Contacts of the helix formed by residues 292 - 313 (chain F) in PDB entry 1R4N
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 VAL 292 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 3.3 26.9 - - + +
19E LEU* 3.6 25.1 - - + -
20E TRP* 4.0 16.4 - - + -
52E PRO* 5.7 1.8 - - + -
89F ASN* 4.5 4.5 - - - +
90F ARG* 4.1 9.0 - - - +
182F THR* 5.8 0.3 - - - +
184F GLY 4.9 1.8 + - - +
185F PHE* 4.4 11.7 - - + -
291F ALA* 1.3 82.7 - - - +
293F ALA* 1.3 66.5 + - - +
294F SER* 3.4 27.4 - - - +
295F THR* 3.9 12.7 + - - +
296F ASN* 3.7 13.5 + - - -
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Residues in contact with ALA 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ASN* 3.8 33.9 - - - +
51E LEU* 4.3 16.2 - - + -
52E PRO* 4.7 5.6 - - + +
62F GLU* 5.0 3.3 - - - +
89F ASN 4.4 4.7 + - - +
90F ARG* 3.7 23.4 - - + +
292F VAL* 1.3 71.2 - - - +
294F SER* 1.3 70.4 + - - +
296F ASN* 2.9 20.2 + - - +
297F ALA* 2.9 9.8 + - - +
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Residues in contact with SER 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ASN* 4.3 10.8 + - - +
52E PRO* 5.5 0.9 - - - +
499E GLY* 3.7 15.9 - - - -
502E ALA* 5.1 0.3 - - - +
503E GLN* 3.3 43.4 + - - +
506E ILE* 4.3 8.7 - - - +
185F PHE* 4.9 0.4 - - - -
292F VAL* 3.4 18.0 - - - +
293F ALA* 1.3 75.5 - - - +
295F THR* 1.3 65.2 + - - +
297F ALA* 3.1 17.7 - - - +
298F VAL* 3.3 11.2 + - - +
326F ASP* 4.8 1.8 - - - -
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Residues in contact with THR 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F THR* 3.3 22.7 - - - +
184F GLY 2.9 27.5 + - - +
185F PHE* 3.4 23.1 + - - +
186F LYS 3.8 18.8 - - - +
187F GLY* 4.6 0.2 - - - -
292F VAL* 3.9 9.0 + - - +
293F ALA 2.9 3.2 + - - -
294F SER* 1.3 76.1 - - - +
296F ASN* 1.3 67.6 + - - +
298F VAL* 2.8 20.2 + - - +
299F ILE* 3.1 17.6 + - + +
324F PHE* 4.9 5.4 - - + -
326F ASP* 4.4 5.4 + - - -
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Residues in contact with ASN 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F GLY* 3.6 29.8 - - - +
59F LEU* 3.8 14.7 - - - +
62F GLU* 4.6 4.7 - - - +
90F ARG* 3.6 33.4 - - - +
182F THR* 3.0 34.6 + - - +
291F ALA* 4.9 1.4 - - - +
292F VAL 3.7 9.0 + - - -
293F ALA* 2.9 9.8 + - - +
295F THR* 1.3 76.5 - - - +
297F ALA* 1.3 66.7 + - - +
299F ILE 4.8 0.2 - - - +
300F ALA* 2.9 29.1 + - - +
176K GLY* 3.9 5.0 + - - +
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Residues in contact with ALA 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLU* 5.9 0.7 - - - +
48E ASN* 3.6 25.8 - - - +
495E ALA* 4.6 6.5 - - + +
499E GLY* 3.8 13.7 - - - +
62F GLU* 3.7 24.7 + - - +
293F ALA 2.9 6.7 + - - +
294F SER 3.1 12.6 - - - +
296F ASN* 1.3 76.2 - - - +
298F VAL* 1.3 53.5 + - - +
300F ALA* 3.8 1.6 - - - +
301F ALA* 2.8 37.4 + - - +
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Residues in contact with VAL 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E PHE* 3.4 40.7 - - + +
499E GLY 3.8 1.6 - - - -
500E ALA* 3.6 26.2 - - + +
294F SER 3.5 14.6 - - - +
295F THR* 2.8 8.4 + - - +
297F ALA* 1.3 73.0 - - - +
299F ILE* 1.3 71.0 + - + +
301F ALA* 3.0 6.4 + - - +
302F VAL* 3.0 24.5 + - + +
324F PHE* 3.6 42.4 - - + -
326F ASP* 5.2 0.7 - - - +
