Contacts of the helix formed by residues 543 - 554 (chain A) in PDB entry 3O8C
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 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A HIS 3.6 1.2 + - - -
542A ILE* 1.3 73.1 - - - +
544A ALA* 1.3 62.1 + - - +
545A HIS* 2.9 33.5 + - - +
546A PHE* 3.1 35.3 + - + +
547A LEU* 3.1 21.0 + - - +
566A THR* 3.1 29.0 + - + +
570A ARG* 4.0 12.2 + - - +
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A ILE* 3.4 7.9 + - - +
543A ASP* 1.3 72.7 + - - +
545A HIS* 1.3 57.3 + - - +
547A LEU* 3.8 7.4 - - - +
548A SER* 2.8 30.0 + - - -
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Residues in contact with HIS 545 (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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543A ASP* 2.9 10.8 + - - +
544A ALA* 1.3 76.7 - - - +
546A PHE* 1.3 71.1 + - - +
548A SER* 3.3 8.1 + - - -
549A GLN* 3.1 48.9 + - + +
587A ARG* 3.2 36.1 + - - -
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Residues in contact with PHE 546 (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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543A ASP* 3.1 36.6 + - + +
545A HIS* 1.3 85.2 - - - +
547A LEU* 1.3 59.1 + - - +
549A GLN* 3.1 17.6 + - - +
550A THR* 2.9 32.7 + - - +
562A ALA* 3.7 16.4 - - + +
565A ALA* 3.7 11.2 - - + -
566A THR* 3.7 17.5 - - - -
569A ALA* 3.4 29.2 - - + -
584A CYS* 4.0 23.8 - - - -
585A LEU* 3.5 23.3 - - + -
587A ARG* 4.6 6.3 - - - -
588A LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A CYS 4.8 2.5 - - - +
500A ALA* 4.1 11.7 - - + +
542A ILE* 4.1 22.4 - - + -
543A ASP 3.1 15.0 + - - +
544A ALA* 3.8 6.3 - - - +
546A PHE* 1.3 77.0 - - - +
548A SER* 1.3 65.7 + - - +
550A THR* 3.3 2.0 + - - +
551A LYS* 3.0 54.1 + - + +
558A PRO 3.9 19.7 - - - +
559A TYR* 3.9 31.4 - - + -
562A ALA* 3.5 10.2 - - + +
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Residues in contact with SER 548 (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 ALA 2.8 19.5 + - - -
545A HIS* 3.5 11.2 - - - -
547A LEU* 1.3 76.3 - - - +
549A GLN* 1.3 61.0 + - - +
551A LYS* 3.9 9.1 - - - +
552A GLN* 3.1 29.1 + - - +
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Residues in contact with GLN 549 (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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545A HIS* 3.1 49.5 + - + +
546A PHE* 3.1 18.8 + - - +
548A SER* 1.3 77.7 - - - +
550A THR* 1.3 66.0 + - - +
552A GLN* 3.3 6.0 + - - +
553A ALA* 3.0 25.3 + - - +
584A CYS* 3.9 29.5 + - + +
587A ARG* 5.3 4.4 - - - +
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Residues in contact with THR 550 (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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546A PHE 2.9 19.5 + - - +
547A LEU* 3.3 8.0 + - - +
549A GLN* 1.3 73.9 - - - +
551A LYS* 1.3 65.4 + - - +
553A ALA* 3.5 12.5 + - - +
554A GLY* 3.6 7.3 + - - -
555A ASP* 4.4 6.1 + - - +
558A PRO* 2.8 39.1 + - - +
561A VAL* 3.7 28.3 - - + -
562A ALA* 3.5 15.1 - - + +
581A MET 5.4 1.3 - - - +
584A CYS* 4.5 13.9 - - + -
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Residues in contact with LYS 551 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A ALA* 3.1 33.5 + - + +
501A TRP* 3.5 56.5 - - + +
547A LEU* 3.0 45.2 + - + +
548A SER* 3.9 7.6 - - - +
550A THR* 1.3 79.5 + - - +
552A GLN* 1.3 61.2 + - - +
554A GLY* 3.4 10.9 + - - -
558A PRO* 4.1 7.4 - - + -
7C U 4.7 1.6 - - - +
8C U 3.1 32.5 + - - +
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Residues in contact with GLN 552 (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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501A TRP* 5.5 2.0 - - - -
548A SER* 3.1 18.5 + - - +
549A GLN* 3.9 6.0 - - - +
550A THR 3.3 0.2 - - - -
551A LYS* 1.3 78.2 - - - +
553A ALA* 1.3 69.2 + - - +
554A GLY* 3.2 2.1 + - - -
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Residues in contact with ALA 553 (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 GLN 3.0 17.7 + - - +
550A THR* 3.5 7.4 + - - +
551A LYS 3.3 0.4 - - - -
552A GLN* 1.3 82.1 + - - +
554A GLY* 1.3 62.0 + - - +
555A ASP* 3.3 16.2 + - + +
583A LYS* 3.9 33.8 + - - +
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Residues in contact with GLY 554 (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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550A THR 3.6 2.8 + - - -
551A LYS 3.4 12.0 + - - -
552A GLN 3.2 5.4 - - - -
553A ALA* 1.3 76.5 - - - +
555A ASP* 1.3 65.8 + - - +
556A ASN* 4.9 0.5 - - - +
5C U 3.9 10.4 - - - +
6C U 3.5 23.5 - - - +
7C U 5.2 2.9 - - - -
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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