Contacts of the strand formed by residues 506 - 511 (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 LEU 506 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504C GLU 2.5 12.5 + - - +
505C LYS* 1.3 115.6 - - + +
507C ALA* 1.3 60.0 + - - +
508C ILE* 5.6 1.3 - - + -
525C LEU* 4.3 15.0 - - + +
527C ALA* 3.1 15.2 - - + +
528C THR 2.8 23.0 + - - -
550C HIS* 3.6 4.8 - - - -
551C GLU* 5.1 2.5 - - + -
552C ALA* 3.6 24.9 - - + +
554C VAL* 4.8 11.4 - - + -
615C ILE* 3.6 34.5 - - + -
618C TRP* 5.8 1.1 - - + -
619C LEU* 4.4 11.4 - - + -
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Residues in contact with ALA 507 (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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506C LEU* 1.3 74.3 - - - +
508C ILE* 1.3 62.1 + - - +
509C LEU* 3.7 5.7 + - + +
528C THR* 3.5 15.0 - - + -
546C MSE 4.4 7.4 - - + -
550C HIS* 3.7 29.4 - - + +
552C ALA 3.2 7.3 + - - -
553C LEU* 3.3 20.6 - - + +
554C VAL* 2.8 25.7 + - - -
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Residues in contact with ILE 508 (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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506C LEU* 5.3 2.0 - - + -
507C ALA* 1.3 73.5 - - - +
509C LEU* 1.3 65.7 + - - +
518C ALA* 4.0 11.9 - - + +
521C VAL* 3.9 19.1 - - + -
522C ALA* 3.8 34.1 - - + +
525C LEU* 5.5 0.9 - - + -
527C ALA* 4.0 13.7 - - + -
528C THR 2.7 15.6 + - - +
529C LEU* 3.6 15.1 - - + +
530C VAL* 3.0 28.9 + - - +
554C VAL* 3.3 22.4 - - + +
556C VAL* 4.0 23.1 - - + -
615C ILE* 4.9 5.4 - - + -
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Residues in contact with LEU 509 (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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507C ALA* 4.4 11.9 - - + +
508C ILE* 1.3 73.0 - - - +
510C ASN* 1.3 61.5 + - - +
511C PHE* 3.8 4.9 - - + -
530C VAL* 3.3 33.7 - - + -
532C MSE 4.0 26.7 - - + -
542C LEU* 6.2 0.2 - - + -
543C ILE* 4.2 20.9 - - + -
546C MSE 4.5 13.5 - - + -
553C LEU* 4.2 21.3 - - + -
554C VAL 2.5 14.8 + - - +
555C THR* 3.2 13.5 - - + -
556C VAL 2.9 25.2 + - - -
569C VAL* 4.3 11.9 - - + -
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Residues in contact with ASN 510 (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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508C ILE* 3.7 1.3 + - + -
509C LEU* 1.3 73.1 - - - +
511C PHE* 1.3 65.6 + - - +
512C GLY 3.0 20.3 + - - +
514C LEU* 3.7 6.3 - - - +
515C MSE 3.3 47.7 - - + +
518C ALA* 3.9 14.9 - - + +
529C LEU* 5.0 2.7 - - + -
530C VAL 3.0 16.9 + - - +
531C ASP* 3.2 17.3 - - - +
532C MSE 3.0 27.6 + - - +
533C ARG 4.3 0.2 + - - -
556C VAL* 3.7 15.0 + - + +
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Residues in contact with PHE 511 (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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437C LEU* 5.2 2.6 - - + +
450C THR* 3.7 17.2 - - + +
475C ARG* 5.8 0.9 + - - -
509C LEU* 3.8 11.2 - - + -
510C ASN* 1.3 78.0 + - - +
512C GLY* 1.3 59.6 + - - +
514C LEU* 5.3 1.0 + - - +
532C MSE 3.5 30.1 - - + -
533C ARG 5.3 0.7 - - - +
534C PHE 3.5 22.7 - - - -
535C VAL* 3.6 22.0 - - + -
538C LEU* 3.6 21.1 - - + -
555C THR* 4.4 8.5 - - - -
556C VAL 2.8 27.0 + - - +
557C GLU* 3.7 19.6 - - + +
558C GLU 4.4 3.5 + - - -
565C ALA* 3.7 20.2 - - + -
569C VAL* 3.9 22.7 - - + -
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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