Contacts of the helix formed by residues 272 - 277 (chain A) in PDB entry 5H2U
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 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLY 4.0 0.2 + - - -
271A SER* 1.3 72.6 - - - +
273A LEU* 1.3 54.2 + - - +
275A LEU* 3.1 15.9 + - + +
276A LEU* 2.7 60.8 + - + +
284A LEU* 5.5 0.2 - - + -
289A LEU* 5.6 0.4 - - + -
292A ILE* 3.9 35.2 - - + -
296A VAL* 5.0 0.4 - - + -
315A ALA* 3.4 15.5 - - + +
318A ILE* 2.7 38.8 + - + +
320A VAL* 4.1 10.4 - - + +
326A CYS* 5.3 0.4 - - - -
376A LEU* 4.4 1.8 - - + -
380A MET* 3.9 32.8 - - + -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A SER* 3.3 3.8 - - - +
272A LEU* 1.3 80.1 - - - +
274A GLU* 1.3 59.4 + - + +
276A LEU* 3.4 3.7 + - + +
277A ARG* 3.0 67.6 + - - +
315A ALA* 3.3 10.9 + - + -
316A ARG* 3.4 68.9 - - + +
379A GLU* 3.8 19.3 - - - +
384A GLY* 3.9 17.7 - - - +
385A GLN 5.7 0.2 - - - +
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU 4.7 9.9 - - - +
269A LYS 6.1 0.2 - - - +
270A GLY* 5.6 1.0 - - - -
271A SER* 3.4 23.6 + - - +
272A LEU 3.3 0.4 - - - -
273A LEU* 1.3 78.1 - - + +
275A LEU* 1.3 64.0 + - - +
277A ARG* 3.4 23.9 + - - +
501A 1N1 3.9 36.3 + - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS* 5.4 7.6 + - + +
271A SER 3.2 10.7 + - - +
272A LEU* 3.1 17.7 + - + +
274A GLU* 1.3 78.4 - - - +
276A LEU* 1.3 61.3 + - - +
279A SER* 3.7 10.9 + - - -
283A VAL* 5.8 7.6 - - + -
284A LEU* 3.6 34.7 - - + +
292A ILE* 5.1 5.4 - - + -
320A VAL* 3.7 37.7 - - + -
324A THR* 5.1 4.9 - - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 2.7 43.5 + - + +
273A LEU* 3.6 6.7 - - - +
274A GLU 3.3 0.2 - - - -
275A LEU* 1.3 73.6 - - - +
277A ARG* 1.3 54.9 + - - +
279A SER* 2.3 32.7 - - - +
284A LEU* 4.0 7.2 - - + -
289A LEU* 3.6 24.5 - - + -
315A ALA* 4.2 11.7 - - + -
379A GLU* 3.5 23.3 - - + +
380A MET* 3.5 31.6 - - + +
383A ARG* 3.3 13.3 - - - +
384A GLY* 3.7 13.9 - - - +
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU* 3.0 49.4 + - - +
274A GLU* 3.7 18.1 - - - +
275A LEU 3.4 1.2 - - - -
276A LEU* 1.3 77.1 - - - +
279A SER* 3.0 23.3 + - - +
316A ARG* 4.5 8.7 - - - +
383A ARG 3.9 5.2 - - - +
384A GLY* 2.8 34.7 + - - +
385A GLN 5.1 0.2 - - - -
386A VAL* 3.6 25.1 - - - +
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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