Contacts of the helix formed by residues 319 - 341 (chain B) in PDB entry 1SZU
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 ASN 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B PHE 3.2 10.6 + - - -
316B GLU 3.4 11.7 + - - +
317B GLN 4.1 5.4 - - - +
318B GLU* 1.3 78.5 - - - +
320B LEU* 1.3 63.7 + - - +
321B LEU 3.3 3.3 + - - +
322B GLN* 3.4 18.5 + - + +
323B LYS* 3.1 27.6 + - + +
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Residues in contact with LEU 320 (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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54B ASN 4.5 4.9 - - - +
55B THR* 3.7 30.3 - - + -
314B VAL* 3.8 19.1 - - + +
315B PHE* 3.2 43.9 + - + -
318B GLU* 3.8 20.0 - - + +
319B ASN* 1.3 74.2 - - - +
321B LEU* 1.3 59.9 + - - +
323B LYS* 3.7 16.0 - - + +
324B ALA* 2.8 29.1 + - - +
403B LEU* 3.8 14.8 - - + +
404B THR* 4.0 24.2 - - + -
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLY* 3.6 32.5 - - - +
249B GLY 3.5 17.4 - - - +
250B THR* 3.6 14.6 - - - -
251B LEU* 3.8 20.2 - - + +
255B GLU* 6.0 0.2 - - - +
315B PHE* 4.0 19.9 + - + +
319B ASN* 3.3 1.2 - - - +
320B LEU* 1.3 77.1 - - - +
322B GLN* 1.3 63.2 + - - +
324B ALA* 3.2 5.8 + - - +
325B ASN* 3.1 28.5 + - - -
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Residues in contact with GLN 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASN* 3.4 23.6 + - + +
320B LEU 3.3 0.2 - - - -
321B LEU* 1.3 78.2 - - - +
323B LYS* 1.3 59.1 + - + +
325B ASN* 3.4 15.3 + - - +
326B ASP* 3.0 58.8 + - - +
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Residues in contact with LYS 323 (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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318B GLU* 3.0 37.7 + - - +
319B ASN* 3.1 14.7 + - + +
320B LEU* 3.7 19.4 - - + +
322B GLN* 1.3 77.2 - - + +
324B ALA* 1.3 55.4 + - - +
326B ASP* 3.6 8.5 - - - +
327B LEU* 2.7 38.3 + - - +
403B LEU* 4.2 17.3 - - - +
404B THR* 5.8 1.3 - - - -
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Residues in contact with ALA 324 (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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246B GLY 3.9 18.4 - - - +
249B GLY 4.3 8.3 - - - +
320B LEU 2.8 14.9 + - - +
321B LEU 3.2 10.1 + - - +
323B LYS* 1.3 76.4 - - - +
325B ASN* 1.3 57.6 + - - +
327B LEU* 3.5 2.9 - - - +
328B GLY 2.9 25.6 + - - -
352B GLY 3.6 7.1 - - - -
353B ALA* 3.6 9.8 - - + +
403B LEU* 3.8 27.5 - - + +
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Residues in contact with ASN 325 (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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248B THR 4.1 1.6 - - - +
249B GLY* 3.4 28.9 + - - -
321B LEU 3.1 20.3 + - - -
322B GLN* 3.7 19.8 - - - +
324B ALA* 1.3 81.8 - - - +
326B ASP* 1.3 64.7 + - - +
328B GLY* 3.5 1.0 + - - -
329B GLN* 3.3 21.3 + - - +
352B GLY* 3.6 15.9 + - - +
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Residues in contact with ASP 326 (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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322B GLN* 3.0 46.5 + - - +
323B LYS* 3.7 8.5 - - - +
325B ASN* 1.3 75.5 - - - +
327B LEU* 1.3 67.5 + - - +
329B GLN* 3.3 6.4 + - - +
330B LYS* 3.0 39.0 + - - +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 4.6 0.7 - - - +
323B LYS 2.7 21.5 + - - +
324B ALA 3.5 3.8 - - - +
326B ASP* 1.3 72.9 - - - +
328B GLY* 1.3 58.7 + - - +
330B LYS* 3.3 4.9 + - - +
331B LEU* 2.9 55.7 + - + +
353B ALA* 4.2 16.6 - - + -
401B VAL* 3.9 24.2 - - + +
402B PRO 4.1 6.1 - - - +
403B LEU* 4.3 14.1 - - + +
405B ILE* 3.9 16.8 - - + -
410B ILE* 3.6 36.6 - - + -
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Residues in contact with GLY 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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324B ALA 2.9 11.2 + - - -
325B ASN 4.0 0.7 - - - -
326B ASP 3.3 0.2 - - - -
327B LEU* 1.3 78.6 - - - +
329B GLN* 1.3 56.3 + - - +
331B LEU* 3.5 1.3 + - - +
332B LYS* 2.9 40.9 + - - +
352B GLY 3.1 25.8 - - - -
353B ALA* 4.3 1.1 - - - +
355B ILE* 3.8 13.2 - - - -
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Residues in contact with GLN 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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325B ASN 3.3 13.0 + - - +
326B ASP* 3.3 9.2 + - - +
328B GLY* 1.3 72.5 - - - +
330B LYS* 1.3 62.6 + - + +
332B LYS* 3.3 13.7 + - - +
333B ASP* 2.8 56.1 + - - +
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Residues in contact with LYS 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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326B ASP* 3.0 30.3 + - - +
327B LEU* 3.8 3.8 - - - +
329B GLN* 1.3 76.1 - - + +
331B LEU* 1.3 58.5 + - - +
333B ASP* 3.3 7.4 + - - +
334B GLY* 2.8 26.9 + - - -
407B ASP* 2.5 32.7 + - - +
410B ILE* 3.9 30.5 - - + +