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Residues in contact with ILE 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F LEU* 3.9 14.4 - - + -
180F GLY* 3.9 8.3 - - - -
181F GLY 3.5 24.2 - - - +
182F THR* 4.2 4.5 - - - +
187F GLY* 3.6 13.0 - - - +
188F ASN* 3.3 43.7 - - - +
189F ALA* 4.1 6.7 - - + +
295F THR* 3.1 10.8 + - + +
296F ASN 4.0 4.0 - - - +
298F VAL* 1.3 81.2 - - + +
300F ALA* 1.3 56.5 + - - +
302F VAL* 2.7 30.3 + - + +
303F CYS* 3.0 19.7 + - - -
322F LEU* 5.3 3.8 - - + +
324F PHE* 4.3 13.2 - - + -
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Residues in contact with ALA 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F LEU* 3.9 16.8 - - + +
62F GLU* 3.5 30.3 - - + -
63F LEU* 3.7 18.2 - - + +
66F ASN* 3.6 5.3 + - - +
296F ASN 2.9 21.2 + - - +
299F ILE* 1.3 75.0 - - - +
301F ALA* 1.3 57.5 + - - +
302F VAL 3.1 0.2 + - - -
303F CYS* 3.3 2.8 + - - -
304F ALA* 2.8 31.4 + - - +
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Residues in contact with ALA 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492E THR 3.4 12.7 - - - +
495E ALA* 3.5 9.6 - - + -
496E PHE* 3.3 33.0 - - + +
522E TYR* 5.2 0.9 + - - -
66F ASN* 3.5 11.6 - - - +
297F ALA 2.8 19.9 + - - +
298F VAL 3.0 5.4 + - - +
300F ALA* 1.3 75.3 - - - +
302F VAL* 1.3 61.4 + - - +
304F ALA* 3.6 3.4 - - - +
305F THR* 3.2 23.7 + - - -
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Residues in contact with VAL 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E PHE* 3.8 24.5 - - + -
522E TYR* 4.3 2.7 - - - +
527E GLN* 3.0 31.6 - - + +
189F ALA* 4.0 20.0 - - + -
298F VAL* 3.0 19.5 + - + +
299F ILE* 2.7 13.8 + - + +
301F ALA* 1.3 74.2 - - - +
303F CYS* 1.3 68.6 + - - +
304F ALA 3.0 0.9 - - - -
305F THR* 2.9 17.0 + - - -
306F GLU* 3.1 15.0 + - + +
318F LEU* 4.9 4.5 - - + -
322F LEU* 4.2 16.8 - - + -
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Residues in contact with CYS 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F LEU* 5.8 0.4 - - - -
63F LEU* 4.2 14.1 - - + -
142F VAL* 4.3 4.0 - - + -
143F CYS 5.4 1.3 - - - -
178F ILE* 3.3 27.9 - - + +
179F ASP 3.9 8.5 - - - -
180F GLY* 4.1 5.4 - - - -
189F ALA* 3.8 21.3 - - - -
299F ILE* 3.0 24.0 + - - -
300F ALA* 3.8 5.8 - - - +
302F VAL* 1.3 75.0 - - - +
304F ALA* 1.3 67.5 + - - +
306F GLU* 3.1 7.6 + - - +
307F VAL* 3.0 23.7 + - - +
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Residues in contact with ALA 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492E THR* 3.5 12.8 - - + -
63F LEU* 4.1 8.9 - - + +
66F ASN* 3.4 33.9 - - + +
67F LEU* 4.7 8.6 - - + +
70F SER* 5.6 0.8 + - - -
300F ALA 2.8 19.5 + - - +
301F ALA 3.6 4.3 - - - +
303F CYS* 1.3 79.1 - - - +
305F THR* 1.3 65.2 + - - +
307F VAL* 2.9 16.2 + - - +
308F PHE* 3.1 10.6 + - - +
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Residues in contact with THR 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E LEU* 5.1 13.5 - - + -
492E THR* 2.8 38.4 + - - +
493E ILE* 4.8 4.0 - - + +
522E TYR* 5.0 1.0 + - - -
524E GLY* 5.1 1.3 - - - +
527E GLN* 3.9 15.9 + - - +
301F ALA 3.2 6.3 + - - -
302F VAL 2.9 9.0 + - - -
304F ALA* 1.3 77.5 - - - +
306F GLU* 1.3 53.1 + - - +
308F PHE* 2.8 14.0 + - + +
309F LYS* 2.7 60.6 + - + +
