Contacts of the helix formed by residues 539 - 550 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495B GLY 3.4 18.9 + - - +
496B LYS* 3.3 21.4 + - - +
497B GLY* 2.8 30.8 + - - +
532B MSE 4.2 16.3 + - + +
534B PHE* 5.1 1.8 + - - +
537B PRO 3.9 0.6 + - - -
538B LEU* 1.3 70.3 - - - +
540B GLU* 1.3 60.9 + - - +
541B ALA* 3.7 7.4 + - - +
542B LEU* 3.1 35.7 + - + +
543B ILE* 3.0 25.5 + - - +
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Residues in contact with GLU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A MSE 6.1 0.9 - - - +
538B LEU* 3.0 14.0 + - + +
539B ASP* 1.3 69.3 + - - +
541B ALA* 1.3 60.1 + - - +
543B ILE* 3.2 9.7 + - - +
544B LEU* 2.9 41.4 + - + +
572B VAL* 3.4 37.7 - - + +
576B HIS* 4.4 11.2 + - + +
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Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B LYS* 6.2 3.4 - - - +
539B ASP* 3.4 7.0 + - - +
540B GLU* 1.3 76.2 - - - +
542B LEU* 1.3 58.3 + - - +
544B LEU* 3.2 9.3 + - - +
545B GLU* 2.8 33.5 + - - +
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B GLY* 3.6 29.6 - - - +
498B ILE* 4.1 3.8 - - - +
499B VAL* 4.3 15.3 - - + -
530B VAL* 4.1 17.9 - - + -
532B MSE 4.5 5.2 - - - -
539B ASP* 3.1 37.0 + - + +
541B ALA* 1.3 77.5 - - - +
543B ILE* 1.3 58.8 + - + +
545B GLU* 3.2 11.0 + - + +
546B MSE 2.9 65.5 + - + +
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Residues in contact with ILE 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B LEU* 4.5 7.4 - - + -
532B MSE 3.7 27.1 - - + -
538B LEU* 4.1 15.3 - - + -
539B ASP 3.0 20.4 + - - +
540B GLU* 3.2 5.8 + - - +
542B LEU* 1.3 77.4 - - - +
544B LEU* 1.3 58.0 + - - +
546B MSE 3.4 6.3 + - - +
547B ALA* 2.9 28.8 + - - +
553B LEU* 4.4 6.3 - - + +
569B VAL* 3.9 35.2 - - + +
572B VAL* 4.2 22.9 - - + -
573B LEU* 4.0 19.3 - - + -
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Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B GLU* 2.9 27.0 + - + +
541B ALA* 3.7 7.2 - - - +
543B ILE* 1.3 75.3 - - - +
545B GLU* 1.3 61.9 + - - +
547B ALA* 3.5 4.4 + - - +
548B ALA* 3.1 24.1 + - - +
572B VAL* 4.2 6.7 - - + -
573B LEU* 4.1 18.6 - - + -
576B HIS* 3.6 55.9 - - + +
578B LYS* 4.8 11.7 - - + -
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Residues in contact with GLU 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B VAL* 5.7 1.2 - - - +
502B ARG* 4.3 12.3 + - - -
541B ALA* 2.8 20.1 + - - +
542B LEU* 3.4 12.3 - - - +
543B ILE 3.2 0.2 - - - -
544B LEU* 1.3 77.2 - - - +
546B MSE 1.3 76.8 + - + +
548B ALA* 3.3 6.8 + - - +
549B SER* 3.0 34.3 + - - +
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Residues in contact with MSE 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B VAL* 4.9 8.5 - - + -
502B ARG* 4.8 13.9 - - - +
507B ALA* 4.3 4.5 - - + -
509B LEU* 4.8 9.9 - - + -
528B THR* 4.3 12.6 - - + -
530B VAL* 4.6 9.4 - - + -
542B LEU* 2.9 44.9 + - + +
543B ILE* 3.7 6.1 - - - +
545B GLU* 1.3 101.1 - - + +
547B ALA* 1.3 62.3 + - - +
549B SER* 2.9 14.8 + - - +
550B HIS* 2.8 43.7 + - + +
553B LEU* 3.9 19.0 - - + +
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Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B ILE 2.9 18.1 + - - +
544B LEU* 3.8 5.2 - - - +
545B GLU 3.3 0.2 - - - -
546B MSE 1.3 77.3 - - - +
548B ALA* 1.3 58.7 + - - +
550B HIS 3.1 21.3 - - - +
553B LEU* 4.3 6.7 - - + +
573B LEU* 3.5 26.7 - - + -
578B LYS* 4.9 4.9 - - + +
580B VAL* 3.6 35.1 - - + +
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Residues in contact with ALA 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B LEU 3.1 17.3 + - - +
545B GLU* 3.6 6.7 - - - +
546B MSE 3.1 0.2 - - - -
547B ALA* 1.3 77.6 - - - +
549B SER* 1.3 62.1 + - - +
550B HIS 3.4 1.4 + - - +
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Residues in contact with SER 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B LYS 4.9 2.4 + - - -
545B GLU* 3.0 21.4 + - - +
546B MSE 2.9 8.8 + - - +
548B ALA* 1.3 79.1 - - - +
550B HIS* 1.3 85.7 + - - +
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Residues in contact with HIS 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B GLY 4.5 2.0 + - - -
504B GLU* 4.0 1.1 - - - -
505B LYS* 3.1 20.6 - - - +
506B LEU 3.4 29.2 - - - -
507B ALA* 3.8 9.9 - - + +
528B THR* 2.8 41.0 + - + +
546B MSE 2.8 35.4 + - + +
547B ALA* 3.1 16.5 - - - +
548B ALA 3.4 2.2 - - - +
549B SER* 1.3 102.3 + - - +
551B GLU* 1.3 66.2 + - - +
552B ALA 3.5 12.3 - - - +
553B LEU* 5.2 0.9 - - + -
580B VAL* 4.9 3.0 - - - +
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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