Contacts of the helix formed by residues 319 - 340 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315D PHE 3.4 6.7 + - - -
316D GLU 3.3 12.2 + - - +
317D GLN 3.5 1.3 - - - +
318D GLU* 1.3 80.3 - - - +
320D LEU* 1.3 58.6 + - - +
321D LEU* 3.4 2.2 - - - +
322D GLN* 3.2 33.8 - - - +
323D LYS* 3.0 30.6 + - - +
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ASN 4.6 4.9 - - - +
55D THR* 3.9 19.1 - - + -
314D VAL* 3.9 35.0 - - + +
315D PHE* 3.3 33.6 + - + -
318D GLU* 3.6 20.2 - - + +
319D ASN* 1.3 74.6 - - - +
321D LEU* 1.3 61.2 + - - +
323D LYS* 3.6 18.4 - - + +
324D ALA* 2.8 30.3 + - - +
403D LEU* 3.9 15.6 - - + +
404D THR* 4.3 24.2 - - + -
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D GLY* 3.8 29.4 - - - +
249D GLY 3.5 17.9 - - - +
250D THR* 3.8 13.2 - - - -
251D LEU* 3.8 22.4 - - + +
315D PHE* 3.8 22.5 + - + +
316D GLU* 5.1 11.2 - - - +
319D ASN* 3.4 1.7 - - - +
320D LEU* 1.3 77.5 - - - +
322D GLN* 1.3 62.9 + - - +
324D ALA* 3.3 12.1 + - - +
325D ASN* 3.4 17.4 + - - -
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Residues in contact with GLN 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ASN* 3.2 36.9 + - - +
320D LEU 3.2 0.2 - - - -
321D LEU* 1.3 80.2 - - - +
323D LYS* 1.3 62.6 + - + +
325D ASN* 3.1 19.0 + - - +
326D ASP* 3.0 46.8 + - - +
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Residues in contact with LYS 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D GLU* 2.9 36.4 + - - +
319D ASN* 3.0 20.6 + - + +
320D LEU* 3.2 19.3 + - + +
322D GLN* 1.3 76.1 - - + +
324D ALA* 1.3 54.8 + - - +
326D ASP* 3.6 11.5 - - + +
327D LEU* 2.7 38.1 + - - +
403D LEU 4.2 18.2 - - - +
404D THR* 5.8 1.6 - - - -
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D GLY 3.8 14.1 - - - +
249D GLY 4.3 5.2 - - - +
320D LEU 2.8 20.0 + - - +
321D LEU 3.5 6.7 - - - +
322D GLN 3.2 0.2 - - - -
323D LYS* 1.3 73.1 - - - +
325D ASN* 1.3 57.4 + - - +
327D LEU* 3.6 0.8 - - - +
328D GLY 2.8 25.3 + - - -
352D GLY 3.5 8.7 - - - -
353D ALA* 3.5 14.1 + - + +
403D LEU* 3.7 35.6 - - + +
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Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D THR 3.9 1.2 - - - +
249D GLY* 3.5 20.5 + - - -
321D LEU 3.4 15.1 + - - -
322D GLN* 3.1 22.0 + - - +
324D ALA* 1.3 74.9 - - - +
326D ASP* 1.3 67.1 + - - +
328D GLY* 3.3 1.0 + - - -
329D GLN* 3.0 23.7 + - - +
352D GLY* 3.4 24.1 + - - +
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Residues in contact with ASP 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D GLN* 3.0 43.1 + - - +
323D LYS* 3.6 15.1 - - + +
325D ASN* 1.3 74.3 - - - +
327D LEU* 1.3 65.1 + - - +
329D GLN* 3.1 7.3 + - - +
330D LYS* 3.0 41.0 + - - +
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Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D LYS 2.7 21.5 + - - +
324D ALA 3.6 3.1 - - - +
326D ASP* 1.3 72.5 - - - +
328D GLY* 1.3 63.5 + - - +
330D LYS* 3.4 5.1 + - - +
331D LEU* 3.0 46.3 + - + +
353D ALA* 3.9 19.7 - - + -
401D VAL* 3.9 24.0 - - + +
402D PRO 4.1 6.5 - - - +
403D LEU* 4.1 12.3 - - + +
405D ILE* 4.0 15.0 - - + -
410D ILE* 3.6 35.0 - - + -
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Residues in contact with GLY 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ALA 2.8 14.9 + - - -
325D ASN 3.8 1.3 - - - -
327D LEU* 1.3 75.2 - - - +
329D GLN* 1.3 55.7 - - - +
331D LEU* 3.5 1.8 + - - +
332D LYS* 3.0 37.7 + - - +
352D GLY 3.1 26.9 - - - -
353D ALA* 4.2 1.1 - - - -
355D ILE* 3.9 13.5 - - - -
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Residues in contact with GLN 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ASN 3.0 13.5 + - - +
326D ASP* 3.5 9.9 - - - +
328D GLY* 1.3 74.0 - - - +
330D LYS* 1.3 65.5 + - + +
332D LYS* 3.4 20.1 + - - +
333D ASP* 3.0 60.0 + - - +
336D LEU* 6.3 0.4 - - - +
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Residues in contact with LYS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D ASP* 3.0 32.2 + - - +
