Contacts of the helix formed by residues 269 - 284 (chain D) in PDB entry 2AXZ
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 LYS 269 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LYS* 5.2 3.8 - - - +
228C ILE* 3.6 15.6 - - - +
233C ASP* 4.3 2.7 + - - +
231D TYR* 3.4 45.2 + - + -
264D PHE* 3.0 30.7 + - + +
267D ILE* 3.4 10.0 - - + +
268D GLY* 1.3 73.4 - - - +
270D GLU* 1.3 58.9 + - - +
271D ASP* 3.4 2.9 - - + -
272D ILE* 3.3 20.6 + - + -
273D HIS* 2.8 28.5 + - - +
301D ASN* 5.8 1.8 - - - +
302D TYR* 3.2 38.2 + - - +
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Residues in contact with GLU 270 (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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265D LYS* 4.2 35.7 - - - +
268D GLY* 2.8 15.6 + - - +
269D LYS* 1.3 70.7 - - - +
271D ASP* 1.3 62.1 + - - +
273D HIS* 3.2 11.7 + - - +
274D ARG* 2.9 49.3 + - - +
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Residues in contact with ASP 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D LYS* 3.4 1.2 - - + -
270D GLU* 1.3 81.4 - - - +
272D ILE* 1.3 63.4 + - + +
274D ARG* 2.9 27.0 + - - +
275D SER* 3.3 11.9 + - - -
294D GLU* 3.2 18.9 - - - +
303D VAL* 5.8 0.4 - - - -
304D ALA* 3.5 38.8 + - + +
305D ILE 5.1 2.1 - - - +
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Residues in contact with ILE 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D GLU* 5.2 0.4 - - - +
264D PHE* 3.6 30.1 - - + -
269D LYS* 3.3 29.3 + - + +
271D ASP* 1.3 73.9 - - + +
273D HIS* 1.3 60.8 + - - +
275D SER* 3.5 4.7 + - - -
276D LEU* 3.0 30.3 + - + +
296D THR* 3.6 14.4 - - + -
302D TYR* 3.3 49.4 - - + +
303D VAL* 3.4 22.0 - - - +
304D ALA* 4.3 0.4 - - + -
1H LEU* 4.5 8.3 - - + -
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Residues in contact with HIS 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASN* 4.9 3.1 - - - -
251A ILE* 4.0 13.9 - - + +
261D ILE* 2.8 33.0 + - + +
262D ASN* 3.9 7.7 - - - -
264D PHE* 4.1 6.3 - - + +
265D LYS* 3.1 53.6 - - + +
269D LYS 2.8 17.7 + - - +
270D GLU* 3.4 11.6 + - - +
272D ILE* 1.3 76.0 - - - +
274D ARG* 1.3 71.0 + - - +
276D LEU* 3.0 7.5 + - - +
277D VAL* 2.9 52.5 + - + +
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Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D GLU* 2.9 34.8 + - - +
271D ASP* 2.9 35.7 + - - +
273D HIS* 1.3 81.1 + - - +
275D SER* 1.3 62.1 + - - +
277D VAL* 3.4 6.7 + - - +
278D GLU* 3.0 23.0 + - + +
294D GLU* 3.1 23.8 + - - +
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Residues in contact with SER 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ASP 3.3 5.9 + - - -
272D ILE 3.6 5.2 - - - -
273D HIS 3.2 0.6 - - - -
274D ARG* 1.3 78.8 - - - +
276D LEU* 1.3 62.2 + - - +
278D GLU* 3.2 8.4 + - - +
279D GLU 3.0 17.0 + - - -
292D PRO* 5.6 4.1 - - - +
294D GLU* 2.8 39.8 + - - +
296D THR* 3.4 16.1 - - - +
1H LEU* 3.6 34.3 - - - +
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Residues in contact with LEU 276 (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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235D GLU* 4.5 12.3 - - + +
238D TYR* 4.4 22.1 + - + +
260D ILE* 6.4 1.1 - - + -
261D ILE* 3.8 33.1 - - + +
264D PHE* 3.2 44.4 - - + -
272D ILE* 3.0 15.8 + - + +
273D HIS* 3.0 9.2 + - - +
275D SER* 1.3 75.2 - - - +
277D VAL* 1.3 64.1 + - - +
279D GLU* 2.9 13.9 + - - +
280D LEU* 2.9 14.2 + - - +
1H LEU* 3.3 33.4 - - + -
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Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 4.2 15.7 - - + -
249A LYS* 3.2 41.3 - - + +
250A ASN* 4.3 0.7 - - - +
251A ILE* 4.5 8.7 - - + +
261D ILE* 3.9 10.5 - - + -
