Contacts of the helix formed by residues 314 - 325 (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 ASP 314 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232N TRP* 4.7 0.2 - - - -
311N LEU* 3.0 16.3 + - + +
312N ALA 3.8 2.6 - - - +
313N LYS* 1.3 80.2 - - + +
315N PRO* 1.3 73.6 - - - +
316N ARG* 2.8 53.9 + - - +
317N ILE* 3.0 32.1 + - + +
318N ALA* 3.0 9.9 + - - +
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Residues in contact with PRO 315 (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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244N VAL 4.6 3.3 - - - +
313N LYS 3.2 10.3 - - - +
314N ASP* 1.3 88.5 - - - +
316N ARG* 1.3 60.2 + - + +
318N ALA* 3.6 10.7 - - + +
319N ALA* 2.9 27.5 + - - +
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Residues in contact with ARG 316 (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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232N TRP* 3.5 49.7 - - + +
236N ASP* 4.1 11.3 + - - -
242N TYR* 2.9 39.8 + - + -
244N VAL* 3.7 24.9 - - + +
298N PRO* 5.1 5.9 - - - +
314N ASP* 2.8 30.1 + - - +
315N PRO* 1.3 80.7 - - + +
317N ILE* 1.3 59.8 + - - +
319N ALA* 3.5 3.6 + - - +
320N THR* 2.9 29.6 + - - -
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Residues in contact with ILE 317 (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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232N TRP* 4.1 13.2 - - + -
294N ASN* 5.9 1.6 - - - +
300N GLY 3.6 27.8 - - - +
301N ALA* 4.2 19.3 - - + -
308N GLU* 5.2 4.5 - - + +
311N LEU* 3.6 42.4 - - + +
312N ALA* 5.0 9.0 - - - +
314N ASP* 3.0 24.7 + - + +
316N ARG* 1.3 75.8 - - - +
318N ALA* 1.3 65.9 + - - +
320N THR* 3.1 8.3 + - - -
321N MET* 3.0 24.5 + - + +
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Residues in contact with ALA 318 (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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312N ALA 4.8 8.6 + - - +
313N LYS 6.1 0.2 - - - -
314N ASP 3.0 12.2 + - - +
315N PRO* 3.6 12.3 - - + +
317N ILE* 1.3 78.2 - - - +
319N ALA* 1.3 57.7 + - - +
321N MET* 3.3 7.4 + - - +
322N GLU* 2.9 28.8 + - - +
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Residues in contact with ALA 319 (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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114N SER* 3.8 2.5 - - - +
244N VAL* 3.4 36.8 - - + +
245N THR* 4.0 11.2 - - - -
246N VAL 4.8 0.4 - - - +
315N PRO 2.9 14.3 + - - +
316N ARG 3.7 5.4 - - - +
317N ILE 3.2 0.2 - - - -
318N ALA* 1.3 73.0 - - - +
320N THR* 1.3 65.7 + - - +
322N GLU* 3.2 13.6 + - - +
323N ASN* 3.0 29.3 + - - -
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Residues in contact with THR 320 (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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110N VAL 4.5 3.8 - - - +
112N ALA* 3.7 30.9 + - - +
114N SER* 3.6 12.5 + - - -
229N PRO* 4.0 13.0 - - + +
232N TRP* 3.4 20.1 - - - -
300N GLY* 5.0 2.9 - - - -
316N ARG 2.9 19.8 + - - -
317N ILE* 3.1 12.5 + - - -
319N ALA* 1.3 74.7 - - - +
321N MET* 1.3 75.8 + - + +
323N ASN* 3.4 1.1 + - - +
324N ALA* 2.9 26.3 + - - +
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Residues in contact with MET 321 (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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92N PHE* 5.7 5.2 - - - -
110N VAL* 3.9 28.7 - - + +
111N GLU 5.1 0.2 - - - +
112N ALA 5.2 0.4 - - - +
301N ALA* 3.6 33.4 - - + -
308N GLU* 5.7 3.1 - - - +
317N ILE* 3.0 21.4 + - + +
318N ALA* 3.8 6.1 - - - +
320N THR* 1.3 102.0 - - + +
322N GLU* 1.3 59.7 + - - +
324N ALA* 4.1 9.9 - - + -
325N GLN* 2.9 56.3 + - - +
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Residues in contact with GLU 322 (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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246N VAL* 3.5 24.8 + - + +
318N ALA 2.9 14.3 + - - +
319N ALA* 3.2 16.2 + - - +
321N MET* 1.3 76.6 - - - +
323N ASN* 1.3 62.3 + - - +
325N GLN* 3.4 5.7 + - - +
326N LYS* 3.1 53.4 + - - +
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Residues in contact with ASN 323 (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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112N ALA* 4.6 0.4 - - + -
113N LEU 3.3 20.0 - - - +
114N SER* 2.9 28.6 + - - +
245N THR 3.1 21.0 + - - -
246N VAL* 3.5 12.0 - - - +
247N LEU* 2.9 31.6 + - - +
255N SER 5.3 1.6 - - - +
257N PRO* 3.4 17.8 - - + +
319N ALA 3.0 15.5 + - - +
320N THR 3.8 3.1 - - - +
322N GLU* 1.3 75.7 - - - +
324N ALA* 1.3 65.5 + - - +
326N LYS* 3.1 15.5 + - - +
327N GLY 3.2 9.0 + - - -
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Residues in contact with ALA 324 (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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110N VAL* 5.1 0.9 - - + -
112N ALA* 3.7 13.1 - - + +
257N PRO* 4.7 0.7 - - - -
259N VAL* 3.3 40.3 - - + +
320N THR 2.9 18.3 + - - +
321N MET* 3.4 22.0 + - + +
323N ASN* 1.3 75.6 - - - +
325N GLN* 1.3 61.3 + - + +
327N GLY* 3.0 19.2 + - - +
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Residues in contact with GLN 325 (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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321N MET* 2.9 41.2 + - - +
322N GLU* 3.9 6.0 - - - +
323N ASN 3.2 0.2 - - - -
324N ALA* 1.3 79.6 - - + +
326N LYS* 1.3 60.0 + - - +
327N GLY 3.4 4.4 - - - +
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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