Contacts of the helix formed by residues 319 - 341 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A PHE 3.3 9.9 + - - -
316A GLU 3.3 8.7 + - - +
317A GLN 3.4 2.4 - - - +
318A GLU* 1.3 80.3 - - - +
320A LEU* 1.3 63.2 + - - +
321A LEU 3.3 3.1 + - - -
322A GLN* 3.0 36.9 + - - +
323A LYS* 3.1 25.9 + - - +
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Residues in contact with LEU 320 (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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54A ASN 4.5 4.0 - - - +
55A THR* 3.8 18.8 - - + -
314A VAL* 3.6 27.6 - - + -
315A PHE* 3.1 41.3 + - + -
318A GLU* 4.1 15.0 - - + +
319A ASN* 1.3 75.8 - - - +
321A LEU* 1.3 61.0 + - - +
323A LYS* 3.7 23.5 - - + +
324A ALA* 2.8 28.8 + - - +
403A LEU* 4.0 19.1 - - + +
404A THR* 3.9 23.8 - - + -
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Residues in contact with LEU 321 (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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246A GLY* 3.6 20.6 - - - +
249A GLY* 3.6 18.2 - - - +
250A THR* 3.6 24.2 - - - -
251A LEU* 3.7 20.0 - - + +
255A GLU* 6.0 0.2 - - - +
315A PHE* 3.7 22.9 + - + +
319A ASN 3.3 1.0 - - - -
320A LEU* 1.3 76.4 - - - +
322A GLN* 1.3 65.7 + - - +
324A ALA* 3.1 13.5 + - - +
325A ASN* 3.2 18.0 + - - -
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Residues in contact with GLN 322 (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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319A ASN* 3.0 37.1 + - - +
321A LEU* 1.3 77.2 - - - +
323A LYS* 1.3 56.5 + - + +
325A ASN* 3.1 17.3 + - - +
326A ASP* 2.8 63.2 + - - +
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Residues in contact with LYS 323 (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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318A GLU* 3.1 36.6 + - - +
319A ASN* 3.1 19.4 + - - +
320A LEU* 3.7 18.5 - - + +
321A LEU 3.2 0.2 - - - -
322A GLN* 1.3 73.6 - - + +
324A ALA* 1.3 57.2 + - - +
326A ASP* 3.9 9.3 - - - +
327A LEU* 2.7 38.1 + - - +
403A LEU 4.4 16.2 - - - +
404A THR* 5.8 2.1 - - - +
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Residues in contact with ALA 324 (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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246A GLY 3.8 19.5 - - - +
249A GLY 4.3 5.4 - - - +
320A LEU 2.8 14.7 + - - +
321A LEU 3.1 10.7 + - - +
323A LYS* 1.3 75.8 - - - +
325A ASN* 1.3 57.9 + - - +
327A LEU* 3.3 3.0 + - - +
328A GLY 2.9 24.3 + - - -
352A GLY 3.5 10.6 - - - -
353A ALA* 3.6 9.8 + - + +
403A LEU* 3.7 28.0 - - + +
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Residues in contact with ASN 325 (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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248A THR 3.9 1.0 - - - +
249A GLY* 3.6 20.4 + - - -
321A LEU 3.2 14.9 + - - -
322A GLN* 3.1 22.8 + - - +
324A ALA* 1.3 80.3 - - - +
326A ASP* 1.3 63.7 + - - +
328A GLY* 3.2 2.4 + - - -
329A GLN* 3.1 21.7 + - - +
352A GLY* 3.4 24.6 + - - +
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Residues in contact with ASP 326 (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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322A GLN* 2.8 50.0 + - - +
323A LYS* 3.9 9.0 - - - +
325A ASN* 1.3 75.8 - - - +
327A LEU* 1.3 62.0 + - - +
329A GLN* 3.3 6.5 + - - +
330A LYS* 3.0 44.0 + - - +
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Residues in contact with LEU 327 (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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323A LYS 2.7 22.6 + - - +
324A ALA 3.5 2.7 - - - +
326A ASP* 1.3 72.8 - - - +
328A GLY* 1.3 58.2 + - - +
330A LYS* 3.4 6.8 + - - +
331A LEU* 2.9 56.5 + - + +
353A ALA* 3.8 19.7 - - + -
401A VAL* 4.1 23.8 - - + +
402A PRO 4.3 2.9 - - - +
403A LEU* 4.3 16.2 - - + +
405A ILE* 3.9 15.9 - - + -
410A ILE* 3.7 33.0 - - + -
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Residues in contact with GLY 328 (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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324A ALA 2.9 11.3 + - - -
325A ASN 3.2 1.5 + - - -
327A LEU* 1.3 77.8 - - - +
329A GLN* 1.3 56.7 - - - +
331A LEU* 3.2 1.2 + - - +
332A LYS* 2.9 37.9 + - - +
352A GLY 3.1 26.2 - - - -
353A ALA* 4.3 1.3 - - - -
355A ILE* 3.9 14.4 - - - -
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Residues in contact with GLN 329 (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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325A ASN 3.1 12.2 + - - +
326A ASP* 3.8 9.4 - - - +
328A GLY* 1.3 74.7 - - - +
330A LYS* 1.3 59.7 + - + +
332A LYS* 3.4 17.5 + - - +
333A ASP* 2.9 68.3 + - - +
336A LEU* 5.9 1.6 - - - +
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Residues in contact with LYS 330 (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 ASP* 3.0 35.4 + - - +
327A LEU* 3.7 4.7 - - - +
329A GLN* 1.3 76.9 - - + +
331A LEU* 1.3 61.4 + - - +
333A ASP* 3.7 8.6 + - - +
