Contacts of the helix formed by residues 2535 - 2543 (chain C) in PDB entry 5Y3R
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 THR2535 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900C GLU* 2.3 36.7 + - + +
901C MET* 4.7 17.0 - - + -
2534C ASN* 1.3 80.5 + - - +
2536C LEU* 1.3 67.8 + - + +
2537C ASP 3.6 0.4 - - - -
2538C ARG* 3.2 5.0 - - - +
2539C LEU* 2.7 38.4 + - + +
2562C LEU* 4.4 12.2 - - + +
2565C MET* 4.0 23.4 + - + +
2566C THR* 4.8 14.2 - - - +
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Residues in contact with LEU2536 (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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900C GLU* 3.4 24.5 - - + +
901C MET* 3.8 25.8 - - + -
2534C ASN* 3.1 7.2 + - - +
2535C THR* 1.3 90.9 - - + +
2537C ASP* 1.3 71.1 + - - +
2539C LEU* 2.9 13.3 - - + +
2540C LEU* 2.9 24.7 + - + +
2815C GLY* 5.0 4.9 - - - +
2819C GLU* 4.5 12.8 - - + +
2823C PHE* 3.6 35.4 - - + -
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Residues in contact with ASP2537 (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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2532C PRO* 5.5 3.8 - - + -
2534C ASN* 2.8 25.3 + - - +
2536C LEU* 1.3 72.4 - - - +
2538C ARG* 1.3 58.9 + - - +
2540C LEU* 2.3 48.9 + - + +
2541C ALA* 2.8 17.3 + - + -
2823C PHE* 6.0 1.6 - - - -
2829C LYS* 5.9 0.9 + - - -
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Residues in contact with ARG2538 (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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2527C HIS* 4.6 9.4 + - - +
2531C LEU* 3.4 48.4 - - + +
2532C PRO* 2.1 43.4 + - + +
2533C SER* 3.2 4.4 - - - +
2534C ASN* 2.7 38.1 + - - +
2535C THR 3.2 8.5 + - - +
2537C ASP* 1.3 75.4 - - - +
2539C LEU* 1.3 49.8 + - - +
2541C ALA* 5.7 0.9 - - - -
2542C LEU* 2.4 48.2 + - + +
2561C PHE* 6.2 0.4 - - - -
2562C LEU* 3.4 22.4 - - + +
2565C MET* 2.7 36.8 - - - +
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Residues in contact with LEU2539 (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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901C MET* 5.4 4.5 - - - -
2535C THR* 2.7 19.5 + - + +
2536C LEU* 2.9 12.8 - - + +
2538C ARG* 1.3 75.4 - - - +
2540C LEU* 1.3 84.0 + - + +
2542C LEU* 2.9 23.1 - - + +
2543C ASN* 2.8 16.7 + - - +
2562C LEU* 3.7 13.6 - - + +
2811C SER* 4.1 9.0 - - - +
2812C LEU* 4.1 17.7 - - + +
2815C GLY* 3.6 40.2 - - - +
2816C ILE* 4.9 4.0 - - + -
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Residues in contact with LEU2540 (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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2536C LEU* 3.1 11.4 - - + +
2537C ASP* 2.3 48.7 + - + +
2539C LEU* 1.3 85.3 - - + +
2541C ALA* 1.3 59.3 + - + +
2542C LEU 2.8 3.8 + - - -
2543C ASN* 2.4 36.4 + - - +
2815C GLY 5.0 3.6 - - - +
2816C ILE* 5.2 2.9 - - + -
2820C MET* 4.2 20.6 - - + -
2823C PHE* 6.3 2.7 - - + -
2829C LYS* 5.8 2.0 - - - +
2832C ILE* 4.4 31.4 - - + -
2836C LEU* 5.1 13.0 - - + +
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Residues in contact with ALA2541 (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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2531C LEU* 6.2 0.9 - - - -
2537C ASP* 2.8 8.5 + - + +
2538C ARG* 5.7 0.7 - - - -
2540C LEU* 1.3 73.9 - - + +
2542C LEU* 1.3 61.1 + - - +
2543C ASN 3.1 0.7 - - - -
2544C SER* 2.7 46.2 + - - +
2545C LEU* 3.8 4.5 + - - +
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Residues in contact with LEU2542 (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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2531C LEU* 5.3 10.0 - - + +
2538C ARG* 2.4 41.2 + - + +
2539C LEU* 2.9 23.3 - - + +
2541C ALA* 1.3 77.5 - - - +
2543C ASN* 1.3 63.6 + - - +
2544C SER 3.0 0.2 + - - -
2545C LEU* 3.5 5.0 + - - +
2546C TYR* 3.0 59.2 - - + +
2558C ALA* 4.0 16.4 - - + +
2561C PHE* 4.9 5.8 - - + -
2562C LEU* 3.5 35.4 - - + -
2812C LEU* 5.8 7.2 - - + -
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Residues in contact with ASN2543 (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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2539C LEU* 2.8 20.0 + - - +
2540C LEU* 2.4 27.2 + - - +
2542C LEU* 1.3 79.3 - - - +
2544C SER* 1.3 55.8 + - - +
2546C TYR* 2.5 46.0 + - + +
2547C SER* 3.4 4.9 + - - -
2812C LEU* 5.5 7.0 - - - +
2836C LEU* 5.0 5.1 - - + +
2839C ASP* 6.1 2.1 - - + +
2840C PHE* 4.0 35.5 - - + -
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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