Contacts of the helix formed by residues 299 - 306 (chain C) in PDB entry 5AQM
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 ARG 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C LEU* 3.0 38.5 + - + +
275C PHE 3.4 7.1 + - - -
276C SER 3.4 21.2 + - - -
277C SER 3.1 23.2 + - - +
278C THR* 2.8 40.2 + - + +
298C THR* 1.3 71.0 - - - +
300C ALA* 1.4 56.8 + - - +
302C PHE* 3.2 5.7 + - + +
303C GLU* 2.9 58.3 + - + +
344C PRO* 3.8 26.3 - - + +
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Residues in contact with ALA 300 (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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298C THR* 3.2 9.2 - - - +
299C ARG* 1.4 77.7 - - - +
301C ARG* 1.3 56.9 + - - +
303C GLU* 3.2 16.7 + - - +
304C GLU* 2.9 42.6 + - - +
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Residues in contact with ARG 301 (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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240C HIS* 3.5 35.9 + - + -
244C GLU* 4.6 7.7 + - - -
247C ARG* 6.0 1.2 - - - +
296C SER 5.0 6.9 + - - -
297C ILE* 3.8 18.4 - - + +
298C THR* 3.0 23.9 + - - +
300C ALA* 1.3 72.7 - - - +
302C PHE* 1.3 66.3 + - - +
304C GLU* 3.1 19.2 + - + +
305C LEU* 3.0 29.2 + - + +
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Residues in contact with PHE 302 (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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233C PHE* 4.2 5.4 - - + -
237C MET* 3.7 37.2 - - + -
271C LYS* 3.7 27.4 - - + -
274C LEU* 3.5 32.3 - - + -
275C PHE* 5.9 0.2 - + - -
297C ILE* 3.9 10.2 - - + +
298C THR 3.0 6.0 + - - +
299C ARG* 3.3 12.6 - - + +
301C ARG* 1.3 75.2 - - - +
303C GLU* 1.3 71.9 + - + +
305C LEU* 3.5 3.7 + - - +
306C ASN* 3.0 48.2 + - - +
310C PHE* 3.6 30.1 - + - -
343C ILE* 4.0 22.9 - - + -
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Residues in contact with GLU 303 (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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299C ARG* 2.9 45.1 + - + +
300C ALA* 3.5 15.5 - - - +
301C ARG 3.2 0.2 - - - -
302C PHE* 1.3 80.9 - - + +
304C GLU* 1.4 56.6 + - + +
306C ASN* 3.4 2.6 + - - +
307C ALA* 2.9 30.2 + - - +
310C PHE* 4.1 10.0 - - + -
343C ILE* 5.6 1.1 - - + +
344C PRO* 5.0 0.9 - - - +
345C LYS* 3.6 52.3 + - + +
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Residues in contact with GLU 304 (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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300C ALA* 2.9 30.9 + - - +
301C ARG* 3.1 18.5 + - - +
303C GLU* 1.4 77.1 - - + +
305C LEU* 1.3 63.3 + - + +
307C ALA* 3.2 20.9 + - - +
308C ASP* 5.4 0.2 - - - +
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Residues in contact with LEU 305 (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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236C ARG* 2.9 47.1 + - + +
237C MET* 4.4 6.5 - - + -
240C HIS* 3.5 48.0 - - + +
297C ILE* 3.8 19.3 - - + -
301C ARG* 3.0 26.0 + - + +
302C PHE* 3.7 6.7 - - - +
304C GLU* 1.3 74.6 - - + +
306C ASN* 1.3 59.9 + - - +
307C ALA 3.6 0.4 + - - -
308C ASP* 4.3 0.2 - - - +
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Residues in contact with ASN 306 (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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233C PHE* 3.2 41.2 + - + -
236C ARG* 3.3 20.9 - - - +
237C MET* 4.8 0.8 - - - +
302C PHE* 3.0 46.7 + - - +
303C GLU 3.5 1.6 - - - -
304C GLU 3.1 0.4 - - - -
305C LEU* 1.3 82.4 - - - +
307C ALA* 1.4 61.2 + - - +
308C ASP* 3.3 3.6 - - - -
309C LEU* 3.0 8.8 + - - +
310C PHE* 2.9 43.6 + - + -
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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