Contacts of the helix formed by residues 327 - 338 (chain B) in PDB entry 1XSK
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B GLU* 4.9 2.7 - - - +
325B PHE 3.3 2.7 - - - -
326B PRO* 1.3 83.2 - - + +
328B PRO* 1.3 71.1 - - - +
329B GLU* 4.6 4.7 + - - +
330B GLY* 3.0 32.8 + - - -
331B MET* 3.2 19.3 + - - +
333B ARG* 5.1 1.6 + - - -
334B ARG* 4.4 10.3 + - - +
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Residues in contact with PRO 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B TRP* 3.4 56.3 - - + +
325B PHE 3.7 6.3 - - - +
326B PRO 3.6 7.0 - - - +
327B ASP* 1.3 83.9 - - - +
329B GLU* 1.3 67.6 + - + +
331B MET* 2.8 27.7 + - + +
332B ILE* 3.0 17.7 + - - +
408B MET* 3.7 11.9 - - + -
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B ASP* 3.6 5.8 - - - +
328B PRO* 1.3 79.3 - - + +
330B GLY* 1.3 60.3 + - - +
332B ILE* 2.8 42.5 - - - +
333B ARG* 3.1 27.5 + - - +
407B ALA 4.5 5.0 - - - +
408B MET* 3.2 45.9 - - + +
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Residues in contact with GLY 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B ASP* 3.0 26.4 + - - -
329B GLU* 1.3 79.4 - - - +
331B MET* 1.3 63.3 + - - +
333B ARG* 3.1 33.3 + - - +
334B ARG* 2.9 28.8 + - - +
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Residues in contact with MET 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B GLU* 3.8 32.7 - - + +
286B VAL* 5.2 0.2 - - - -
305B PHE* 3.8 19.3 - - + -
320B TRP* 3.5 37.5 - - + -
325B PHE* 3.5 28.7 - - + -
327B ASP 3.2 11.2 + - - +
328B PRO* 2.8 20.0 + - + +
330B GLY* 1.3 77.3 - - - +
332B ILE* 1.3 61.3 + - + +
334B ARG* 3.1 13.9 + - - +
335B LEU* 2.9 44.0 + - + +
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B PHE* 5.3 2.9 - - + -
320B TRP* 5.1 10.5 - - + -
328B PRO 3.0 10.2 + - - +
329B GLU* 2.8 33.0 - - - +
331B MET* 1.3 82.4 - - + +
333B ARG* 1.3 88.1 + - + +
335B LEU* 3.8 6.7 - - - +
336B LYS* 2.8 46.0 + - + +
342B ILE* 4.8 19.7 - - + -
408B MET* 2.9 36.8 - - + +
409B GLY* 4.1 12.8 - - - -
410B VAL* 5.2 3.8 - - + -
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B ASP* 5.1 1.0 + - - -
329B GLU* 3.1 43.4 + - - +
330B GLY* 3.1 22.5 + - - +
332B ILE* 1.3 92.5 - - + +
334B ARG* 1.3 56.4 + - + +
336B LYS* 3.3 3.7 + - - +
337B ALA* 2.7 38.2 + - - +
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B GLU* 3.3 27.6 + - - +
287B ASN* 5.2 8.1 - - - +
327B ASP* 4.4 13.3 + - - +
330B GLY* 2.9 36.1 + - - +
331B MET 3.1 9.4 - - - +
333B ARG* 1.3 78.0 - - + +
335B LEU* 1.3 64.8 + - + +
337B ALA* 3.3 15.3 + - - +
338B LYS* 3.3 23.8 + - - +
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B VAL* 3.6 13.5 - - + -
287B ASN* 3.5 24.0 - - - +
290B ILE* 3.3 31.4 - - + -
303B PHE* 5.6 1.3 - - + -
305B PHE* 3.8 26.0 - - + -
331B MET* 2.9 42.7 + - + +
332B ILE* 3.8 6.1 - - - +
334B ARG* 1.3 77.9 - - + +
336B LYS* 1.3 60.9 + - - +
338B LYS* 3.2 17.7 + - - +
340B LEU* 3.4 20.1 - - - +
342B ILE* 4.1 15.7 - - + -
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Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ILE* 2.8 37.0 + - + +
333B ARG* 3.9 3.1 - - - +
335B LEU* 1.3 68.4 - - - +
337B ALA* 1.3 61.5 + - - +
338B LYS 3.0 5.4 - - - -
339B GLY* 3.0 13.7 + - - -
340B LEU 3.4 23.4 + - - +
341B LYS* 5.6 2.1 - - + +
342B ILE* 4.2 12.6 - - + +
409B GLY* 2.9 40.1 + - - +
411B ASP* 3.2 29.7 + - - +
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ARG 2.7 22.1 + - - +
334B ARG* 3.4 11.2 - - - +
335B LEU 3.2 0.2 - - - -
336B LYS* 1.3 71.8 - - - +
338B LYS* 1.3 57.9 + - + +
339B GLY 3.1 4.2 + - - -
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ASN* 2.6 36.2 + - - +
290B ILE* 3.8 25.9 - - + +
291B ASP* 3.5 26.7 + - - +
334B ARG* 3.3 20.2 - - - +
335B LEU* 3.2 12.5 + - - +
336B LYS 3.0 1.4 - - - -
337B ALA* 1.3 77.3 - - + +
339B GLY* 1.3 62.7 + - - +
340B LEU* 3.5 5.4 - - + +
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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