327D LEU* 3.8 3.8 - - - +
329D GLN* 1.3 76.3 - - + +
331D LEU* 1.3 58.0 + - - +
333D ASP* 3.3 7.6 + - - +
334D GLY* 2.9 26.9 + - - -
407D ASP* 2.5 32.1 + - - +
410D ILE* 4.3 30.1 - - + +
414D LEU* 4.1 6.9 - - + +
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PHE* 4.5 13.5 - - + -
327D LEU* 3.0 48.8 + - + +
328D GLY 3.7 3.8 - - - +
330D LYS* 1.3 76.7 - - - +
332D LYS* 1.3 56.6 + - - +
334D GLY* 3.2 1.4 + - - -
335D LEU* 2.8 38.1 + - + +
353D ALA 5.3 2.5 - - - +
355D ILE* 4.1 26.5 - - + -
399D ILE* 3.7 39.7 - - + -
401D VAL* 4.8 0.7 - - + -
410D ILE* 4.6 7.4 - - + -
414D LEU* 3.9 22.1 - - + +
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Residues in contact with LYS 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D GLY 3.0 22.9 + - - +
329D GLN* 4.0 23.4 + - - +
331D LEU* 1.3 76.3 - - - +
333D ASP* 1.3 59.7 + - - +
335D LEU* 4.4 0.9 - - - -
336D LEU* 2.9 40.0 + - + +
348D VAL* 3.9 26.4 - - + +
349D ARG* 4.1 14.5 - - - +
350D GLY 2.9 28.2 + - - +
352D GLY 5.4 0.7 - - - -
355D ILE* 3.8 22.7 - - + -
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Residues in contact with ASP 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D GLN* 3.0 48.0 + - - +
330D LYS* 3.7 6.3 - - - +
332D LYS* 1.3 73.9 - - - +
334D GLY* 1.3 66.0 - - - +
336D LEU* 3.2 13.3 + - - +
337D ALA* 3.1 23.0 + - - +
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Residues in contact with GLY 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D LYS 2.9 14.8 + - - -
331D LEU 3.7 2.9 - - - -
333D ASP* 1.3 79.9 - - - +
335D LEU* 1.3 59.0 + - - +
337D ALA* 3.4 7.3 + - - +
338D ILE* 3.3 25.1 + - - +
414D LEU* 3.9 23.7 - - - +
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Residues in contact with LEU 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D LEU 2.8 31.4 + - - +
332D LYS* 4.0 4.5 - - - +
334D GLY* 1.3 75.7 - - - +
336D LEU* 1.3 58.2 + - - +
338D ILE* 3.3 10.8 + - + +
339D ALA* 2.9 27.2 + - - +
345D ILE* 4.6 4.9 - - + +
348D VAL* 4.2 8.3 - - + +
355D ILE* 3.9 12.6 - - + -
357D ILE* 3.7 39.5 - - + -
399D ILE* 3.8 28.9 - - + -
414D LEU* 4.0 15.5 - - + -
417D ILE* 4.3 23.8 - - + -
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D GLN* 6.3 0.2 - - - +
332D LYS* 2.9 32.9 + - + +
333D ASP* 3.7 13.0 - - - +
335D LEU* 1.3 73.6 - - - +
337D ALA* 1.3 60.7 + - - +
339D ALA* 3.5 8.9 + - + +
340D GLU* 2.9 29.9 + - - +
348D VAL* 3.5 31.6 - - + +
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D ASP 3.1 11.9 + - - +
334D GLY* 3.5 12.1 - - - +
335D LEU 3.2 0.2 - - - -
336D LEU* 1.3 74.9 - - - +
338D ILE* 1.3 67.4 + - + +
340D GLU* 3.2 33.4 + - - +
341D LYS* 4.1 9.4 + - - +
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Residues in contact with ILE 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D GLY 3.3 17.0 + - - +
335D LEU* 3.3 17.0 + - + +
337D ALA* 1.3 79.0 - - + +
339D ALA* 1.3 57.0 + - - +
341D LYS* 3.0 20.7 + - - +
342D HIS* 3.2 29.6 - - + -
345D ILE* 3.9 16.4 - - + -
414D LEU* 3.7 13.2 - - + +
417D ILE* 4.0 13.7 - - + -
418D SER* 3.7 41.7 - - - +
421D PHE* 4.2 14.4 - - + -
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Residues in contact with ALA 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D LEU 2.9 17.0 + - - +
336D LEU* 3.6 15.0 - - + +
337D ALA 3.2 0.4 - - - -
338D ILE* 1.3 72.2 - - - +
340D GLU* 1.3 55.7 + - - +
341D LYS 2.9 9.6 + - - -
342D HIS 3.3 17.9 + - - +
343D PRO* 4.3 2.3 - - - +
345D ILE* 3.6 40.2 - - + +
348D VAL* 4.7 3.8 - - + -
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Residues in contact with GLU 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D LEU* 2.9 25.6 - - - +
337D ALA* 3.4 24.2 - - - +
338D ILE 3.1 1.2 - - - -
339D ALA* 1.3 75.1 - - - +
341D LYS* 1.3 64.3 + - + +
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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