9 22.2 + - - -
590A LEU* 3.0 40.9 + - + +
592A SER* 4.2 13.5 - - - -
599A LEU* 3.7 25.4 - - + -
602A ALA* 4.4 5.8 - - - -
603A LEU* 3.5 27.4 - - - -
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Residues in contact with ARG 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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579A PRO* 6.1 1.0 - - - +
582A LYS* 2.6 55.8 + - + +
583A GLU* 3.5 43.1 + - - +
585A CYS* 1.3 73.2 - - + +
587A ALA* 1.3 59.2 + - - +
589A GLY* 2.9 18.8 + - - -
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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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559A TYR* 5.5 7.2 - - + +
583A GLU 2.9 16.6 + - - +
584A ALA* 3.2 9.2 + - - +
586A ARG* 1.3 78.4 - - - +
588A TYR* 1.3 71.9 + - + +
589A GLY 3.2 1.0 + - - -
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Residues in contact with TYR 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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559A TYR 3.1 18.8 + - - -
560A SER* 4.0 0.9 - - - -
561A GLU* 3.0 51.3 + - + +
564A LEU* 3.8 10.6 - - + +
584A ALA* 3.1 18.6 + - - -
585A CYS 3.4 0.2 + - - -
587A ALA* 1.3 87.4 - - + +
589A GLY* 1.3 66.0 + - - +
590A LEU* 2.6 26.4 + - + +
603A LEU* 5.0 2.2 - - + -
606A HIS* 3.6 33.8 + + + +
607A PHE* 3.6 22.4 - + - -
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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