Contacts of the helix formed by residues 288 - 312 (chain D) in PDB entry 4PE5
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 GLY 288 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D GLU 4.2 9.2 + - - -
285D TRP 4.6 1.7 + - - -
286D ASP 3.8 3.2 + - - -
287D TYR* 1.3 76.6 - - - +
289D LEU* 1.3 67.5 + - - -
290D PRO* 3.4 7.0 - - - -
291D ALA* 3.2 10.3 + - - +
292D ARG* 2.9 21.9 + - - +
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Residues in contact with LEU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 4.4 11.4 - - + -
45D SER* 4.1 27.6 - - - -
46D ASP 5.4 2.7 - - - +
50D ILE* 6.2 1.8 - - + -
100D ALA* 3.7 27.4 - - + -
126D ILE* 4.3 7.2 - - + -
127D HIS* 4.0 27.5 - - + +
288D GLY* 1.3 70.7 - - - -
290D PRO* 1.4 72.1 - - + +
292D ARG* 2.9 19.3 + - - +
293D VAL* 2.9 23.1 + - + +
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Residues in contact with PRO 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ASP* 5.3 2.5 - - + +
49D ALA* 3.8 13.7 - - + +
50D ILE* 3.8 29.8 - - + +
53D ALA* 3.7 30.2 - - + +
54D HIS* 5.8 0.2 - - - +
288D GLY* 3.5 6.3 - - - -
289D LEU* 1.4 93.6 - - + +
291D ALA* 1.3 55.3 + - - +
293D VAL* 3.9 5.3 - - + +
294D ARG* 2.9 28.6 + - - +
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Residues in contact with ALA 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ALA* 5.2 1.1 - - - +
286D ASP 5.5 1.1 - - - +
287D TYR* 4.6 6.7 - - + -
288D GLY 3.2 21.0 + - - +
290D PRO* 1.3 80.9 - - - +
292D ARG* 1.3 58.3 + - + +
294D ARG* 3.1 8.9 - - - +
295D ASP* 2.9 37.2 + - - +
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Residues in contact with ARG 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ILE* 2.4 60.9 + - + +
127D HIS* 3.6 28.5 - - - +
131D SER* 5.1 2.2 + - - -
146D PHE* 4.4 9.7 - - + -
282D TYR* 3.4 41.4 + - + +
283D ASP 4.2 0.8 - - - -
284D GLU* 3.4 36.5 - - - +
287D TYR* 3.0 20.6 + - + +
288D GLY 2.9 18.8 + - - +
289D LEU* 2.9 12.7 + - - +
291D ALA* 1.3 77.8 - - - +
293D VAL* 1.3 56.5 + - - +
295D ASP* 3.4 7.5 + - - +
296D GLY* 2.9 25.5 + - - -
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Residues in contact with VAL 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 3.8 33.2 - - + -
41D LEU* 4.5 11.7 - - + -
50D ILE* 5.3 13.0 - - + +
54D HIS* 5.1 7.0 - - + -
70D LEU* 5.6 3.1 - - + -
98D VAL* 4.2 4.7 - - + +
126D ILE* 3.6 20.2 - - + +
289D LEU* 2.9 23.5 + - + +
290D PRO* 3.9 7.2 - - + +
292D ARG* 1.3 72.5 - - - +
294D ARG* 1.3 66.8 + - - +
296D GLY* 3.2 0.9 + - - -
297D ILE* 2.9 43.8 + - + +
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Residues in contact with ARG 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ALA* 3.8 19.3 - - + +
54D HIS* 5.4 2.9 - - - +
59D PHE* 5.8 4.0 - - + -
290D PRO 2.9 16.1 + - - +
291D ALA* 3.1 14.8 - - - +
293D VAL* 1.3 77.7 - - - +
295D ASP* 1.3 62.5 + - - +
297D ILE* 3.2 8.0 + - - +
298D ALA* 2.9 28.3 + - - +
344D PHE* 5.3 6.4 - - + -
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Residues in contact with ASP 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D PHE* 4.1 19.2 - - + -
291D ALA* 2.9 22.4 + - - +
292D ARG* 4.0 4.9 - - - +
294D ARG* 1.3 75.0 - - - +
296D GLY* 1.3 55.9 + - - +
298D ALA* 3.4 8.2 - - - +
299D ILE* 2.9 38.2 + - + +
344D PHE* 3.8 23.8 - - + -
349D LEU* 5.2 9.8 - - + +
