Contacts of the helix formed by residues 322 - 341 (chain D) in PDB entry 1AX4
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 GLU 322 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232D TYR* 4.6 14.3 - - + -
235D LYS* 3.1 47.2 + - - +
245D THR* 5.1 1.4 - - - -
246D ILE* 4.0 24.7 + - + +
320D THR 3.4 3.4 + - - -
321D GLU* 1.3 67.9 - - - +
323D GLU* 1.3 71.2 + - + +
325D LEU* 3.1 4.6 + - - +
326D HIS* 2.7 35.7 + - + +
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Residues in contact with GLU 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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16B LYS* 4.5 9.0 + - - -
8D PRO* 3.6 22.7 - - + +
321D GLU* 4.1 19.8 - - - +
322D GLU* 1.3 92.3 + - + +
324D TYR* 1.4 63.0 + - - +
326D HIS* 3.9 6.9 - - - +
327D TYR* 3.3 21.7 + - - +
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Residues in contact with TYR 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 3.9 13.8 - - + +
9D PHE* 5.1 2.7 - + + -
229D GLU* 5.1 0.3 + - - -
267D ASP 5.2 1.1 - - - -
269D LEU* 3.6 8.7 - - + +
318D GLU 3.9 14.1 - - - +
319D GLY* 4.1 14.4 - - - -
321D GLU* 3.1 24.3 + - + +
323D GLU* 1.4 80.7 + - - +
325D LEU* 1.3 88.8 + - + +
327D TYR* 3.1 9.2 + + - +
328D ARG* 2.8 48.6 + - + +
419D ARG* 3.2 37.7 + - + +
420D ARG* 3.7 42.2 - - + +
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Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D CYS* 3.8 33.9 - - + +
229D GLU* 4.2 15.5 - - + +
232D TYR* 3.8 15.7 - - + -
246D ILE* 4.0 24.9 - - + -
267D ASP* 5.7 0.9 - - - -
319D GLY 3.7 24.2 - - - +
320D THR* 3.9 12.6 - - - +
321D GLU 2.9 18.9 + - - +
322D GLU 3.7 3.4 - - - +
324D TYR* 1.3 87.7 - - + +
326D HIS* 1.3 62.8 + - - +
328D ARG* 4.2 3.8 - - + -
329D ILE* 2.9 33.3 + - + +
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Residues in contact with HIS 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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3D LYS* 4.7 10.1 + - - -
5D ILE* 3.6 36.3 - - + +
232D TYR* 2.7 38.5 + - + -
322D GLU* 2.7 24.2 + - + +
323D GLU* 3.9 7.9 - - - +
325D LEU* 1.3 70.1 - - - +
327D TYR* 1.3 56.7 + - - +
329D ILE* 4.4 0.5 - - - +
330D GLY* 2.9 27.7 + - - -
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Residues in contact with TYR 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 5.9 0.9 - - - +
5D ILE* 3.5 38.6 - - + +
6D VAL 3.6 12.6 - - - +
7D GLU* 2.8 40.2 + - + +
8D PRO* 3.7 18.6 - - + -
9D PHE* 4.0 20.9 - + - -
323D GLU 3.3 11.8 + - - +
324D TYR* 3.1 13.6 + + - +
326D HIS* 1.3 76.0 - - - +
328D ARG* 1.3 86.2 + - + +
330D GLY 3.4 0.7 + - - -
331D GLN* 2.9 49.6 + - + +
420D ARG* 5.0 11.1 - - + -
422D TYR 3.7 7.8 + - - -
424D ASN* 4.6 5.4 - - - -
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Residues in contact with ARG 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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51D ASP* 3.8 0.2 + - - -
229D GLU* 2.8 29.0 + - - -
324D TYR* 2.8 49.4 + - + +
325D LEU* 3.6 6.1 - - + +
327D TYR* 1.3 84.5 - - + +
329D ILE* 1.3 66.0 + - - +
331D GLN* 3.2 16.2 + - - +
332D VAL* 3.3 16.2 + - - +
352D GLY 3.2 17.6 + - - -
