Contacts of the helix formed by residues 539 - 550 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495C GLY 3.2 20.6 + - - +
496C LYS* 3.1 19.1 - - - +
497C GLY* 2.6 34.5 + - - +
532C MSE 4.3 15.9 + - + +
534C PHE* 5.0 1.8 + - - +
537C PRO 3.9 0.6 + - - -
538C LEU* 1.3 69.4 - - - +
540C GLU* 1.3 63.7 + - - +
541C ALA* 3.7 8.1 + - - +
542C LEU* 3.0 35.3 + - + +
543C ILE* 3.0 24.3 + - - +
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Residues in contact with GLU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C LEU* 2.6 19.7 + - + +
539C ASP* 1.3 71.0 - - - +
541C ALA* 1.3 64.1 + - - +
543C ILE* 3.2 4.5 + - - +
544C LEU* 3.0 31.4 + - + +
572C VAL* 3.6 36.0 - - + +
576C HIS* 3.1 27.4 + - - +
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Residues in contact with ALA 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C LYS* 5.9 4.5 - - - -
539C ASP* 3.3 6.8 + - - +
540C GLU* 1.3 78.0 - - - +
542C LEU* 1.3 58.6 + - - +
544C LEU* 3.3 9.7 + - - +
545C GLU* 2.9 30.5 + - - +
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Residues in contact with LEU 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497C GLY* 3.9 26.7 - - - +
498C ILE 4.1 2.9 - - - +
499C VAL* 4.0 18.2 - - + -
530C VAL* 4.2 15.3 - - + -
532C MSE 4.5 8.5 - - - -
539C ASP* 3.0 36.6 + - + +
541C ALA* 1.3 77.2 - - - +
543C ILE* 1.3 62.4 + - - +
545C GLU* 3.2 14.7 + - - +
546C MSE 2.9 57.2 + - + +
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Residues in contact with ILE 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C LEU* 4.2 8.5 - - + -
532C MSE 3.4 30.3 - - + -
538C LEU* 4.2 16.6 - - + -
539C ASP 3.0 18.2 + - - +
540C GLU* 3.2 7.4 + - - +
542C LEU* 1.3 75.8 - - - +
544C LEU* 1.3 58.5 + - - +
546C MSE 3.2 7.7 + - - +
547C ALA* 2.9 26.9 + - - +
553C LEU* 4.3 6.0 - - + +
569C VAL* 3.8 39.7 - - + -
572C VAL* 4.3 15.5 - - + -
573C LEU* 3.9 23.3 - - + -
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Residues in contact with LEU 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C GLU* 3.0 25.3 + - + +
541C ALA* 3.6 7.6 - - - +
543C ILE* 1.3 75.2 - - - +
545C GLU* 1.3 58.7 + - - +
547C ALA* 3.2 6.2 + - + +
548C ALA* 2.9 31.9 + - - +
572C VAL* 4.7 2.5 - - + -
573C LEU* 4.3 16.4 - - + -
576C HIS* 3.7 54.5 - - + +
578C LYS* 4.3 11.7 - - + -
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Residues in contact with GLU 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541C ALA 2.9 18.1 + - - +
542C LEU* 3.2 22.9 + - - +
544C LEU* 1.3 76.2 - - - +
546C MSE 1.3 63.1 + - + +
548C ALA* 3.8 5.9 + - - +
549C SER* 2.7 32.0 + - - -
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Residues in contact with MSE 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C VAL* 4.7 7.2 - - + -
502C ARG* 3.6 20.2 - - - +
507C ALA* 4.4 3.4 - - + -
509C LEU* 4.5 6.7 - - + -
528C THR* 3.8 29.2 - - - -
530C VAL* 4.3 16.4 - - + -
542C LEU* 2.9 40.8 + - + +
543C ILE* 3.7 5.8 - - - +
544C LEU 3.1 0.2 - - - -
545C GLU* 1.3 98.5 - - + +
547C ALA* 1.3 65.8 + - - +
548C ALA 3.2 0.4 - - - -
549C SER* 3.6 4.0 - - - +
550C HIS* 2.9 37.1 + - - +
553C LEU* 3.8 15.9 - - + +
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Residues in contact with ALA 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C ILE 2.9 16.0 + - - +
544C LEU* 3.6 5.2 - - - +
546C MSE 1.3 78.7 - - - +
548C ALA* 1.3 56.8 + - - +
550C HIS 3.1 20.7 - - - +
553C LEU* 3.9 15.0 - - + +
573C LEU* 3.7 21.1 - - + -
578C LYS* 5.6 3.1 - - + -
580C VAL* 3.6 35.6 - - + +
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Residues in contact with ALA 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C LEU 2.9 16.0 + - - +
545C GLU* 4.1 7.2 - - - +
547C ALA* 1.3 79.8 - - - +
549C SER* 1.3 57.8 + - - +
550C HIS 3.5 1.8 + - - +
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Residues in contact with SER 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502C ARG* 4.6 8.5 + - - -
505C LYS* 5.3 1.9 + - - -
545C GLU* 2.7 23.2 + - - +
546C MSE 3.3 6.3 + - - +
548C ALA* 1.3 78.4 - - - +
550C HIS* 1.3 84.6 + - - +
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Residues in contact with HIS 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502C ARG* 3.8 19.0 + - - -
503C GLY 4.4 2.4 + - - -
504C GLU* 4.4 1.8 - - - -
505C LYS* 3.4 17.9 - - - +
506C LEU 3.6 27.8 - - - -
507C ALA* 3.7 11.1 - - + +
528C THR* 2.6 34.3 + - - -
546C MSE 2.9 30.6 + - - +
547C ALA 3.1 15.9 - - - +
548C ALA 3.5 2.0 - - - +
549C SER* 1.3 98.1 + - - +
551C GLU* 1.3 63.1 + - - +
552C ALA 3.4 11.7 - - - +
553C LEU* 4.6 1.6 - - + -
580C VAL* 4.3 2.6 - - - +
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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