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Residues in contact with GLY 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D VAL* 4.0 10.8 - - - -
124D LEU* 3.4 29.4 - - - +
146D PHE* 4.2 7.6 - - - -
292D ARG 2.9 15.4 + - - -
293D VAL 3.6 3.6 - - - -
294D ARG 3.1 0.4 - - - -
295D ASP* 1.3 73.8 - - - +
297D ILE* 1.3 64.7 + - - +
299D ILE 3.0 11.4 + - - -
300D ILE* 3.0 12.5 + - - +
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Residues in contact with ILE 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 3.7 36.4 - - + +
39D VAL* 4.2 1.6 - - + -
54D HIS* 4.2 18.2 - - + +
59D PHE* 5.7 6.1 - - + -
66D PRO* 3.8 22.9 - - + -
68D VAL* 3.5 32.3 - - + -
98D VAL* 4.1 6.0 - - + +
293D VAL* 2.9 39.2 + - + +
294D ARG* 3.7 4.3 - - - +
296D GLY* 1.3 74.6 - - - +
298D ALA* 1.3 56.9 + - - +
300D ILE* 3.4 0.9 + - - -
301D THR* 2.9 28.6 + - - -
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Residues in contact with ALA 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D PHE* 5.5 6.7 - - + -
294D ARG 2.9 13.8 + - - +
295D ASP* 3.4 13.9 - - - +
296D GLY 3.0 0.2 - - - -
297D ILE* 1.3 79.0 - - - +
299D ILE* 1.3 57.3 + - - +
301D THR* 3.9 3.3 - - - -
302D THR* 2.8 37.0 + - - -
342D VAL* 4.6 1.1 - - - -
344D PHE* 3.5 46.0 - - + -
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Residues in contact with ILE 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 4.4 7.6 - - + -
146D PHE* 3.5 27.4 - - + -
295D ASP 2.9 20.1 + - - +
296D GLY* 3.0 6.7 + - - +
298D ALA* 1.3 75.3 - - + +
300D ILE* 1.3 58.1 + - - +
303D ALA* 2.9 32.1 + - - +
339D LEU* 4.0 34.1 - - + +
342D VAL* 3.5 24.6 - - + +
344D PHE* 6.1 0.4 - - + -
349D LEU* 3.6 33.2 - - + +
351D PHE* 3.6 16.6 - - + -
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Residues in contact with ILE 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE* 4.1 9.2 - - + -
37D ILE* 3.6 29.4 - - + -
95D GLN* 4.9 3.8 - - + +
96D GLY* 3.9 17.5 - - - +
97D VAL 3.8 26.2 - - - +
98D VAL* 4.0 15.7 - - + -
122D PRO* 4.8 7.6 - - + -
124D LEU* 3.8 24.7 - - + -
296D GLY 3.0 12.3 + - - +
299D ILE* 1.3 75.0 - - - +
301D THR* 1.3 60.0 + - - +
303D ALA* 3.9 4.2 - - - +
304D ALA* 3.0 27.9 + - + +
335D LEU* 5.6 4.4 - - + +
339D LEU* 4.6 12.8 - - + -
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Residues in contact with THR 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE* 4.3 11.0 - - - -
37D ILE* 5.0 0.2 - - - -
59D PHE* 5.9 4.7 - - - -
62D LEU* 5.2 4.9 - - - -
64D VAL* 3.4 11.4 - - - +
66D PRO* 4.3 29.2 - - - -
297D ILE* 2.9 19.3 + - - -
298D ALA* 3.9 4.3 - - - -
300D ILE* 1.3 76.0 - - - +
302D THR* 1.3 61.9 + - - +
304D ALA 3.3 0.5 + - - -
305D SER* 2.9 31.1 + - - -
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Residues in contact with THR 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU* 5.3 5.1 - - - +
298D ALA* 2.8 24.3 + - - -
301D THR* 1.3 71.9 - - - +
303D ALA* 1.3 59.2 + - - +
305D SER* 3.3 7.4 + - - -
306D ASP* 2.9 51.8 + - - +
342D VAL* 3.5 30.1 - - + +
343D THR 4.6 12.4 + - - +
344D PHE* 4.9 8.0 - - - -
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D ILE 2.9 21.2 + - - +
300D ILE 3.9 3.6 - - - +
301D THR 3.2 0.2 - - - -
302D THR* 1.3 75.5 - - - +
304D ALA* 1.3 63.5 + - - +
306D ASP* 3.2 6.5 + - - +
307D MET* 3.0 17.7 + - - +
335D LEU* 3.6 15.7 - - + +
338D TYR* 3.7 13.6 - - + +
339D LEU* 3.8 37.0 - - + +
342D VAL* 4.0 3.6 - - + +