273D HIS* 2.9 48.1 + - + +
274D ARG* 3.7 8.1 - - - +
276D LEU* 1.3 75.6 - - - +
278D GLU* 1.3 63.5 + - - +
279D GLU 3.1 0.2 + - - -
280D LEU* 3.2 7.4 + - - +
281D THR* 3.0 26.7 + - - -
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Residues in contact with GLU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LYS* 5.4 15.7 - - + +
274D ARG* 3.0 13.9 + - + +
275D SER* 3.2 10.5 + - - +
277D VAL* 1.3 78.2 - - - +
279D GLU* 1.3 59.3 - - - +
281D THR* 3.6 7.9 - - - -
282D LYS* 2.6 63.2 + - - +
292D PRO* 3.9 15.2 - - + +
293D LYS* 3.7 48.6 + - - +
294D GLU* 4.1 13.7 - - - +
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Residues in contact with GLU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D THR* 3.4 18.7 - - - +
203D MSE 3.4 17.9 - - + +
238D TYR* 2.7 28.4 + - - +
239D LEU* 3.9 4.0 - - - +
275D SER 3.0 10.3 + - - +
276D LEU* 2.9 10.8 + - - +
278D GLU* 1.3 76.7 - - - +
280D LEU* 1.3 66.0 + - - +
282D LYS* 3.1 11.7 + - - +
283D ILE* 3.0 28.5 + - + +
1H LEU* 2.9 51.2 + - + +
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Residues in contact with LEU 280 (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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245A PHE* 4.2 11.0 - - + -
251A ILE* 4.1 13.2 - - + -
238D TYR* 4.4 2.9 + - + -
242D ILE* 3.7 32.3 - - + -
254D TYR* 3.5 24.9 - - + +
257D ALA* 5.0 1.8 - - + -
258D VAL* 3.9 27.1 - - + -
261D ILE* 3.7 26.7 - - + -
276D LEU 2.9 10.7 + - - +
277D VAL* 3.2 8.5 + - - +
279D GLU* 1.3 75.8 - - - +
281D THR* 1.3 52.0 + - - +
283D ILE* 3.2 11.5 + - + +
284D SER* 2.7 38.4 + - - -
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Residues in contact with THR 281 (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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245A PHE* 4.7 13.1 + - - +
246A LEU* 4.8 19.1 - - + +
249A LYS* 3.7 42.9 - - + +
277D VAL* 3.0 15.1 + - - +
278D GLU* 3.6 10.8 - - - -
280D LEU* 1.3 76.5 - - - +
282D LYS* 1.3 59.0 + - + +
284D SER* 2.9 9.4 - - - +
285D ALA* 2.8 35.9 + - + +
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Residues in contact with LYS 282 (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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249A LYS* 6.1 1.0 - - - +
203D MSE 4.6 14.8 - - + -
278D GLU* 2.6 55.9 + - - +
279D GLU* 3.1 11.8 + - - +
281D THR* 1.3 76.7 - - + +
283D ILE* 1.3 62.3 + - - +
285D ALA* 3.9 6.1 - - - -
286D LYS 2.8 24.8 + - - -
287D GLU* 2.9 56.4 + - + +
288D LYS 5.5 0.4 - - - +
290D THR* 4.8 16.4 - - + +
292D PRO* 5.1 4.9 - - - -
293D LYS* 5.0 3.4 - - - +
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Residues in contact with ILE 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ILE* 3.8 22.9 - - + -
203D MSE 4.0 22.9 - - + +
205D ARG* 2.8 48.8 + - - +
238D TYR* 3.9 22.4 - - + +
239D LEU* 4.5 4.7 - - + -
242D ILE* 3.8 31.0 - - + -
246D LEU* 5.0 1.6 - - + -
254D TYR* 6.4 1.3 - - + -
279D GLU* 3.0 22.5 + - + +
280D LEU* 3.6 10.5 - - + +
282D LYS* 1.3 76.0 - - - +
284D SER* 1.3 56.9 + - - +
285D ALA 3.0 3.7 + - - -
286D LYS* 3.6 4.3 + - - +
287D GLU 5.3 1.6 - - - -
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Residues in contact with SER 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 4.0 22.2 + - - -
245A PHE* 5.5 3.9 - - - -
246A LEU* 4.9 8.9 - - - +
284A SER* 3.1 31.6 + - - -
285A ALA* 5.7 1.1 - - - +
286A LYS* 4.1 13.8 + - - +
254D TYR* 3.8 17.9 + - - -
280D LEU* 2.7 18.3 + - - -
281D THR* 2.9 10.7 - - - +
283D ILE* 1.3 76.3 - - - +
285D ALA* 1.3 54.6 + - - +
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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