353D HIS* 3.2 20.0 - - - +
417D ILE* 2.6 44.5 + - - +
418D ALA 3.6 10.9 + - - -
419D ARG* 3.4 27.8 - - + +
420D ARG 5.6 1.1 - - - +
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Residues in contact with ILE 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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229D GLU* 4.1 24.7 - - + +
232D TYR* 3.4 47.1 - - + -
233D PHE* 3.6 31.2 - - + -
325D LEU* 2.9 21.4 + - + +
326D HIS 4.4 0.7 - - - +
328D ARG* 1.3 76.4 - - - +
330D GLY* 1.3 59.7 + - - +
332D VAL* 3.3 4.0 + - - +
333D LYS* 2.9 29.4 + - + +
350D THR* 5.7 0.9 - - - +
351D GLY 4.5 5.3 - - - +
352D GLY* 3.8 19.5 - - - +
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Residues in contact with GLY 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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3D LYS 4.3 4.9 - - - +
5D ILE* 3.8 24.2 + - - -
326D HIS 2.9 20.7 + - - -
327D TYR 3.7 0.4 - - - -
329D ILE* 1.3 75.5 - - - +
331D GLN* 1.4 56.9 + - - +
333D LYS* 3.7 12.3 - - - +
334D TYR* 2.9 28.1 + - - +
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Residues in contact with GLN 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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5D ILE* 5.5 0.6 - - - +
327D TYR* 2.9 38.4 + - + +
328D ARG* 3.2 11.6 + - - +
330D GLY* 1.4 76.8 - - - +
332D VAL* 1.3 65.0 + - - +
334D TYR* 3.3 3.6 + - - +
335D LEU* 3.1 21.1 + - - +
417D ILE* 3.7 21.4 - - + +
418D ALA 4.8 2.8 - - - +
420D ARG 5.6 2.6 + - - -
422D TYR* 3.0 28.7 + - - +
423D THR 3.4 13.1 + - - -
424D ASN* 3.2 29.7 + - - +
427D MET* 3.6 19.5 - - + +
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ARG* 3.3 17.5 + - - +
329D ILE 3.3 7.7 + - - +
331D GLN* 1.3 73.6 - - - +
333D LYS* 1.3 66.5 + - - +
334D TYR 3.2 0.2 + - - -
335D LEU* 3.2 8.8 + - - +
336D GLY* 3.1 17.8 + - - -
350D THR* 4.2 4.7 - - - +
351D GLY 3.6 18.4 - - - +
352D GLY 3.7 16.4 - - - +
353D HIS* 4.1 5.8 - - - -
354D ALA 3.6 32.1 - - - +
355D VAL* 3.6 8.0 - - + +
417D ILE* 4.0 27.4 - - + -
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Residues in contact with LYS 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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3D LYS* 6.4 1.6 - - - -
329D ILE* 2.9 20.3 + - + +
330D GLY* 3.8 10.8 - - - +
332D VAL* 1.3 77.3 - - - +
334D TYR* 1.3 54.7 + - - +
336D GLY* 3.2 1.4 + - - -
337D ASP* 2.8 60.4 + - - +
348D TYR* 5.2 10.6 + - + -
349D PRO* 6.5 0.7 - - - -
350D THR* 3.4 22.5 + - + +
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Residues in contact with TYR 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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2D ALA* 3.6 31.9 - - + -
3D LYS 3.7 24.9 - - - +
4D ARG* 3.4 33.1 + - + -
5D ILE 5.9 0.2 - - - +
330D GLY 2.9 18.1 + - - +
331D GLN* 3.6 7.4 - - - +
332D VAL 3.2 0.2 - - - -
333D LYS* 1.3 72.3 - - - +
335D LEU* 1.4 69.8 + - - +
337D ASP* 3.4 5.0 + - - +
338D ARG* 2.8 39.2 + - + +
424D ASN* 3.9 29.8 - - + +
427D MET* 4.1 10.5 - - + -
428D ASP* 2.3 39.4 + - - -
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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 GLN 3.1 10.1 + - - +
