Contacts of the helix formed by residues 578 - 591 (chain A) in PDB entry 1RQG
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 LYS 578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A TYR* 1.3 75.9 - - - +
579A ARG* 1.3 60.7 + - - +
580A GLU* 4.2 23.4 + - + +
581A ASP* 2.9 40.4 + - - +
582A VAL* 3.2 12.1 + - - +
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Residues in contact with ARG 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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570A ARG* 3.9 11.5 - - - +
574A ASP* 2.7 35.5 + - + +
577A TYR 3.8 0.4 + - - -
578A LYS* 1.3 72.9 - - - +
580A GLU* 1.3 60.9 - - + +
582A VAL* 3.9 1.2 - - - +
583A ILE* 2.9 38.2 + - + +
602A TYR* 3.2 62.5 - - + +
604A ASP 5.2 5.5 + - - -
605A ILE* 6.1 0.4 - - - +
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Residues in contact with GLU 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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578A LYS* 3.1 22.6 + - + +
579A ARG* 1.3 79.3 - - + +
581A ASP* 1.3 61.1 + - - +
583A ILE* 4.1 11.1 - - + +
584A ARG* 3.6 18.7 + - - +
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Residues in contact with ASP 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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554A ILE* 4.7 4.0 - - + -
577A TYR* 5.0 7.6 - - + -
578A LYS* 2.9 38.4 + - - +
580A GLU* 1.3 78.9 - - - +
582A VAL* 1.3 65.9 + - - +
583A ILE 3.2 1.1 - - - -
584A ARG* 3.2 34.3 + - - +
585A VAL* 3.0 26.9 + - + +
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Residues in contact with VAL 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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554A ILE* 3.7 38.1 - - + -
558A LEU* 4.0 10.5 - - + -
573A LEU* 3.9 22.7 - - + -
577A TYR* 3.9 13.0 - - + -
578A LYS 3.2 12.3 + - - +
579A ARG 3.5 4.2 + - - +
581A ASP* 1.3 76.6 - - - +
583A ILE* 1.3 52.1 + - - +
585A VAL* 3.2 2.6 + - - +
586A ALA* 2.7 33.1 + - - +
598A LEU* 4.0 10.3 - - + -
602A TYR* 3.3 28.3 - - + +
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Residues in contact with ILE 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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579A ARG* 2.9 30.4 + - + +
580A GLU* 4.1 11.7 - - + +
581A ASP 3.2 0.2 - - - -
582A VAL* 1.3 77.3 - - + +
584A ARG* 1.3 53.9 + - - +
586A ALA* 2.9 2.9 + - - +
587A LYS* 2.5 57.9 + - + +
598A LEU* 3.6 35.9 - - + -
602A TYR* 5.5 3.1 - - + -
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Residues in contact with ARG 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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551A ASP* 4.0 17.4 + - - -
580A GLU 3.6 11.7 + - - +
581A ASP* 3.2 33.0 + - - +
583A ILE* 1.3 80.2 - - - +
585A VAL* 1.3 62.3 + - - +
587A LYS* 3.6 6.3 - - - +
588A GLU* 2.9 54.5 + - + +
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Residues in contact with VAL 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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551A ASP* 3.6 49.4 - - - +
554A ILE* 3.7 35.7 - - + -
555A TYR* 4.3 7.4 - - - +
558A LEU* 5.3 0.7 - - + -
581A ASP* 3.0 16.2 + - + +
582A VAL 3.6 6.7 - - - +
584A ARG* 1.3 83.2 - - - +
586A ALA* 1.3 61.4 + - - +
588A GLU* 3.5 11.6 + - - +
589A LYS* 2.8 38.1 + - + +
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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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558A LEU* 3.6 16.4 - - + -
582A VAL 2.7 21.9 + - - +
583A ILE 3.3 4.0 - - - +
585A VAL* 1.3 75.1 - - - +
587A LYS* 1.3 55.8 + - - +
590A PHE* 2.9 41.8 + - + -
594A ALA* 2.9 13.9 - - + +
597A VAL* 5.6 0.4 - - + -
598A LEU* 3.5 30.5 - - + -
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Residues in contact with LYS 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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583A ILE* 2.5 42.6 + - + +
584A ARG* 3.6 7.0 - - - +
586A ALA* 1.3 74.4 - - - +
588A GLU* 1.3 57.6 + - + +
589A LYS 3.1 4.2 + - - -
591A GLY* 3.6 23.6 + - - +
594A ALA* 3.6 16.2 - - + -
595A GLU* 3.1 31.3 + - - +
598A LEU* 5.0 1.8 - - + -
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Residues in contact with GLU 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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551A ASP* 3.9 14.3 - - - +
584A ARG* 2.9 48.0 + - - +
585A VAL* 3.8 9.5 - - - +
587A LYS* 1.3 75.1 - - + +
589A LYS* 1.3 66.5 + - + +
591A GLY 5.1 0.7 - - - -
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Residues in contact with LYS 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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551A ASP* 5.2 10.3 - - - +
555A TYR* 3.4 48.3 - - + -
585A VAL* 2.8 25.8 - - + +
586A ALA* 3.9 2.5 - - - +
587A LYS 3.1 1.0 + - - -
588A GLU* 1.3 86.2 + - + +
590A PHE* 1.3 77.8 + - + +
591A GLY 3.6 2.0 - - - -
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Residues in contact with PHE 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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555A TYR* 3.8 35.9 - + - -
558A LEU* 3.7 34.5 - - + -
559A ASN* 3.9 26.5 - - + -
585A VAL* 6.3 0.4 - - + -
586A ALA* 2.9 33.3 + - + +
589A LYS* 1.3 88.3 - - + +
591A GLY* 1.3 65.5 + - - +
592A ASP* 3.1 2.6 + - - +
593A GLU* 2.9 22.8 + - + +
594A ALA* 3.5 18.6 - - - +
597A VAL* 4.4 16.4 - - + -
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Residues in contact with GLY 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 LYS* 3.6 18.2 + - - +
589A LYS 3.6 2.6 + - - +
590A PHE* 1.3 75.3 - - - +
592A ASP* 1.3 59.4 + - - -
593A GLU 3.0 5.9 + - - -
594A ALA* 3.6 11.6 + - - +
595A GLU 5.2 0.2 + - - -
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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