Contacts of the helix formed by residues 539 - 550 (chain A) in PDB entry 2O1S
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 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A GLY 3.0 21.1 + - - +
496A LYS* 3.1 28.9 + - - +
497A GLY* 2.7 35.2 + - - +
532A MSE 4.3 15.7 - - + +
534A PHE* 5.0 2.4 + - - +
537A PRO 3.9 0.4 + - - -
538A LEU* 1.3 68.3 - - - +
540A GLU* 1.3 61.2 + - - +
541A ALA 3.8 1.0 + - - -
542A LEU* 3.0 31.0 + - + +
543A ILE* 3.1 22.2 + - - +
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Residues in contact with GLU 540 (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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538A LEU* 2.7 21.5 + - + +
539A ASP* 1.3 71.3 - - - +
541A ALA* 1.3 64.5 + - - +
543A ILE* 2.9 7.2 + - - +
544A LEU* 2.9 28.1 + - + +
572A VAL* 3.4 36.1 - - + +
576A HIS* 3.1 28.1 + - - +
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Residues in contact with ALA 541 (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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496A LYS* 4.3 14.1 - - - +
539A ASP* 3.4 5.7 + - - +
540A GLU* 1.3 76.9 - - - +
542A LEU* 1.3 57.4 + - - +
544A LEU* 3.4 10.7 + - - +
545A GLU* 2.9 30.6 + - - +
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Residues in contact with LEU 542 (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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497A GLY 5.2 6.7 - - - +
499A VAL* 4.1 23.1 - - + +
509A LEU* 5.0 0.9 - - + -
530A VAL* 3.9 27.6 - - + -
532A MSE 4.4 9.0 - - - -
539A ASP* 3.0 35.8 + - + +
541A ALA* 1.3 73.7 - - - +
543A ILE* 1.3 66.5 + - - +
545A GLU* 3.2 23.3 + - - +
546A MSE 2.9 39.1 + - + +
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Residues in contact with ILE 543 (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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509A LEU* 4.5 6.5 - - + -
532A MSE 3.4 33.7 - - + -
538A LEU* 4.2 10.1 - - + -
539A ASP 3.1 9.9 + - - +
540A GLU* 2.9 9.6 + - - +
542A LEU* 1.3 77.8 - - - +
544A LEU* 1.3 61.4 + - + +
546A MSE 3.0 7.1 + - - +
547A ALA* 2.9 27.2 + - - +
553A LEU* 4.3 6.3 - - + +
569A VAL* 3.9 36.8 - - + +
572A VAL* 4.2 25.4 - - + -
573A LEU* 4.0 20.6 - - + -
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Residues in contact with LEU 544 (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 GLU* 2.9 20.0 + - + +
541A ALA* 3.6 11.7 - - - +
543A ILE* 1.3 77.2 - - - +
545A GLU* 1.3 56.8 + - - +
547A ALA* 3.4 5.4 + - - +
548A ALA* 3.0 30.0 + - - +
572A VAL* 4.2 7.2 - - + -
573A LEU* 3.9 22.2 - - + -
576A HIS* 3.5 54.1 - - + +
578A LYS* 4.7 12.2 - - + +
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Residues in contact with GLU 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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502A ARG* 4.2 12.0 + - - -
541A ALA 2.9 17.7 + - - +
542A LEU* 3.4 20.0 - - - +
543A ILE 3.1 0.2 - - - -
544A LEU* 1.3 77.4 - - - +
546A MSE 1.3 73.6 + - + +
548A ALA* 3.4 6.8 + - - +
549A SER* 2.7 34.3 + - - +
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Residues in contact with MSE 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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499A VAL* 4.6 3.6 - - + -
502A ARG* 4.3 11.9 - - - +
507A ALA* 4.2 12.6 - - + -
509A LEU* 4.3 9.0 - - + -
528A THR* 3.9 28.0 - - - -
530A VAL* 3.9 15.0 - - + -
542A LEU* 2.9 39.3 + - + +
543A ILE* 3.6 5.4 - - - +
545A GLU* 1.3 107.8 - - + +
547A ALA* 1.3 60.6 + - - +
549A SER* 3.6 10.3 - - - +
550A HIS* 2.9 42.4 + - + +
553A LEU* 3.8 7.6 - - + +
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Residues in contact with ALA 547 (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 ILE 2.9 16.1 + - - +
544A LEU* 3.6 5.6 - - - +
546A MSE 1.3 78.4 - - - +
548A ALA* 1.3 57.2 + - - +
550A HIS 3.0 21.0 - - - +
553A LEU* 3.7 15.2 - - + +
573A LEU* 3.7 21.3 - - + -
578A LYS* 5.0 3.8 - - + +
580A VAL* 3.6 32.7 - - + +
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Residues in contact with ALA 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 LEU 3.0 18.0 + - - +
545A GLU* 3.8 7.6 - - - +
546A MSE 3.3 0.2 - - - -
547A ALA* 1.3 77.4 - - - +
549A SER* 1.3 58.4 + - - +
550A HIS 3.6 1.1 + - - -
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Residues in contact with SER 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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505A LYS 5.1 2.4 + - - -
545A GLU* 2.7 23.0 + - - +
546A MSE 3.6 7.8 - - - +
547A ALA 3.2 0.2 - - - -
548A ALA* 1.3 79.2 - - - +
550A HIS* 1.3 90.1 + - - +
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Residues in contact with HIS 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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502A ARG* 6.3 0.2 - - - -
503A GLY 4.6 4.6 + - - -
504A GLU* 4.4 0.6 - - - -
505A LYS* 3.7 16.2 - - - +
506A LEU 3.4 33.2 - - - -
507A ALA* 3.5 9.6 - - + -
528A THR* 2.6 32.4 + - + -
546A MSE 2.9 36.6 + - + +
547A ALA 3.0 17.0 - - - +
548A ALA 3.6 0.9 - - - -
549A SER* 1.3 105.2 + - - +
551A GLU* 1.3 65.4 + - - +
552A ALA 3.4 11.4 - - - +
553A LEU* 4.4 1.6 - - + -
580A VAL* 4.2 3.7 - - - +
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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