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Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE* 3.7 20.4 - - + -
64D VAL* 3.7 17.7 - - + -
95D GLN* 5.3 4.0 - - + -
300D ILE 3.0 19.4 + - - +
303D ALA* 1.3 76.0 - - - +
305D SER* 1.3 65.3 + - - +
307D MET* 3.0 4.8 + - - +
308D LEU* 2.9 22.3 + - - +
313D PHE 5.4 0.2 - - - +
314D ILE* 5.4 11.0 - - + +
335D LEU* 4.0 17.4 - - + +
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Residues in contact with SER 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D HIS 5.0 0.5 + - - -
62D LEU* 3.9 10.9 - - - -
63D SER* 2.9 37.0 + - - -
64D VAL* 3.3 12.2 - - - +
301D THR 2.9 17.9 + - - -
302D THR* 3.4 6.9 + - - -
304D ALA* 1.3 75.8 - - - +
306D ASP* 1.3 56.9 + - - +
308D LEU* 2.9 5.9 + - - +
309D SER* 2.8 37.1 + - - -
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Residues in contact with ASP 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D THR* 2.9 41.8 + - - +
303D ALA* 3.5 7.4 - - - +
305D SER* 1.3 76.5 + - - +
307D MET* 1.3 57.6 + - - +
309D SER* 3.2 12.2 + - - -
310D GLU* 3.0 30.7 + - - +
338D TYR* 3.6 25.6 - - + +
341D ASN 4.9 7.6 - - - +
342D VAL* 4.9 1.0 - - - +
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Residues in contact with MET 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ALA 3.0 10.0 + - - +
304D ALA 3.0 6.0 + - - +
306D ASP* 1.3 75.3 - - - +
308D LEU* 1.3 61.9 + - - +
309D SER 3.2 0.7 - - - -
310D GLU 3.8 0.4 - - - +
311D HIS* 3.0 30.2 + - - +
313D PHE* 3.3 44.4 - - + +
314D ILE* 4.5 1.3 - - - -
315D PRO* 3.6 36.1 - - + -
334D MET* 3.8 21.8 - - + -
335D LEU* 3.6 24.9 - - + -
338D TYR* 3.4 31.9 - - + -
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Residues in contact with LEU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D SER* 4.9 11.0 - - - +
64D VAL* 5.7 3.8 - - + -
304D ALA 2.9 11.2 + - - +
305D SER* 3.6 8.5 - - - +
307D MET* 1.3 78.2 - - - +
309D SER* 1.3 58.3 + - - +
310D GLU 3.1 2.8 + - - -
312D SER* 2.8 27.0 + - - -
313D PHE* 3.9 19.5 + - - +
314D ILE* 5.6 3.8 - - + -
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Residues in contact with SER 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D SER* 4.5 12.6 - - - -
305D SER* 2.8 16.5 + - - -
306D ASP* 3.2 17.8 + - - -
308D LEU* 1.3 77.0 - - - +
310D GLU* 1.3 58.0 + - - +
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Residues in contact with GLU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D ASP 3.0 12.4 + - - +
309D SER* 1.3 81.0 - - - +
311D HIS* 1.3 78.8 + - + +
337D ARG* 5.9 0.5 - - - -
338D TYR* 2.7 38.5 + - - +
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Residues in contact with HIS 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D MET* 3.0 20.4 + - + +
310D GLU* 1.3 97.1 + - - +
312D SER* 1.3 70.4 + - - +
313D PHE* 3.1 32.4 + + + +
334D MET* 4.0 23.2 - - + +
337D ARG* 4.4 13.2 + - - -
338D TYR* 2.9 33.8 + + - -
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Residues in contact with SER 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D LEU* 2.8 22.4 + - - -
310D GLU 3.9 0.2 - - - -
311D HIS* 1.3 79.3 - - - +
313D PHE* 1.3 61.4 + - - +
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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
------------------------------------------------------------
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