Contacts of the helix formed by residues 329 - 345 (chain B) in PDB entry 2XWU
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 HIS 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B LEU* 3.6 51.1 - - + +
283B ILE* 6.2 0.4 - - + -
323B LEU 5.6 1.6 - - - +
326B GLN* 3.2 16.9 + - + +
327B VAL 3.0 1.4 - - - -
328B GLU* 1.3 88.6 - - + +
330B TRP* 1.3 53.6 + - - +
331B GLN* 3.0 4.0 - - - -
332B SER* 2.7 45.5 + - - +
333B PHE* 3.4 5.6 + - + +
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Residues in contact with TRP 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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323B LEU 5.7 0.7 - - - -
326B GLN 3.9 2.1 + - - -
327B VAL* 3.0 33.3 + - + +
328B GLU* 4.3 7.9 - - - -
329B HIS* 1.3 76.9 - - - +
331B GLN* 1.3 99.1 + - + +
333B PHE* 3.4 8.4 + - - +
334B LEU* 2.9 49.1 + - + +
382B TYR* 3.9 29.3 - + + +
385B VAL* 4.3 30.3 - - + -
386B TYR* 4.6 2.4 + - - -
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU 5.9 0.9 - - - +
329B HIS* 2.7 6.2 + - - +
330B TRP* 1.3 119.4 - - + +
332B SER* 1.3 63.7 + - - +
334B LEU* 3.4 5.9 + - - +
335B ALA* 3.1 21.3 + - - +
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Residues in contact with SER 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 5.9 1.1 - - - -
283B ILE* 3.7 33.3 - - - +
284B PRO* 5.8 1.0 - - - +
287B LEU* 5.0 3.1 - - - +
329B HIS* 2.7 30.9 + - - +
331B GLN* 1.3 75.1 - - - +
333B PHE* 1.3 61.1 + - - -
335B ALA* 3.2 16.2 + - - +
336B LEU 3.2 8.7 + - - -
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Residues in contact with PHE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 4.3 8.2 - - + +
316B GLY* 4.4 4.5 - - - -
320B SER* 4.1 24.9 - - - -
323B LEU* 3.7 46.4 - - + +
324B LEU* 3.6 28.5 - - + -
329B HIS* 3.4 5.1 + - + +
330B TRP* 3.7 12.3 - - - +
331B GLN 3.3 0.2 - - - -
332B SER* 1.3 80.8 - - - +
334B LEU* 1.3 56.7 + - - +
336B LEU* 3.0 25.3 + - + +
337B VAL* 2.9 45.9 + - + +
363B PHE* 4.4 11.0 - + - -
367B LEU* 4.1 8.1 - - + -
386B TYR* 3.3 19.3 - - - -
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B TRP* 2.9 39.0 + - + +
331B GLN* 3.6 7.9 - - - +
332B SER 3.3 0.2 - - - -
333B PHE* 1.3 78.4 - - - +
335B ALA* 1.3 59.5 + - - +
337B VAL* 3.3 4.6 + - + -
338B ASN* 2.8 42.3 + - - +
385B VAL* 4.3 10.5 - - + +
386B TYR* 3.3 40.1 + - + +
389B VAL* 4.4 11.9 - - + -
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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
----------------------------------------------------------
287B LEU* 3.6 28.9 - - + +
290B GLN* 4.2 5.3 + - - +
331B GLN 3.1 12.0 + - - +
332B SER* 3.5 10.8 - - - +
333B PHE 3.2 0.2 - - - -
334B LEU* 1.3 77.2 - - - +
336B LEU* 1.3 62.6 + - - +
338B ASN* 3.1 11.8 + - - +
339B MET* 3.0 18.0 + - - +
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Residues in contact with LEU 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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283B ILE* 4.3 13.7 - - + +
286B VAL* 3.5 31.6 - - + -
287B LEU* 3.6 10.0 - - + +
312B ALA* 4.2 15.7 - - + +
315B LEU* 4.2 18.2 - - + -
316B GLY* 3.8 31.9 - - - +
323B LEU* 5.0 0.4 - - + -
332B SER 3.2 9.8 + - - +
333B PHE* 3.0 22.2 + - + +
335B ALA* 1.3 79.3 - - - +
337B VAL* 1.3 62.2 + - + +
339B MET* 3.1 5.6 + - + +
340B ILE* 3.1 27.4 + - + +
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PHE* 2.9 47.8 + - + +
334B LEU* 3.6 9.9 - - + +
335B ALA 3.2 0.2 - - - -
336B LEU* 1.3 77.5 - - - +
338B ASN* 1.3 56.0 + - - +
340B ILE* 3.3 12.0 + - - +
341B MET 3.0 21.0 + - - -
363B PHE* 4.0 9.6 - - + -
364B TRP* 3.5 29.8 - - + -
367B LEU* 4.2 3.1 - - + -
386B TYR* 3.8 27.6 - - + +
