Contacts of the helix formed by residues 328 - 340 (chain B) in PDB entry 2XYX
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 ILE 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294B LEU* 5.2 4.0 - - + -
303B LEU* 3.8 26.5 - - + -
317B LEU* 3.8 31.0 - - + -
325B SER 5.3 5.2 - - - +
327B ILE* 1.3 76.1 - - - +
329B GLU* 1.3 70.7 + - - +
330B PRO 3.5 0.4 - - - -
331B LYS* 3.1 23.6 + - + -
332B PHE* 3.3 25.0 + - + -
1441B Z00 3.5 64.3 - - + +
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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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314B ARG* 2.7 49.6 + - - +
317B LEU* 6.0 0.3 - - - +
318B ARG* 3.1 36.9 + - + +
325B SER 4.9 9.2 + - - +
326B ASP* 4.4 6.8 + - - +
327B ILE 3.4 0.6 - - - -
328B ILE* 1.3 81.4 - - - +
330B PRO* 1.4 67.1 - - + +
332B PHE* 3.2 18.5 + - - +
333B GLU* 3.3 27.7 + - - +
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Residues in contact with PRO 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASP 4.0 7.9 - - - +
327B ILE 3.3 16.8 - - - +
329B GLU* 1.4 90.1 - - + +
331B LYS* 1.3 65.6 + - - +
332B PHE 3.4 0.2 - - - -
333B GLU* 3.6 16.6 + - + +
334B PHE* 3.2 17.2 + - - +
409B LEU* 3.5 26.5 - - + +
412B GLU* 5.7 6.7 - - + -
416B MET* 4.0 17.9 - - + -
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Residues in contact with LYS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PHE* 3.7 35.9 - - + -
294B LEU* 3.9 18.9 - - + +
298B VAL* 5.8 1.1 - - - -
327B ILE* 2.8 30.3 + - - +
328B ILE* 3.1 13.1 + - + +
330B PRO* 1.3 81.8 - - + +
332B PHE* 1.4 55.4 + - - +
334B PHE* 3.4 8.0 + - - +
335B ALA* 2.9 35.5 + - - +
409B LEU* 4.5 10.4 + - + -
413B HIS* 3.1 43.2 - - - +
416B MET* 4.1 7.7 - - - -
1441B Z00 3.5 18.6 - - - +
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Residues in contact with PHE 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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298B VAL* 3.6 22.0 - - + -
299B ASN 3.4 21.8 - - - -
300B LYS* 4.9 0.2 - - - -
302B GLY* 3.8 16.6 - - - -
303B LEU* 3.7 21.8 - - + -
314B ARG* 3.7 57.4 - - + +
317B LEU* 4.3 2.7 - - + -
328B ILE* 3.3 50.1 + - + -
329B GLU* 3.2 9.9 + - - +
331B LYS* 1.4 75.7 - - - +
333B GLU* 1.3 63.8 + - - +
335B ALA* 3.2 4.1 + - - +
336B VAL* 3.0 32.3 + - + +
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ARG* 4.3 8.1 + - - +
329B GLU* 3.3 38.3 + - - +
330B PRO* 3.6 16.0 - - + +
331B LYS 3.4 0.2 - - - -
332B PHE* 1.3 76.3 - - - +
334B PHE* 1.3 61.1 + - - +
336B VAL* 4.5 2.6 - - - +
337B LYS* 3.3 46.4 + - - +
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Residues in contact with PHE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PHE* 4.2 17.7 - - + -
292B ALA* 4.3 2.9 - - - -
295B ALA* 5.2 0.4 - - + -
330B PRO 3.2 15.0 + - - +
331B LYS 3.6 7.9 - - - +
333B GLU* 1.3 76.6 - - - +
335B ALA* 1.4 54.3 + - - +
337B LYS* 3.2 9.0 + - + +
338B PHE* 2.8 73.4 + + + +
402B LYS* 3.9 27.1 - - + -
405B ASP* 4.3 14.1 - - + -
406B LEU* 3.5 42.0 - - + -
409B LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 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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291B PHE 5.7 0.7 - - - +
294B LEU* 6.0 1.1 - - + -
295B ALA* 3.8 27.8 - - + +
298B VAL* 3.5 31.4 - - + -
331B LYS 2.9 21.6 + - - +
332B PHE 3.2 2.2 + - - +
334B PHE* 1.4 75.4 - - + +
336B VAL* 1.3 56.5 + - - +
338B PHE* 3.9 0.4 - - - +
339B ASN* 2.9 38.1 + - - +
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Residues in contact with VAL 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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298B VAL* 5.4 0.4 - - + -
299B ASN* 4.5 5.6 - - - +
300B LYS* 3.9 38.1 - - + +
314B ARG* 4.8 5.6 - - - +
332B PHE* 3.0 21.0 + - - +
333B GLU* 4.6 2.7 - - - +
335B ALA* 1.3 77.1 - - + +
337B LYS* 1.3 64.4 + - + +
339B ASN* 3.5 6.6 + - - +
340B ALA* 3.3 19.9 + - - +
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Residues in contact with LYS 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 GLU* 3.3 36.1 + - - +
334B PHE* 3.2 10.0 + - + +
336B VAL* 1.3 79.2 - - + +
338B PHE* 1.3 60.1 + - - +
340B ALA* 3.3 20.7 - - - +
341B LEU* 4.1 4.7 + - - +
402B LYS* 4.4 21.4 - - - +
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Residues in contact with PHE 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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194B LYS* 5.4 2.7 + - - -
292B ALA* 3.7 18.2 - - + -
295B ALA* 3.7 19.5 - - + -
334B PHE* 2.8 46.0 + + + +
335B ALA* 3.9 4.9 - - - +
336B VAL 3.4 0.2 - - - -
337B LYS* 1.3 69.4 - - - +
339B ASN* 1.4 61.7 + - - +
340B ALA 3.2 4.9 - - - -
341B LEU* 3.3 24.1 + - + +
342B GLU 4.3 0.9 + - - -
343B LEU* 3.8 22.3 + - + +
348B LEU* 3.9 15.9 - - + -
351B PHE* 3.7 33.2 - + - -
399B LEU* 3.7 22.2 - - + -
402B LYS* 3.9 20.6 - - + +
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Residues in contact with ASN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LYS* 4.0 21.3 + - - +
198B ARG* 3.6 13.6 - - - +
295B ALA* 2.8 41.6 + - - +
298B VAL* 3.0 16.2 + - - +
299B ASN* 5.2 1.2 - - - +
335B ALA 2.9 28.2 + - - +
336B VAL* 4.0 7.3 - - - +
337B LYS 3.4 0.2 - - - -
338B PHE* 1.4 72.9 - - - +
340B ALA* 1.4 62.0 + - - +
341B LEU 3.2 1.8 - - - -
342B GLU* 3.2 22.7 + - - +
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Residues in contact with ALA 340 (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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336B VAL 3.3 11.3 + - - +
337B LYS* 3.3 18.4 - - - +
338B PHE 3.2 0.6 - - - -
339B ASN* 1.4 75.1 - - - +
341B LEU* 1.4 61.2 + - + +
342B GLU* 3.5 11.2 + - - +
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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