414B LEU* 4.0 7.0 - - + +
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Residues in contact with LEU 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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46B PHE* 4.6 14.4 - - + -
247B ARG* 5.8 0.2 - - - +
327B LEU* 2.9 43.0 + - + +
328B GLY 3.7 4.0 - - - +
330B LYS* 1.3 76.7 - - - +
332B LYS* 1.3 58.0 + - - +
334B GLY* 3.3 1.2 + - - -
335B LEU* 2.7 39.0 + - + +
353B ALA 5.3 2.5 - - - +
355B ILE* 4.1 24.0 - - + -
399B ILE* 3.7 36.6 - - + -
401B VAL* 4.9 0.7 - - + -
405B ILE* 6.5 0.2 - - + -
410B ILE* 4.2 18.6 - - + -
414B LEU* 4.0 19.0 - - + +
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Residues in contact with LYS 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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328B GLY 2.9 25.4 + - - +
329B GLN* 4.0 14.6 - - - +
331B LEU* 1.3 74.2 - - - +
333B ASP* 1.3 61.4 + - - +
335B LEU* 4.4 0.7 - - - -
336B LEU* 2.8 41.5 + - + +
348B VAL* 3.7 21.0 - - + +
349B ARG* 3.9 17.2 - - - +
350B GLY 2.8 28.3 + - - +
352B GLY 5.2 0.7 - - - -
355B ILE* 3.6 30.1 - - + -
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Residues in contact with ASP 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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329B GLN* 2.8 51.0 + - - +
330B LYS* 3.6 7.7 - - - +
332B LYS* 1.3 72.9 - - - +
334B GLY* 1.3 64.0 + - - +
336B LEU* 3.3 12.3 + - - +
337B ALA* 3.1 21.5 + - - +
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Residues in contact with GLY 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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330B LYS 2.8 15.3 + - - -
331B LEU 3.6 2.9 - - - -
333B ASP* 1.3 77.8 - - - +
335B LEU* 1.3 60.8 + - - +
337B ALA* 3.2 21.2 + - - +
338B ILE* 3.3 12.7 + - - +
414B LEU* 4.1 21.5 - - - -
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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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331B LEU 2.7 25.0 + - - +
332B LYS 4.0 2.9 - - - +
334B GLY* 1.3 70.2 - - - +
336B LEU* 1.3 67.3 + - - +
338B ILE* 3.1 10.9 + - + +
339B ALA* 2.9 22.0 + - - +
345B ILE* 4.6 4.4 - - + +
348B VAL* 4.1 8.4 - - + +
355B ILE* 3.9 18.6 - - + -
356B ALA 5.3 0.4 - - - -
357B ILE* 3.5 42.0 - - + -
399B ILE* 3.9 23.1 - - + -
414B LEU* 4.1 16.8 - - + -
417B ILE* 4.2 29.4 - - + -
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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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332B LYS* 2.8 30.1 + - + +
333B ASP* 3.6 12.8 - - - +
334B GLY 3.3 0.2 - - - -
335B LEU* 1.3 75.8 - - - +
337B ALA* 1.3 62.9 + - - +
339B ALA* 3.2 16.2 + - + +
340B GLU* 3.3 16.3 + - - +
348B VAL* 3.7 30.5 - - + +
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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 ASP 3.1 11.7 + - - +
334B GLY* 3.2 14.1 - - - +
336B LEU* 1.3 77.1 - - - +
338B ILE* 1.3 64.2 + - + +
340B GLU* 3.1 35.9 + - - +
341B LYS* 4.0 13.4 + - - +
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Residues in contact with ILE 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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334B GLY 3.3 15.5 + - - +
335B LEU* 3.1 16.5 + - + +
337B ALA* 1.3 77.2 - - + +
339B ALA* 1.3 62.4 + - - +
341B LYS* 3.2 18.7 + - - +
342B HIS* 3.3 27.6 + - + +
345B ILE* 3.9 16.2 - - + -
414B LEU* 3.7 12.3 - - + +
417B ILE* 4.0 12.8 - - + -
418B SER* 3.4 47.3 - - - +
421B PHE* 4.1 14.6 - - + -
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Residues in contact with ALA 339 (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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335B LEU 2.9 13.2 + - - +
336B LEU* 3.4 17.9 - - + +
337B ALA 3.1 0.2 - - - -
338B ILE* 1.3 77.0 - - - +
340B GLU* 1.3 62.3 + - - +
341B LYS 3.2 0.2 - - - -
342B HIS 3.1 24.8 + - - +
343B PRO* 4.1 2.6 - - - +
345B ILE* 3.6 34.5 - - + +
348B VAL* 4.8 3.6 - - + -
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Residues in contact with GLU 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 LEU 3.3 14.1 + - - +
337B ALA* 3.1 24.5 + - - +
339B ALA* 1.3 78.0 - - - +
341B LYS* 1.3 65.5 + - + +
342B HIS 3.5 0.4 - - - -
343B PRO* 5.7 1.7 - - - +
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Residues in contact with LYS 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 ALA* 4.3 17.6 - - - +
338B ILE* 3.2 6.5 + - - +
339B ALA 3.2 0.6 - - - -
340B GLU* 1.3 82.8 - - + +
342B HIS* 1.3 82.9 + - + +
343B PRO* 4.1 5.9 - - - +
418B SER* 5.2 8.5 + - - +
422B ASP* 5.1 9.6 + - - +
425B LYS* 4.5 11.4 + - - +
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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
------------------------------------------------------------
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