Contacts of the helix formed by residues 578 - 588 (chain A) in PDB entry 3QFS
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 TYR 578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ARG* 4.4 2.9 - - - -
295A LEU* 3.7 32.5 + - + +
305A HIS* 2.8 41.2 - + - -
462A ALA* 4.3 3.5 - - + +
475A CYS* 3.3 40.3 - - + +
540A VAL* 4.2 4.9 - - + -
544A ILE* 3.4 53.2 - - + -
576A TYR 3.5 1.0 + - - -
577A LEU* 1.3 79.7 - - + +
579A ARG* 1.3 65.4 + - - +
580A GLU 3.2 2.5 - - - -
581A GLU* 3.3 31.5 + - + +
582A LEU* 2.8 26.3 + - + +
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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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297A GLN* 4.4 10.3 + - - +
572A SER* 3.2 34.3 + - - -
573A ASP* 4.6 5.5 - - - +
576A TYR* 3.4 59.2 + - + +
577A LEU 3.1 2.2 + - - -
578A TYR* 1.3 77.1 - - - +
580A GLU* 1.3 65.8 + - + +
582A LEU* 4.0 0.9 - - - +
583A ALA* 3.0 26.9 + - + +
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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 TYR 3.2 0.4 - - - -
579A ARG* 1.3 79.6 - - + +
581A GLU* 1.3 75.4 + - - +
583A ALA* 3.3 6.9 + - - +
584A GLN* 3.1 23.4 + - - +
587A ARG* 4.4 3.3 + - - +
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Residues in contact with GLU 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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293A ARG* 2.9 32.3 + - - -
295A LEU* 5.6 0.3 - - - +
544A ILE* 6.0 3.8 - - + -
578A TYR* 3.4 36.6 - - + +
580A GLU* 1.3 82.7 + - - +
582A LEU* 1.3 59.1 + - + +
584A GLN* 3.2 7.8 + - - +
585A PHE* 2.9 48.1 + - + -
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Residues in contact with LEU 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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540A VAL* 4.8 5.6 - - + -
544A ILE* 4.1 15.0 - - + -
547A ILE* 3.8 28.9 - - + -
565A LEU* 3.9 22.2 - - + -
567A TYR* 4.9 3.6 - - + -
576A TYR* 4.2 13.7 - - + +
577A LEU 3.6 23.6 - - - +
578A TYR* 2.8 24.5 + - + +
579A ARG* 4.1 2.9 - - - +
581A GLU* 1.3 69.8 - - - +
583A ALA* 1.3 66.5 + - - +
585A PHE* 3.3 10.6 + - + +
586A HIS* 2.9 24.4 + - - +
591A LEU* 3.9 7.7 - - + +
594A LEU* 3.8 20.3 - - + +
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Residues in contact with ALA 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* 3.0 21.9 + - + +
580A GLU* 3.5 6.1 - - - +
582A LEU* 1.3 76.0 - - - +
584A GLN* 1.3 58.1 + - - +
586A HIS* 3.3 7.6 + - - +
587A ARG* 2.9 47.6 + - + +
594A LEU* 4.3 7.4 - - + +
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Residues in contact with GLN 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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580A GLU 3.1 13.0 + - - +
581A GLU* 3.6 10.3 - - - +
583A ALA* 1.3 75.1 - - - +
585A PHE* 1.3 62.5 + - + +
587A ARG* 2.8 39.0 + - - +
588A ASP* 2.8 60.7 + - - +
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Residues in contact with PHE 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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544A ILE* 4.8 9.2 - - + -
547A ILE* 3.4 30.3 - - + -
548A GLN* 3.9 33.0 - - + -
551A ALA* 3.6 31.4 - - + -
555A GLN* 5.4 2.2 - - - -
581A GLU* 2.9 40.0 + - + +
582A LEU* 3.3 14.3 + - + +
584A GLN* 1.3 79.5 - - + +
586A HIS* 1.3 60.6 + - - +
588A ASP* 3.6 3.5 + - + -
589A GLY 3.2 2.8 + - - -
590A ALA* 2.9 33.4 + - + -
591A LEU* 3.0 8.3 + - + -
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Residues in contact with HIS 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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582A LEU 2.9 13.7 + - - +
583A ALA* 3.4 9.8 - - - +
584A GLN 3.1 0.2 - - - -
585A PHE* 1.3 74.5 - - - +
587A ARG* 1.3 68.1 + - - +
589A GLY* 3.1 14.0 + - - -
591A LEU* 3.2 28.8 - - + +
592A THR 3.8 15.7 + - - -
593A GLN* 4.4 0.6 - - - -
594A LEU* 4.2 33.0 + - + +
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Residues in contact with ARG 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 GLU* 4.4 3.2 + - - +
583A ALA* 2.9 27.4 + - - +
584A GLN* 2.8 44.9 - - - +
586A HIS* 1.3 79.4 - - + +
588A ASP* 1.3 64.8 + - - +
589A GLY* 3.4 0.7 + - - -
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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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554A ARG* 3.4 15.2 + - - -
584A GLN* 2.8 48.8 + - - +
585A PHE* 4.2 6.8 - - + +
587A ARG* 1.3 78.1 - - - +
589A GLY* 1.3 57.8 + - - +
590A ALA* 3.4 5.1 + - + +
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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