Contacts of the helix formed by residues 315 - 323 (chain A) in PDB entry 5J0O
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 SER 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A TYR* 3.7 18.4 - - - -
313A VAL* 3.1 20.8 - - - +
314A ASP* 1.3 82.6 - - - +
316A GLU* 1.3 65.5 + - - +
317A LYS* 3.4 10.9 + - - +
318A ASP* 3.1 31.9 + - - -
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Residues in contact with GLU 316 (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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182A ARG* 2.9 33.1 + - - -
266A TYR* 3.7 21.4 - - + +
269A VAL* 4.3 5.6 - - + -
270A LEU* 3.3 37.0 + - + -
315A SER* 1.3 74.3 - - - +
317A LYS* 1.3 62.6 + - - +
319A ILE* 3.3 16.1 + - + +
320A PHE* 3.1 19.3 - - + -
327A TYR* 3.3 14.4 + - + -
333A ARG* 2.7 42.1 + - - +
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Residues in contact with LYS 317 (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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315A SER* 3.1 9.4 - - - +
316A GLU* 1.3 78.6 - - - +
318A ASP* 1.3 68.3 + - - +
320A PHE* 2.9 15.6 + - + +
321A ASP* 2.9 38.2 + - - +
327A TYR* 3.8 34.9 - - + +
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Residues in contact with ASP 318 (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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312A PRO 4.4 2.1 - - - +
313A VAL* 3.9 13.7 - - + -
314A ASP* 2.9 31.2 + - - +
315A SER* 3.1 24.0 + - - +
317A LYS* 1.3 78.1 - - - +
319A ILE* 1.3 62.1 + - - +
321A ASP* 3.4 11.3 + - - +
322A TYR* 2.9 38.7 + - + -
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Residues in contact with ILE 319 (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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266A TYR 4.0 9.0 - - - +
267A CYS* 3.7 34.5 - - - +
270A LEU* 3.7 34.8 - - + -
282A MET* 4.4 5.6 - - + -
293A ILE* 3.9 25.4 - - + -
298A ILE* 4.3 6.8 - - + +
313A VAL* 3.6 23.6 - - + -
315A SER 4.1 0.2 - - - +
316A GLU* 3.4 13.9 - - - +
317A LYS 3.1 0.8 - - - -
318A ASP* 1.3 77.0 - - - +
320A PHE* 1.3 65.0 + - + +
322A TYR* 3.3 24.3 + - - +
323A ILE* 3.5 8.5 + - - +
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Residues in contact with PHE 320 (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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270A LEU* 4.1 10.8 - - + -
278A PHE* 4.1 16.8 - + - -
282A MET* 3.3 28.0 - - + -
316A GLU 3.1 24.5 - - - -
317A LYS* 2.9 7.5 + - - +
319A ILE* 1.3 80.0 - - + +
321A ASP* 1.3 62.3 + - - +
323A ILE* 3.4 10.1 - - - +
324A GLN 3.1 5.4 + - - -
325A TRP* 2.9 55.8 + + - +
326A LYS 3.9 13.5 - - - -
327A TYR* 3.7 28.9 - + + +
328A ARG* 3.8 26.0 - - + -
333A ARG* 3.9 13.2 - - - -
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Residues in contact with ASP 321 (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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317A LYS* 2.9 54.1 + - - +
318A ASP* 3.8 11.6 - - - +
320A PHE* 1.3 74.1 - - - +
322A TYR* 1.3 67.9 + - - +
324A GLN* 2.8 21.6 + - - +
325A TRP 4.3 7.0 - - - +
327A TYR 5.6 0.5 + - - -
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Residues in contact with TYR 322 (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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289A LYS* 5.5 0.2 - - - +
291A PHE* 3.0 27.2 - + + -
298A ILE* 3.5 22.0 - - + -
311A LEU* 3.4 39.7 - - + -
312A PRO* 2.6 51.2 + - - +
313A VAL* 4.1 8.7 - - + -
318A ASP* 2.9 33.7 + - + -
319A ILE* 3.4 11.7 - - - +
321A ASP* 1.3 76.7 - - - +
323A ILE* 1.3 59.0 - - - +
324A GLN* 3.6 4.5 + - - +
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Residues in contact with ILE 323 (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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282A MET* 4.0 44.0 - - + +
285A HIS* 3.3 29.5 + - + -
286A ALA* 4.0 13.0 - - + +
289A LYS* 3.7 17.9 - - + +
291A PHE* 3.5 33.2 - - + -
293A ILE* 4.2 5.2 - - + -
298A ILE* 4.2 9.9 - - + -
319A ILE 3.6 7.0 - - - +
320A PHE 3.4 12.6 - - - +
322A TYR* 1.3 75.4 - - - +
324A GLN* 1.3 74.7 + - - +
325A TRP* 4.3 6.7 - - + -
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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