Contacts of the helix formed by residues 327 - 339 (chain A) in PDB entry 3OJX
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 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ALA 3.8 0.4 + - - -
326A ASN* 1.3 71.2 - - - +
328A SER* 1.3 58.8 + - - +
329A ALA* 2.5 44.9 + - - +
330A LEU* 2.8 37.6 + - + +
331A VAL* 3.2 10.1 + - - +
487A LYS* 4.5 21.3 + - + +
489A VAL* 5.6 1.4 - - - +
492A SER* 6.1 5.1 - - - -
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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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326A ASN 3.1 7.6 + - - -
327A ASP* 1.3 71.7 + - - +
329A ALA* 1.3 59.3 + - - +
331A VAL* 3.6 11.3 - - - +
332A ASN* 3.0 36.1 + - - +
368A ARG* 5.3 1.5 + - - -
372A THR* 5.8 2.9 - - - -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASP* 2.5 22.6 + - - +
328A SER* 1.3 75.9 + - - +
330A LEU* 1.3 59.2 + - - +
332A ASN* 3.7 8.6 - - - +
333A GLN* 3.2 34.8 + - - +
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Residues in contact with LEU 330 (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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327A ASP* 2.8 26.2 + - + +
329A ALA* 1.3 76.0 - - - +
331A VAL* 1.3 65.1 + - - +
333A GLN* 3.4 10.5 + - - +
334A ILE* 3.2 30.3 + - + +
377A ILE* 3.9 24.2 - - + +
378A THR* 3.7 30.1 - - + -
426A HIS* 4.8 16.2 - - + +
428A LEU* 3.5 36.6 - - + -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASN* 4.4 3.4 - - + -
327A ASP 3.2 9.3 + - - +
328A SER* 3.6 12.8 - - - +
330A LEU* 1.3 77.8 - - - +
332A ASN* 1.3 64.8 + - - +
334A ILE* 3.1 9.8 + - - +
335A GLY 3.1 16.5 + - - -
342A LEU* 3.7 18.4 - - + +
368A ARG* 4.3 16.6 - - + +
371A LEU* 3.8 35.8 - - + +
372A THR* 3.5 29.2 - - + +
377A ILE* 4.2 11.4 - - + -
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Residues in contact with ASN 332 (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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328A SER* 3.0 24.7 + - - +
329A ALA* 3.7 8.9 - - - +
330A LEU 3.3 0.2 - - - -
331A VAL* 1.3 76.0 - - - +
333A GLN* 1.3 58.6 - - + +
335A GLY* 3.0 4.5 + - - -
336A GLU* 2.9 33.5 + - + +
342A LEU* 3.9 5.8 - - - +
368A ARG* 2.8 36.8 - - - +
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Residues in contact with GLN 333 (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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329A ALA* 3.2 25.3 + - - +
330A LEU* 3.7 11.9 - - - +
331A VAL 3.3 0.2 - - - -
332A ASN* 1.3 79.6 - - + +
334A ILE* 1.3 57.6 + - - +
336A GLU* 3.7 8.2 - - - +
337A ILE* 2.9 30.9 + - - +
428A LEU* 3.9 27.3 - - + +
432A GLN* 4.5 9.9 - - - +
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Residues in contact with ILE 334 (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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330A LEU* 3.3 17.7 - - + +
331A VAL* 3.1 8.5 + - - +
333A GLN* 1.3 76.1 - - - +
335A GLY* 1.3 62.5 + - - +
337A ILE* 2.9 27.7 - - + +
338A LEU* 3.0 29.3 + - + +
371A LEU* 4.4 17.7 - - + -
377A ILE* 4.0 37.9 - - + -
427A ILE* 4.0 16.6 - - + -
428A LEU* 4.2 20.9 - - + -
431A LEU* 4.5 8.5 - - + -
444A LEU* 4.6 7.4 - - + -
448A LEU* 6.3 0.2 - - + -
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Residues in contact with GLY 335 (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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331A VAL 3.1 6.7 + - - -
332A ASN 3.0 8.2 + - - -
334A ILE* 1.3 77.9 - - - +
336A GLU* 1.3 56.6 + - - +
338A LEU* 3.4 5.1 + - - +
339A GLY 2.9 7.4 + - - -
340A ALA* 2.8 34.2 + - - -
342A LEU* 3.6 32.0 - - - +
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Residues in contact with GLU 336 (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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332A ASN* 2.9 19.4 + - + +
333A GLN* 3.7 10.5 - - - +
334A ILE 3.3 0.2 - - - -
335A GLY* 1.3 72.9 - - - +
337A ILE* 1.3 60.5 + - - +
339A GLY* 2.8 21.5 + - - +
340A ALA 5.4 1.6 - - - +
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Residues in contact with ILE 337 (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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333A GLN 2.9 15.6 + - - +
334A ILE* 2.9 30.3 - - - +
336A GLU* 1.3 76.2 - - - +
338A LEU* 1.3 60.5 + - + +
339A GLY 3.6 0.3 + - - -
428A LEU* 4.2 9.4 - - + -
431A LEU* 3.9 47.6 - - + +
432A GLN* 4.5 18.8 - - + +
438A ARG* 5.8 4.2 - - - +
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Residues in contact with LEU 338 (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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334A ILE* 3.0 30.7 + - + +
335A GLY 3.9 3.1 - - - +
337A ILE* 1.3 81.9 - - + +
339A GLY* 1.3 66.1 + - - +
340A ALA* 4.4 9.5 - - + +
371A LEU* 5.9 0.2 - - + -
431A LEU* 4.2 15.5 - - + -
437A LEU 6.0 0.2 - - - +
438A ARG* 5.6 1.1 - - - -
439A PRO* 3.5 42.7 - - + +
441A ILE* 3.8 31.8 + - + +
444A LEU* 3.7 24.5 - - + -
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Residues in contact with GLY 339 (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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335A GLY 2.9 1.3 + - - -
336A GLU* 2.8 18.3 + - - -
337A ILE 3.2 0.6 + - - -
338A LEU* 1.3 81.0 - - - +
340A ALA* 1.3 59.1 + - - +
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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