389B VAL* 4.1 12.1 - - + -
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Residues in contact with ASN 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 2.8 37.2 + - - +
335B ALA* 3.1 12.1 + - - +
337B VAL* 1.3 74.2 - - - +
339B MET* 1.3 61.2 + - - +
341B MET* 3.2 12.4 + - + +
342B PHE* 2.9 26.2 + - - +
389B VAL* 4.8 13.2 - - - +
392B GLN* 4.6 11.4 + - - +
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Residues in contact with MET 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 3.4 44.9 - - + +
287B LEU* 4.0 3.4 - - - -
289B LEU* 4.4 2.7 - - + -
290B GLN* 3.5 39.5 - - + +
293B LEU* 4.3 16.2 - - + -
308B ILE* 3.9 27.8 - - + -
312B ALA* 4.1 11.2 - - + -
335B ALA 3.0 11.5 + - - +
336B LEU* 3.1 12.1 + - + +
338B ASN* 1.3 76.0 - - - +
340B ILE* 1.3 64.4 + - + +
342B PHE* 3.0 23.0 + - + +
343B CYS* 3.2 10.5 + - - -
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B CYS* 6.0 0.2 - - - -
312B ALA* 3.9 35.9 - - + +
313B VAL* 4.6 8.1 - - + +
316B GLY* 4.6 2.5 - - - -
336B LEU* 3.1 24.6 + - + +
337B VAL 3.5 5.8 - - - +
339B MET* 1.3 76.6 - - - +
341B MET* 1.3 56.5 + - - +
343B CYS* 3.0 10.8 + - - +
344B THR* 2.8 29.3 + - - -
360B THR* 3.6 25.8 - - + -
363B PHE* 3.7 52.3 - - + -
364B TRP* 3.8 5.6 - - + -
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Residues in contact with MET 341 (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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337B VAL* 3.0 14.3 + - + +
338B ASN* 3.2 17.9 - - - +
339B MET 3.2 0.2 - - - -
340B ILE* 1.3 76.2 - - - +
342B PHE* 1.3 62.9 + - - +
344B THR* 3.4 3.3 + - - -
345B GLY* 3.0 19.9 + - - -
364B TRP* 3.6 13.2 - - + -
389B VAL* 3.3 42.8 - - + +
392B GLN* 4.1 25.4 - - - +
393B LEU* 3.8 38.4 - - + +
396B VAL* 4.1 16.1 - - + +
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Residues in contact with PHE 342 (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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290B GLN 5.5 0.2 - - - -
293B LEU* 3.5 40.6 - - + -
294B ARG* 4.3 39.0 - - + -
297B VAL* 3.9 30.1 - - + -
338B ASN 2.9 12.5 + - - +
339B MET* 3.0 15.4 + - - +
341B MET* 1.3 78.5 - - - +
343B CYS* 1.3 55.6 + - - +
345B GLY* 3.3 3.5 + - - -
346B ILE* 2.9 29.7 + - + +
347B PRO* 5.0 11.0 - - + -
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Residues in contact with CYS 343 (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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293B LEU* 3.8 30.1 - - - -
309B CYS* 3.5 46.7 - - - -
312B ALA* 5.9 2.2 - - - -
339B MET* 3.2 8.3 + - - +
340B ILE* 3.0 10.4 + - - +
342B PHE* 1.3 77.0 - - - +
344B THR* 1.3 65.2 + - - +
346B ILE* 3.1 27.1 + - - +
356B THR* 3.8 8.1 - - + -
357B SER* 3.4 16.7 - - - -
360B THR* 4.0 2.5 - - + -
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Residues in contact with THR 344 (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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340B ILE 2.8 15.6 + - - -
341B MET* 3.7 7.6 - - - -
343B CYS* 1.3 75.6 - - - +
345B GLY* 1.3 59.3 + - - +
357B SER* 3.4 21.9 - - - +
360B THR* 3.0 23.3 + - - +
361B LEU* 4.6 3.6 - - + -
364B TRP* 3.0 33.6 + - + +
393B LEU* 4.1 7.0 - - + -
396B VAL* 3.9 4.0 - - + -
397B LEU* 4.0 25.6 - - + -
400B LYS* 3.6 13.5 - - - +
423B TYR* 4.6 0.2 + - - -
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B MET 3.0 13.6 + - - -
342B PHE* 3.4 5.4 - - - -
344B THR* 1.3 78.1 - - - +
346B ILE* 1.3 68.6 + - - +
347B PRO* 3.3 5.2 - - - +
396B VAL* 3.3 24.0 - - - +
400B LYS* 4.3 7.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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