332D VAL 3.6 8.1 - - - +
334D TYR* 1.4 84.4 - - - +
336D GLY* 1.3 63.0 + - - +
338D ARG* 3.3 4.3 + - - +
339D LEU* 3.2 37.4 + - + +
355D VAL* 3.9 18.4 - - + -
415D LEU* 4.2 15.3 - - + -
417D ILE* 3.9 18.4 - - + -
427D MET* 3.8 45.5 - - - +
430D ILE* 4.2 13.0 - - + -
431D ALA* 4.0 17.9 - - + +
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Residues in contact with GLY 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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332D VAL 3.1 13.1 + - - -
333D LYS 3.2 3.3 + - - -
335D LEU* 1.3 77.8 - - - +
337D ASP* 1.3 57.4 + - - +
339D LEU* 3.1 5.8 + - - +
340D ARG* 2.9 28.8 + - - +
346D ILE* 3.7 25.1 - - - +
350D THR* 4.0 4.0 - - - -
355D VAL* 3.8 14.6 - - - +
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Residues in contact with ASP 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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2D ALA* 3.8 25.0 - - + -
3D LYS 4.9 2.6 + - - -
333D LYS* 2.8 51.8 + - - +
334D TYR* 3.9 1.3 - - - +
336D GLY* 1.3 73.0 - - - +
338D ARG* 1.3 66.4 + - - +
340D ARG* 4.2 10.7 + - - -
341D GLU* 3.0 41.5 + - - +
348D TYR* 4.3 17.8 + - - -
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Residues in contact with ARG 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ALA* 4.1 11.9 - - + -
334D TYR* 2.8 51.5 + - + +
335D LEU* 3.7 5.8 - - - +
336D GLY 3.2 0.2 - - - -
337D ASP* 1.3 79.0 - - - +
339D LEU* 1.3 64.0 + - - +
341D GLU* 3.9 6.8 + - - +
342D ALA* 3.5 19.8 + - - +
427D MET 5.8 0.2 - - - +
428D ASP* 2.8 40.9 + - - +
431D ALA* 3.9 13.8 - - + +
432D ASP* 2.7 29.9 + - - -
435D ILE* 3.7 26.4 - - - +
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Residues in contact with LEU 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* 3.3 20.2 - - + +
336D GLY 3.1 7.5 + - - +
338D ARG* 1.3 79.9 - - - +
340D ARG* 1.3 59.3 + - - +
342D ALA* 3.2 7.9 + - - -
343D GLY 3.3 0.2 + - - -
344D ILE* 2.9 44.7 + - + +
346D ILE* 4.2 7.0 - - + -
355D VAL* 4.0 17.5 - - + -
357D VAL* 4.4 6.1 - - + -
415D LEU* 3.9 27.8 - - + -
430D ILE* 6.2 0.2 - - + -
431D ALA* 3.8 28.0 - - + +
434D LEU* 3.8 27.8 - - + -
435D ILE* 4.6 2.9 - - + -
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Residues in contact with ARG 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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158D GLU* 5.1 4.6 + - - +
336D GLY 2.9 15.3 + - - +
337D ASP* 3.8 12.5 + - - +
339D LEU* 1.3 72.4 - - - +
341D GLU* 1.3 65.7 + - + +
343D GLY* 3.1 13.9 + - - -
344D ILE 3.7 11.6 - - - +
345D PRO* 6.2 0.2 - - + -
346D ILE* 4.4 14.1 - - + +
348D TYR* 3.3 66.1 + - - +
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Residues in contact with GLU 341 (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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2D ALA* 3.0 35.4 + - - +
337D ASP* 3.0 31.3 + - - +
338D ARG* 4.0 8.0 + - - +
340D ARG* 1.3 77.2 - - + +
342D ALA* 1.3 58.5 + - - +
343D GLY 3.6 0.7 + - - -
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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