Contacts of the helix formed by residues 371 - 382 (chain A) in PDB entry 3OX4
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 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A LEU* 3.7 5.8 - - - -
370A GLY* 1.3 73.6 - - - -
372A GLN* 1.3 68.1 + - - +
373A LYS* 3.7 32.3 + - - +
374A GLU* 3.0 30.2 + - - +
375A VAL* 3.1 22.3 + - - +
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Residues in contact with GLN 372 (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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351A PRO* 3.1 22.9 + - - +
354A ALA* 3.4 8.5 - - - +
355A ASP* 3.5 29.6 - - - +
358A LEU* 3.7 14.4 - - + +
371A ASP* 1.3 76.0 - - - +
373A LYS* 1.3 67.2 + - + +
375A VAL* 3.3 1.6 + - - +
376A GLU* 2.5 63.0 + - - +
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Residues in contact with LYS 373 (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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371A ASP* 3.3 19.5 + - - +
372A GLN* 1.3 81.9 - - + +
374A GLU* 1.3 59.0 + - + +
376A GLU* 3.3 8.6 + - - +
377A GLU* 2.9 48.3 + - - +
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Residues in contact with GLU 374 (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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291A TYR* 2.8 38.6 + - + +
368A ARG* 3.7 21.7 + - - -
369A GLN 4.4 1.8 - - - +
370A GLY* 3.6 8.3 - - - -
371A ASP* 3.0 29.5 + - - +
373A LYS* 1.3 78.9 - - + +
375A VAL* 1.3 57.8 + - - +
377A GLU* 4.0 7.0 - - - +
378A LEU* 3.0 28.2 + - - +
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Residues in contact with VAL 375 (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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261A TYR* 4.4 17.5 - - + -
265A MET* 4.5 10.5 - - + -
291A TYR* 5.4 0.2 - - - +
354A ALA* 3.5 33.2 - - + +
357A ALA* 4.1 9.0 - - + -
358A LEU* 3.4 30.1 - - + -
370A GLY* 4.5 3.4 - - - +
371A ASP 3.1 15.7 + - - +
372A GLN 3.9 1.3 - - - +
374A GLU* 1.3 74.1 - - - +
376A GLU* 1.3 62.1 + - - +
378A LEU* 3.3 8.1 + - + +
379A PHE* 2.9 37.8 + - + -
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Residues in contact with GLU 376 (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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350A VAL* 3.1 26.9 - - + +
351A PRO* 3.5 29.9 - - + +
354A ALA* 3.5 8.5 - - + -
372A GLN* 2.5 55.4 + - - +
373A LYS* 3.6 8.5 - - - +
375A VAL* 1.3 78.6 - - - +
377A GLU* 1.3 57.9 + - + +
379A PHE 3.2 0.9 + - - -
380A LEU* 3.0 31.3 + - + +
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Residues in contact with GLU 377 (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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373A LYS* 2.9 35.0 + - - +
374A GLU* 4.1 5.8 - - - +
376A GLU* 1.3 75.2 - - + +
378A LEU* 1.3 64.5 + - - +
380A LEU* 3.5 15.0 + - + +
381A SER* 3.1 23.2 + - - -
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Residues in contact with LEU 378 (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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261A TYR* 4.2 11.7 - - + -
265A MET* 3.8 27.6 - - + -
287A HIS* 3.8 32.3 - - + +
288A VAL* 4.4 7.9 - - + +
291A TYR* 3.9 42.0 - - + -
374A GLU 3.0 18.5 + - - +
375A VAL* 3.4 9.0 - - - +
376A GLU 3.2 0.2 - - - -
377A GLU* 1.3 73.4 - - - +
379A PHE* 1.3 65.8 + - - +
381A SER* 2.4 29.9 + - - +
382A ALA* 3.3 6.1 + - + +
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Residues in contact with PHE 379 (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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265A MET* 3.5 50.5 - - + +
268A GLN* 4.7 0.7 - - + -
269A LEU* 4.0 25.6 - - + -
284A LEU* 5.0 0.7 - - + -
340A LEU* 3.9 18.2 - - + -
350A VAL* 3.6 15.3 - - + -
353A LEU* 3.6 26.9 - - + -
354A ALA* 3.6 34.8 - - + -
357A ALA* 4.3 0.2 - - + -
375A VAL* 2.9 25.5 + - + -
376A GLU 3.3 8.7 - - - +
378A LEU* 1.3 76.5 - - - +
380A LEU* 1.3 54.9 + - - +
382A ALA* 2.5 34.7 + - - +
383A PHE* 3.2 10.3 - + - -
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Residues in contact with LEU 380 (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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347A LYS* 3.4 48.8 + - + +
350A VAL* 3.4 27.6 - - + -
376A GLU* 3.0 24.0 + - + +
377A GLU* 3.8 15.0 - - + +
379A PHE* 1.3 79.7 - - - +
381A SER* 1.3 60.8 + - - +
383A PHE* 3.3 15.1 + - - +
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Residues in contact with SER 381 (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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287A HIS* 3.5 22.5 + - - +
377A GLU 3.1 12.9 + - - -
378A LEU* 2.4 38.1 + - - +
380A LEU* 1.3 72.7 - - - +
382A ALA* 1.3 59.1 + - - +
383A PHE 3.1 10.9 + - - -
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Residues in contact with ALA 382 (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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265A MET* 5.6 0.7 - - + -
283A VAL* 4.6 0.7 - - + +
284A LEU* 3.8 15.7 - - + -
287A HIS* 3.8 28.5 + - + -
339A ASN* 3.2 10.3 - - - +
340A LEU* 3.0 40.5 + - + +
378A LEU* 3.9 6.5 - - + +
379A PHE* 2.5 21.7 + - - +
381A SER* 1.3 74.6 + - - +
383A PHE* 1.3 56.9 + - - -
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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