Contacts of the helix formed by residues 304 - 312 (chain N) in PDB entry 3O3U
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 304 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N LYS* 3.6 32.3 - - + +
89N LEU* 3.8 17.2 - - + +
108N ILE 4.7 0.6 + - - -
285N LEU* 3.8 19.9 - - + +
286N THR* 3.6 37.2 - - - -
287N ASP* 3.6 5.4 - - - +
290N LEU* 3.6 22.4 - - + -
302N VAL* 3.2 2.6 - - + +
303N ALA* 1.3 76.2 - - - +
305N LYS* 1.3 66.6 + - - +
306N SER* 3.5 23.1 - - - +
307N TYR* 3.3 2.7 + - + -
308N GLU* 2.9 23.0 + - - +
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Residues in contact with LYS 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87N ASP* 2.9 30.6 + - - +
88N LYS* 3.0 18.4 + - - +
89N LEU 3.5 20.3 + - - -
90N TYR* 3.8 43.1 - - + +
91N PRO* 4.5 7.9 - - - +
303N ALA 3.4 1.2 + - - -
304N LEU* 1.3 70.8 - - - +
306N SER* 1.3 64.3 + - - +
308N GLU* 3.2 1.0 + - - +
309N GLU* 2.9 41.2 + - - +
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Residues in contact with SER 306 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N LYS 4.8 0.4 + - - -
287N ASP* 2.7 31.8 + - - +
304N LEU* 3.5 15.0 - - - +
305N LYS* 1.3 80.0 - - - +
307N TYR* 1.3 60.2 + - - +
309N GLU* 3.6 12.6 + - - +
310N GLU* 3.3 17.3 + - - +
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Residues in contact with TYR 307 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287N ASP* 3.3 33.9 - - + +
290N LEU* 3.7 21.8 - - + -
291N GLU* 3.3 47.9 + - + +
294N ASN* 4.6 7.9 + - + +
295N LYS* 5.4 3.3 - - - -
302N VAL* 3.9 15.5 - - + -
304N LEU* 3.3 10.1 + - + +
305N LYS 3.3 0.2 - - - -
306N SER* 1.3 78.3 + - - +
308N GLU* 1.3 66.2 - - - +
309N GLU 3.2 0.2 - - - -
310N GLU* 3.1 43.9 + - - +
311N LEU* 3.2 50.2 + - + +
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Residues in contact with GLU 308 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90N TYR* 2.5 35.7 + - + -
301N ALA* 4.4 16.4 - - + +
302N VAL* 3.4 35.5 - - - +
304N LEU 2.9 18.1 + - - +
305N LYS 3.7 2.7 - - - +
307N TYR* 1.3 77.4 - - - +
309N GLU* 1.3 61.6 + - - +
311N LEU* 3.2 5.3 + - - +
312N ALA* 2.9 42.2 + - - +
317N ILE* 5.2 3.9 - - + +
321N MET* 5.7 2.4 - - - +
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Residues in contact with GLU 309 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90N TYR* 4.3 9.9 + - - +
305N LYS* 2.9 35.9 + - - +
306N SER* 3.6 9.5 - - - +
308N GLU* 1.3 81.7 - - - +
310N GLU* 1.3 63.1 + - - +
311N LEU 3.4 0.3 + - - -
312N ALA* 3.5 14.1 + - - +
313N LYS 4.9 1.0 + - - -
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Residues in contact with GLU 310 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287N ASP* 4.8 8.1 - - - +
291N GLU* 5.1 5.4 - - - +
306N SER 3.3 9.3 + - - +
307N TYR* 3.1 41.6 + - + +
309N GLU* 1.3 81.1 - - - +
311N LEU* 1.3 64.5 + - + +
312N ALA 3.8 0.2 + - - -
313N LYS* 4.1 22.6 + - - +
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Residues in contact with LEU 311 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294N ASN* 3.7 26.2 - - - +
300N GLY 5.0 4.5 - - - +
302N VAL* 5.0 6.5 - - + -
307N TYR* 3.2 59.1 + - + +
308N GLU* 4.1 3.1 - - - +
310N GLU* 1.3 84.2 - - + +
312N ALA* 1.3 66.7 + - - +
313N LYS* 2.9 7.6 + - - +
314N ASP* 3.0 22.3 + - + +
317N ILE* 3.6 24.4 - - + +
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Residues in contact with ALA 312 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308N GLU* 2.9 31.7 + - - +
309N GLU* 3.5 12.3 + - - +
310N GLU 3.5 1.8 - - - -
311N LEU* 1.3 76.6 - - - +
313N LYS* 1.3 60.2 + - - +
314N ASP 3.1 8.5 + - - +
317N ILE* 5.0 7.9 - - - +
318N ALA* 4.8 10.4 + - - +
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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