Contacts of the helix formed by residues 269 - 288 (chain H) in PDB entry 1UW9
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 TYR 269 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H HIS* 3.3 15.3 + - - -
268H ASP* 1.3 73.3 - - - +
270H LEU* 1.3 84.7 + - + +
273H GLY* 2.9 28.7 + - - -
274H PHE* 3.5 34.7 + + - -
277H ASN* 3.4 26.9 - - + +
293H ILE* 3.1 27.1 - - + -
294H HIS 3.4 5.6 + - - -
295H ARG* 3.8 17.5 - - + -
311H PHE* 4.1 8.0 - - - -
314H LEU* 2.9 36.0 + - - +
318H LEU* 3.5 26.7 - - + +
326H LEU* 3.8 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H PHE* 6.0 0.4 - - + -
268H ASP 3.2 0.8 - - - -
269H TYR* 1.3 117.1 - - + +
271H THR* 1.3 65.1 + - - +
273H GLY* 3.7 4.0 + - - -
274H PHE* 4.1 16.4 - - + -
294H HIS 4.7 0.2 + - - -
295H ARG 3.8 5.6 - - - +
296H ALA 3.4 11.1 + - - +
297H MET* 3.9 10.8 - - + -
298H HIS* 3.7 39.9 - - + +
301H ILE* 4.8 4.9 - - + -
314H LEU* 4.3 17.0 - - + -
1477H EDO 2.9 45.9 + - - +
273R GLY* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H ASP* 3.1 20.8 - - - +
270H LEU* 1.3 74.9 - - - +
272H GLY* 1.3 62.5 + - - +
296H ALA* 3.7 19.0 + - + +
297H MET* 3.9 22.7 - - + -
1477H EDO 5.7 0.2 - - - -
114R THR* 2.9 29.8 + - - +
117R PHE* 4.2 8.5 - - + -
118R THR* 2.8 42.0 + - - +
274R PHE* 3.9 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 272 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H HIS* 4.0 12.6 - - - -
268H ASP 2.9 14.6 + - - -
271H THR* 1.3 78.8 + - - +
273H GLY* 1.3 60.5 + - - +
276H ALA* 4.0 3.3 - - - +
114R THR* 3.7 7.5 - - - +
272R GLY 4.7 0.2 - - - +
273R GLY 3.8 1.4 - - - -
274R PHE 3.6 3.8 + - - -
275R THR* 3.2 45.5 + - - -
276R ALA 4.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H HIS* 4.0 0.7 + - - -
269H TYR 2.9 19.6 + - - -
270H LEU 4.0 7.4 - - - -
271H THR 3.5 0.4 - - - -
272H GLY* 1.3 79.8 - - - +
274H PHE* 1.3 60.1 + - - -
275H THR 3.4 2.5 - - - -
276H ALA 3.5 2.6 + - - -
277H ASN* 2.9 28.9 + - - +
1477H EDO 4.6 3.8 - - - -
272R GLY 3.9 0.4 - - - -
273R GLY* 3.8 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 3.5 24.7 - - + -
114H THR* 3.5 22.0 - - - +
117H PHE* 3.9 30.5 - + + -
269H TYR* 3.5 39.0 + + - -
270H LEU* 4.1 15.5 - - + -
273H GLY* 1.3 69.6 - - - -
275H THR* 1.3 58.2 + - - +
277H ASN* 3.7 3.7 - - + +
278H THR* 2.7 38.5 + - - +
314H LEU* 5.0 1.3 - - + -
317H ALA* 3.7 28.0 - - + -
321H SER* 4.0 14.8 - - - -
1477H EDO 4.8 9.4 + - - -
245R GLY 4.5 0.4 - - - -
271R THR* 3.9 13.7 + - - +
272R GLY 3.6 3.2 + - - -
297R MET* 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H THR* 3.1 8.7 + - - +
274H PHE* 1.3 75.2 - - - +
276H ALA* 1.3 63.1 + - - +
279H SER* 3.3 23.2 + - - -
244R ALA 2.8 22.9 + - - +
245R GLY 3.6 8.1 - - - -
246R THR* 3.3 33.9 - - - +
247R CYS* 3.4 6.8 + - - +
250R MET* 4.7 7.9 - - + -
267R HIS* 4.9 1.1 - - + -
272R GLY* 3.1 23.7 + - - -
276R ALA* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H CYS* 4.1 5.8 - - - -
250H MET* 3.5 20.5 - - - +
267H HIS* 4.3 4.5 - - - +
272H GLY 4.0 3.8 - - - +
273H GLY 3.5 7.7 + - - +
275H THR* 1.3 80.7 - - - +
277H ASN* 1.3 56.3 + - - +
279H SER* 3.3 4.0 + - - -
280H LEU* 3.0 24.6 + - - +
247R CYS* 3.7 11.1 - - - -
272R GLY 4.3 0.8 + - - -
275R THR* 3.8 36.1 - - + -
276R ALA* 4.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 277 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H HIS* 2.8 34.6 + - + +
269H TYR* 3.4 16.1 - - + +
273H GLY 2.9 19.5 + - - +
274H PHE* 3.7 6.1 - - + +
276H ALA* 1.3 77.1 - - - +
278H THR* 1.3 57.6 + - - +
280H LEU* 3.2 3.1 + - - +
281H ALA* 2.8 27.5 + - - +
291H LEU* 4.4 2.8 - - - +
293H ILE* 3.2 24.8 - - - +
318H LEU* 3.6 5.8 - - - +
321H SER* 3.0 19.9 + - - +
322H GLY 3.0 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 278 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H GLY 4.4 14.4 + - - +
113H VAL* 5.3 4.2 + - - +
148H PHE* 6.0 0.7 - - + -
149H VAL* 6.3 1.3 - - + -
274H PHE* 2.7 20.7 + - - +
276H ALA 3.4 0.2 - - - -
