Contacts of the helix formed by residues 330 - 336 (chain A) in PDB entry 3W3K
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 GLY 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A GLU* 2.8 32.0 + - - -
329A SER* 1.3 84.9 + - - +
331A ALA* 1.3 65.5 + - - +
332A PHE* 3.1 9.9 - - - -
333A LEU* 3.2 24.4 + - - +
360A SER* 4.9 1.8 - - - -
362A ASN* 4.0 7.4 + - - +
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Residues in contact with ALA 331 (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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302A ILE 5.8 1.3 - - - +
304A ALA* 4.3 13.5 - - + +
326A GLU* 4.1 3.2 + - - -
329A SER* 3.7 1.8 + - - -
330A GLY* 1.3 73.3 - - - +
332A PHE* 1.3 58.2 + - - +
333A LEU 2.9 6.1 + - - -
334A THR* 3.0 24.2 + - - -
335A MET* 4.4 2.8 - - - +
362A ASN* 4.7 8.5 - - - +
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Residues in contact with PHE 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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302A ILE* 3.5 49.8 + - + +
304A ALA* 3.9 23.2 - - - +
307A PHE* 4.1 14.0 - + + -
316A LEU* 4.2 7.4 - - + -
318A LEU* 3.7 23.1 - - + -
323A LEU* 5.7 0.4 - - + -
326A GLU* 3.5 33.8 + - + -
327A ILE* 5.9 2.5 - - + -
330A GLY* 3.1 4.7 - - - -
331A ALA* 1.3 77.7 - - - +
333A LEU* 1.3 85.9 + - + +
334A THR 3.2 0.4 - - - -
335A MET* 3.3 18.3 + - - +
336A LEU* 3.7 15.8 - - + +
342A LEU* 5.1 5.4 - - + -
344A LEU* 5.1 11.2 - - + -
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Residues in contact with LEU 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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326A GLU 5.4 0.4 - - - +
327A ILE* 6.2 0.4 - - - -
330A GLY* 3.5 15.5 - - - +
331A ALA 2.9 1.6 + - - -
332A PHE* 1.3 115.2 - - + +
334A THR* 1.3 62.9 + - - +
335A MET 3.1 3.6 + - - -
336A LEU* 3.6 8.6 + - + -
342A LEU* 5.0 3.8 - - + -
360A SER* 5.6 1.1 - - - +
362A ASN* 3.6 13.2 - - + +
363A PHE* 3.3 66.0 - - + +
365A LYS* 3.7 15.6 - - - +
366A LEU* 3.7 27.1 - - + +
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Residues in contact with THR 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 GLY 4.6 0.2 + - - -
331A ALA* 3.0 15.7 + - - -
333A LEU* 1.3 78.3 - - - +
335A MET* 1.3 72.8 + - - +
336A LEU 3.5 0.9 + - - -
337A PRO* 4.5 6.6 - - - +
362A ASN* 4.4 17.1 + - - +
365A LYS* 4.3 20.8 - - + +
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Residues in contact with MET 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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304A ALA* 3.7 33.2 - - + +
307A PHE* 3.8 24.2 - - + +
308A LYS* 3.4 60.6 - - + +
310A MET 4.9 4.3 - - - +
311A PRO* 6.0 0.5 - - - +
331A ALA 4.4 1.1 - - - +
332A PHE* 3.6 15.7 - - - +
333A LEU 3.1 1.4 - - - -
334A THR* 1.3 92.4 - - - +
336A LEU* 1.3 65.3 + - - +
337A PRO* 3.4 12.8 - - - +
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Residues in contact with LEU 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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307A PHE* 3.8 18.6 - - + -
310A MET 5.3 1.6 - - - +
313A LEU* 3.7 34.1 - - + -
316A LEU* 3.8 26.9 - - + -
332A PHE* 3.7 26.9 - - + +
333A LEU* 3.6 5.1 + - + -
334A THR 3.4 2.8 - - - -
335A MET* 1.3 89.6 - - - +
337A PRO* 1.3 63.9 - - - +
338A ARG 3.2 2.9 - - - +
339A LEU* 3.3 31.7 + - + +
342A LEU* 5.7 0.9 - - + -
365A LYS 4.7 0.9 - - - -
366A LEU* 3.5 30.3 - - + +
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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