Contacts of the helix formed by residues 319 - 329 (chain A) in PDB entry 3QOW
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 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ALA 3.2 25.3 + - - -
259A ASN 4.6 0.8 - - - -
260A MET 3.0 29.3 + - - +
261A LYS* 4.1 1.0 - - - +
262A GLU* 2.7 41.3 + - - +
290A ILE* 3.7 40.3 - - + +
317A ILE* 3.5 13.8 - - + +
318A ASP* 1.3 70.1 - - - +
320A THR* 1.3 60.0 + - - +
321A ILE 3.0 7.0 + - - -
322A LEU* 3.0 18.6 + - + +
323A GLU* 3.1 26.0 + - + +
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Residues in contact with THR 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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262A GLU* 4.6 7.4 - - - +
318A ASP* 2.6 26.6 + - - +
319A ARG* 1.3 78.3 - - - +
321A ILE* 1.3 53.4 + - - +
323A GLU* 2.9 19.4 + - - +
324A ASN* 2.8 49.6 + - - +
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Residues in contact with ILE 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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277A PHE* 5.9 1.3 - - + -
279A ILE* 3.6 27.6 - - + +
288A GLY 4.8 4.0 - - - +
289A THR 3.7 10.1 - - - +
291A MET 3.7 29.4 - - - +
292A ARG* 4.0 18.4 - - + -
318A ASP* 3.6 22.9 - - - +
319A ARG 3.0 0.4 + - - -
320A THR* 1.3 76.0 - - - +
322A LEU* 1.3 63.9 + - - +
324A ASN* 3.7 9.2 - - - +
325A TYR* 3.3 16.1 + - - +
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Residues in contact with LEU 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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279A ILE* 3.9 7.9 - - + -
284A LEU* 4.1 23.3 - - + +
289A THR* 3.5 31.2 + - - +
290A ILE* 4.4 18.4 - - + -
319A ARG* 3.0 12.3 + - + +
321A ILE* 1.3 75.8 - - - +
323A GLU* 1.3 65.8 + - + +
325A TYR* 3.3 9.4 + - + +
326A PHE* 3.1 48.7 + - + -
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Residues in contact with GLU 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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262A GLU* 5.5 1.2 - - - +
319A ARG* 3.1 23.6 + - + +
320A THR* 2.9 32.3 + - - +
322A LEU* 1.3 77.0 - - + +
324A ASN* 1.3 63.0 + - - +
326A PHE* 3.2 10.1 + - - +
327A SER* 3.1 23.8 + - - -
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Residues in contact with ASN 324 (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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320A THR* 2.8 39.4 + - - +
321A ILE* 3.7 9.6 - - - +
323A GLU* 1.3 75.5 - - - +
325A TYR* 1.3 62.6 + - - +
327A SER* 3.2 9.9 + - - -
328A SER* 3.0 23.4 + - - -
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Residues in contact with TYR 325 (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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279A ILE* 3.7 37.7 - - + -
280A ASN* 4.3 7.6 - - - -
281A SER* 3.7 25.1 + - - -
284A LEU* 3.7 33.9 - - + -
321A ILE 3.3 12.7 + - - +
322A LEU* 3.3 8.4 + - + +
324A ASN* 1.3 78.1 - - - +
326A PHE* 1.3 67.5 + + - +
328A SER* 2.7 27.2 + - - -
329A LEU* 3.3 48.2 + - + +
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Residues in contact with PHE 326 (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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284A LEU* 4.5 20.0 - - + -
322A LEU* 3.1 47.3 + - + -
323A GLU* 3.2 10.4 + - - +
324A ASN 3.2 0.8 - - - -
325A TYR* 1.3 85.9 - + - +
327A SER* 1.3 59.6 + - - +
328A SER 3.1 1.6 - - - -
329A LEU* 2.9 39.8 + - + +
330A LYS* 3.6 21.3 - - - +
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Residues in contact with SER 327 (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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323A GLU 3.1 14.2 + - - -
324A ASN* 3.6 11.6 - - - -
326A PHE* 1.3 75.0 - - - +
328A SER* 1.3 60.1 + - - +
330A LYS* 3.4 30.6 + - - +
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Residues in contact with SER 328 (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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324A ASN 3.0 12.3 + - - -
325A TYR* 2.7 30.7 + - - -
326A PHE 3.1 0.2 - - - -
327A SER* 1.3 71.9 - - - +
329A LEU* 1.3 61.6 + - - +
330A LYS 3.1 10.9 + - - +
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Residues in contact with LEU 329 (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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284A LEU* 6.1 0.9 - - + -
325A TYR* 3.3 54.0 + - + +
326A PHE* 2.9 30.0 + - + +
328A SER* 1.3 78.8 + - - +
330A LYS* 1.3 60.0 + - + +
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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