334A GLY 3.2 15.8 + - - -
407A ASP* 3.9 19.4 + - - +
410A ILE* 3.9 32.4 - - + +
411A ARG* 6.3 0.9 - - - +
414A LEU* 3.7 11.0 - - - +
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Residues in contact with LEU 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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46A PHE* 4.6 14.1 - - + -
327A LEU* 2.9 51.0 + - + +
328A GLY 3.7 3.6 - - - +
330A LYS* 1.3 75.4 - - - +
332A LYS* 1.3 60.7 + - - +
334A GLY* 3.3 2.3 + - - -
335A LEU* 2.8 37.3 + - + +
353A ALA* 5.1 2.2 - - + +
355A ILE* 3.9 24.2 - - + -
399A ILE* 3.7 41.7 - - + -
401A VAL* 5.0 1.3 - - + -
410A ILE* 4.4 9.4 - - + -
414A LEU* 3.8 20.8 - - + +
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Residues in contact with LYS 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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328A GLY 2.9 24.6 + - - +
329A GLN* 4.0 19.2 + - - +
331A LEU* 1.3 72.1 - - - +
333A ASP* 1.3 57.3 + - - +
335A LEU* 3.1 1.8 + - - +
336A LEU* 2.6 48.0 + - + +
348A VAL* 3.8 19.5 - - + +
349A ARG* 4.0 23.9 - - - +
350A GLY 2.9 27.1 + - - +
352A GLY 5.5 0.7 - - - -
355A ILE* 3.8 22.9 - - + -
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Residues in contact with ASP 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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329A GLN* 2.9 55.2 + - - +
330A LYS* 3.9 7.6 - - - +
332A LYS* 1.3 76.5 - - - +
334A GLY* 1.3 56.8 + - - +
336A LEU* 3.2 11.7 + - - +
337A ALA* 3.0 28.3 + - - +
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Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A LYS 3.2 8.9 + - - -
331A LEU 3.7 2.9 - - - -
333A ASP* 1.3 78.6 - - - +
335A LEU* 1.3 61.4 + - - +
337A ALA* 3.4 7.8 + - - +
338A ILE* 3.1 28.5 + - - +
414A LEU* 3.9 27.4 - - - -
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Residues in contact with LEU 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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331A LEU 2.8 27.1 + - - +
332A LYS* 3.5 4.3 - - - +
334A GLY* 1.3 75.8 - - - +
336A LEU* 1.3 60.3 + - - +
338A ILE* 3.2 17.6 + - + +
339A ALA* 2.9 29.0 + - - +
345A ILE* 4.8 3.9 - - + +
348A VAL* 4.0 12.5 - - + +
355A ILE* 3.6 31.0 - - + -
356A ALA* 5.7 0.2 - - - -
357A ILE* 3.7 35.7 - - + -
399A ILE* 4.1 14.1 - - + -
414A LEU* 4.2 13.9 - - + -
417A ILE* 4.5 16.4 - - + -
421A PHE* 6.2 0.2 - - + -
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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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329A GLN* 5.9 1.1 - - - +
332A LYS* 2.6 31.5 + - + +
333A ASP* 3.6 13.2 - - - +
335A LEU* 1.3 72.9 - - - +
337A ALA* 1.3 62.5 + - - +
339A ALA* 3.3 8.4 + - + +
340A GLU* 3.1 28.9 + - - +
348A VAL* 3.7 29.2 - - + -
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Residues in contact with ALA 337 (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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333A ASP 3.0 13.3 + - - +
334A GLY* 3.5 12.6 - - - +
335A LEU 3.1 0.4 - - - -
336A LEU* 1.3 74.3 - - - +
338A ILE* 1.3 66.4 + - + +
340A GLU* 3.0 31.2 + - - +
341A LYS* 3.8 4.5 + - - +
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Residues in contact with ILE 338 (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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334A GLY 3.1 19.5 + - - +
335A LEU* 3.5 15.3 - - + +
337A ALA* 1.3 77.3 - - + +
339A ALA* 1.3 60.4 + - - +
341A LYS* 3.1 12.9 + - - +
342A HIS* 3.2 30.8 - - + -
345A ILE* 4.0 6.7 - - + -
414A LEU* 3.8 26.0 - - + +
417A ILE* 3.9 13.7 - - + -
418A SER* 3.9 29.2 - - - +
421A PHE* 4.0 20.6 - - + -
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Residues in contact with ALA 339 (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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335A LEU 2.9 16.8 + - - +
336A LEU* 3.5 12.8 - - + +
337A ALA 3.1 0.4 - - - -
338A ILE* 1.3 73.3 - - - +
340A GLU* 1.3 60.5 + - - +
341A LYS 2.9 6.8 + - - -
342A HIS 3.0 18.7 + - - +
343A PRO* 4.2 2.1 - - - +
345A ILE* 3.9 39.5 - - + +
348A VAL* 4.7 4.3 - - + -
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Residues in contact with GLU 340 (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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336A LEU* 3.1 19.5 + - - +
337A ALA* 3.0 21.1 + - - +
339A ALA* 1.3 74.7 - - - +
341A LYS* 1.3 57.8 + - + +
342A HIS 3.6 0.2 - - - -
343A PRO* 5.9 0.2 - - - +
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Residues in contact with LYS 341 (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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337A ALA 4.6 3.8 - - - +
338A ILE* 3.1 11.1 + - - +
339A ALA 2.9 0.8 - - - -
340A GLU* 1.3 81.2 - - + +
342A HIS* 1.3 73.6 + - + +
343A PRO* 4.0 6.7 - - - +
422A ASP* 4.1 26.4 + - - +
425A LYS* 4.1 4.5 + - - +
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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