277H ASN* 1.3 75.7 - - - +
279H SER* 1.3 62.2 + - - +
281H ALA* 3.3 2.4 + - - +
282H ILE* 3.0 32.3 + - + +
320H MET 5.6 0.2 - - - +
321H SER* 2.9 35.2 + - - +
245R GLY 3.1 24.8 + - - +
246R THR* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 279 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H MET* 4.5 0.7 - - - -
251H MET* 3.8 19.5 - - - +
275H THR 3.3 4.6 + - - -
276H ALA 3.4 8.7 - - - -
277H ASN 3.3 0.4 - - - -
278H THR* 1.3 77.9 - - - +
280H LEU* 1.3 57.0 + - - +
282H ILE* 3.3 8.3 + - - +
283H TYR* 3.0 26.9 + - - +
246R THR* 3.4 4.3 - - - +
247R CYS* 2.8 31.6 + - - +
248R GLU* 2.6 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H ALA* 4.2 8.7 - - + -
250H MET* 3.9 22.2 - - + -
251H MET* 4.1 12.8 - - - +
254H ALA* 3.7 28.7 - - + -
265H ILE* 3.8 15.9 - - + -
267H HIS* 3.6 35.9 - - + +
276H ALA 3.0 16.8 + - - +
277H ASN* 3.2 6.0 + - - +
279H SER* 1.3 76.7 - - - +
281H ALA* 1.3 56.7 + - - +
283H TYR* 3.2 5.3 + - + +
284H CYS* 2.9 34.1 + - - -
291H LEU* 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 281 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H VAL* 5.5 0.6 - - - +
150H GLY 4.5 4.7 - - - +
152H PRO* 3.5 15.4 - - + +
277H ASN 2.8 16.7 + - - +
278H THR 3.6 1.8 - - - +
280H LEU* 1.3 75.8 - - - +
282H ILE* 1.3 59.0 + - + +
284H CYS 3.3 0.7 + - - -
285H ARG* 3.0 26.9 + - - +
291H LEU* 3.7 12.7 - - + +
321H SER 3.6 20.9 - - - +
322H GLY* 3.8 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H VAL* 4.2 32.5 - - + -
278H THR* 3.0 25.9 + - + +
279H SER* 3.6 9.0 - - - +
281H ALA* 1.3 74.4 - - + +
283H TYR* 1.3 64.6 + - - +
285H ARG* 3.4 7.8 + - + +
286H ASP* 3.0 38.4 + - - +
246R THR* 3.8 25.6 - - + -
248R GLU* 5.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H MET* 4.3 24.2 - - + -
254H ALA* 3.8 31.0 - - + -
255H VAL* 3.4 33.3 - - + +
258H LYS* 3.3 25.6 - - - +
279H SER 3.0 13.5 + - - +
280H LEU* 3.2 10.3 + - + +
282H ILE* 1.3 78.0 - - - +
284H CYS* 1.3 62.7 + - - +
286H ASP* 3.2 3.4 + - - -
287H ASN* 2.9 61.7 + - + +
289H LEU* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 284 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H PRO* 3.8 11.4 - - + -
153H HIS* 3.7 1.0 + - - -
265H ILE* 3.7 30.3 - - - -
280H LEU* 2.9 23.9 + - - +
281H ALA 3.6 5.4 - - - +
282H ILE 3.2 0.2 - - - -
283H TYR* 1.3 75.9 - - - +
285H ARG* 1.3 59.2 + - - +
288H GLY* 2.8 27.7 + - - -
289H LEU* 3.0 42.9 + - - +
290H PHE 4.5 0.2 - - - -
291H LEU* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E ARG* 3.6 48.2 - - - +
214E TRP* 6.4 0.2 - - - +
215E ARG* 3.7 15.8 - - - +
216E ASP* 5.9 2.0 - - - -
149H VAL* 3.3 39.4 + - + +
151H HYP 2.8 24.7 + - - -
152H PRO* 2.8 31.7 + - + +
153H HIS* 4.7 4.9 - - - +
281H ALA 3.0 13.8 + - - +
282H ILE* 3.5 11.2 - - + +
284H CYS* 1.3 78.3 - - - +
286H ASP* 1.3 69.9 + - - +
287H ASN 3.3 0.9 + - - -
288H GLY* 3.6 6.2 + - - -
372H PRO* 5.0 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 286 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214E TRP* 5.2 11.9 + - + -
215E ARG* 3.0 19.0 + - - +
252E LYS* 3.4 35.6 + - - -
282H ILE* 3.0 34.6 + - - +
283H TYR* 3.2 5.7 + - - +
285H ARG* 1.3 86.0 - - - +
287H ASN* 1.3 69.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 287 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ARG* 3.4 20.8 + - - +
258H LYS* 2.8 38.1 + - + +
283H TYR* 2.9 66.1 + - + +
284H CYS* 4.7 0.4 - - - +
286H ASP* 1.3 88.2 - - - +
288H GLY* 1.3 65.3 + - - +
289H LEU* 3.4 5.0 + - + +
63J VAL* 6.0 0.2 - - - -
65J CYS* 4.0 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 288 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ARG* 3.5 17.9 - - - +
153H HIS* 3.7 18.8 - - - -
161H LYS* 4.0 5.7 + - - -
284H CYS 2.8 9.6 + - - -
285H ARG 3.6 4.7 + - - -
287H ASN* 1.3 79.0 - - - +
289H LEU* 1.3 56.8 + - - -
65J CYS* 3.7 15.0 - - - +
66J LEU* 3.4 20.1 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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