Contacts of the helix formed by residues 2544 - 2550 (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 SER2544 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2541C ALA* 2.7 43.1 + - - +
2543C ASN* 1.3 74.8 - - - +
2545C LEU* 1.3 70.4 + - - +
2546C TYR 3.3 0.2 + - - -
2547C SER* 3.7 13.0 + - - -
2548C PRO* 3.7 5.7 - - - +
2839C ASP* 5.3 10.1 + - - -
2842C ARG* 4.6 5.6 + - - +
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Residues in contact with LEU2545 (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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2500C LYS* 6.0 1.6 - - - +
2503C LYS* 3.9 38.6 - - + +
2507C ILE* 3.8 29.9 - - + +
2530C ARG* 4.2 20.6 - - + +
2541C ALA 4.7 3.6 - - - +
2542C LEU 3.5 6.2 + - - +
2543C ASN 3.2 0.2 - - - -
2544C SER* 1.3 88.5 - - - +
2546C TYR* 1.3 66.0 + - + +
2548C PRO* 3.1 26.0 - - + +
2549C LYS* 4.5 3.6 + - - +
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Residues in contact with TYR2546 (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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2507C ILE* 5.1 10.1 - - + -
2510C LEU* 5.2 7.9 - - + -
2542C LEU* 3.0 59.8 + - + +
2543C ASN* 2.5 38.0 + - + +
2545C LEU* 1.3 80.8 - - + +
2547C SER* 1.3 65.3 + - - +
2549C LYS* 2.9 50.7 - - - +
2554C PHE* 5.1 5.2 - + + -
2555C LEU* 6.5 0.9 - - + -
2558C ALA* 3.3 29.8 - - + +
2561C PHE* 4.1 7.5 - + - -
2843C PHE* 4.3 13.3 - - + -
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Residues in contact with SER2547 (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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2543C ASN 3.4 4.3 + - - -
2544C SER 3.9 5.2 - - - -
2546C TYR* 1.3 78.3 - - - +
2548C PRO* 1.3 64.5 - - - +
2549C LYS 2.7 7.8 + - - -
2550C ILE* 3.6 13.2 + - - +
2839C ASP* 4.0 7.9 + - - -
2842C ARG* 2.3 55.2 + - - +
2843C PHE* 3.9 18.6 + - - -
2846C THR* 4.2 8.9 + - - +
2847C THR* 4.7 0.7 - - - +
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Residues in contact with PRO2548 (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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2504C ASP* 5.9 7.2 - - - +
2507C ILE* 4.7 13.0 - - + -
2544C SER 3.7 4.7 - - - +
2545C LEU* 3.1 32.3 - - + +
2547C SER* 1.3 95.3 - - - +
2549C LYS* 1.3 65.3 + - - +
2550C ILE* 3.3 16.6 + - + +
2846C THR* 6.1 0.9 - - + -
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Residues in contact with LYS2549 (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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2507C ILE* 6.2 4.0 - - - -
2511C ILE* 6.1 2.9 - - + -
2545C LEU 4.5 2.5 - - - +
2546C TYR* 2.9 57.4 + - - +
2547C SER 2.7 1.4 + - - -
2548C PRO* 1.3 83.2 - - - +
2550C ILE* 1.3 70.3 + - - +
2551C GLU* 3.1 52.8 - - + +
2552C VAL 5.6 0.2 - - - +
2554C PHE* 3.1 46.4 - - + +
2843C PHE* 5.7 1.3 - - + -
2847C THR* 5.6 0.7 - - + -
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Residues in contact with ILE2550 (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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2547C SER 3.6 3.9 + - - +
2548C PRO* 3.4 19.0 - - + +
2549C LYS* 1.3 76.4 - - - +
2551C GLU* 1.3 62.0 + - - +
2846C THR* 3.3 50.7 - - + +
2847C THR* 3.6 13.6 - - - +
2848C PHE 4.4 1.3 - - - +
2850C PHE* 3.2 26.8 - - + -
3075C LYS* 4.6 8.5 + - - +
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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