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Residues in contact with GLU 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527E GLN* 3.3 28.8 + - - +
178F ILE* 4.3 6.5 - - + -
191F VAL* 3.2 34.1 - - + -
302F VAL* 3.1 10.8 + - + +
303F CYS* 3.1 13.6 + - - +
305F THR* 1.3 76.7 - - - +
307F VAL* 1.3 52.6 + - - +
309F LYS* 2.9 28.5 + - - +
310F ILE* 2.6 41.6 + - + +
317F PRO* 3.4 3.1 - - + +
318F LEU* 2.6 34.9 + - + +
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Residues in contact with VAL 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F VAL* 4.7 3.6 - - + -
67F LEU* 3.7 16.4 - - + -
72F PHE* 3.7 19.7 - - + -
140F ILE* 3.7 34.3 - - + -
142F VAL* 3.5 31.9 - - + -
178F ILE* 4.2 5.4 - - + +
303F CYS 3.0 17.3 + - - +
304F ALA* 2.9 9.6 + - - +
306F GLU* 1.3 73.6 - - - +
308F PHE* 1.3 56.7 + - - +
310F ILE* 3.0 6.5 + - - +
311F ALA* 2.7 33.4 + - - +
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Residues in contact with PHE 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492E THR* 5.6 1.8 - - + +
20F VAL* 3.6 19.1 - - + -
23F PHE* 4.5 16.8 - + + -
24F LEU* 3.6 22.9 - - + -
45F LEU* 4.1 3.4 - - + -
70F SER* 3.6 36.8 - - - +
72F PHE* 4.0 23.1 - + + -
304F ALA 3.1 6.5 + - - +
305F THR* 2.8 16.5 + - + +
307F VAL* 1.3 79.9 - - - +
309F LYS* 1.3 60.0 + - + +
312F THR* 2.6 63.6 + - + +
314F ALA* 4.3 11.4 - - + -
315F TYR* 5.7 2.5 - + - -
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Residues in contact with LYS 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E LEU* 5.1 2.0 - - - -
524E GLY 2.9 28.5 + - - -
525E MET* 3.2 14.6 + - - +
527E GLN* 3.6 10.3 - - - +
305F THR* 2.7 36.2 + - + +
306F GLU* 3.1 34.8 + - - +
308F PHE* 1.3 74.5 - - + +
310F ILE* 1.3 59.4 + - - +
312F THR* 4.1 3.1 - - - -
313F SER* 2.4 37.2 + - - +
314F ALA* 4.7 2.7 - - - +
315F TYR* 3.9 41.1 - - + +
316F ILE 3.7 14.7 + - - +
317F PRO* 4.7 4.7 - - + -
318F LEU 4.6 0.4 - - - +
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Residues in contact with ILE 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F ILE* 3.9 13.5 - - + -
176F PRO* 3.8 31.0 - - + -
178F ILE* 3.6 32.1 - - + -
191F VAL* 4.3 18.2 - - + -
193F LEU* 4.9 4.3 - - + -
306F GLU* 2.6 21.7 + - - +
307F VAL 3.5 4.3 - - - +
309F LYS* 1.3 75.0 - - - +
311F ALA* 1.3 61.9 + - - +
313F SER* 3.7 12.2 + - - +
317F PRO* 4.0 24.9 - - + +
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Residues in contact with ALA 311 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 4.0 11.0 - - + +
49F CYS* 4.1 8.9 - - - -
72F PHE* 3.7 23.1 - - + -
140F ILE* 3.6 19.1 - - + -
307F VAL 2.7 19.5 + - - +
308F PHE 4.1 0.9 - - - +
310F ILE* 1.3 76.9 - - - +
312F THR* 1.3 60.5 + - - +
313F SER* 4.6 1.0 + - - -
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Residues in contact with THR 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F LEU* 3.4 31.4 - - + +
35F PHE* 4.1 9.5 - - - -
41F SER 6.1 0.2 - - - +
45F LEU* 3.9 21.5 - - + -
308F PHE* 2.6 43.6 + - + +
309F LYS 3.7 0.2 + - - -
311F ALA* 1.3 77.2 - - - +
313F SER* 1.3 73.1 + - - +
314F ALA* 3.4 18.1 + - - +
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Residues in contact with SER 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F HIS* 3.5 28.7 - - - +
34F ASP* 4.7 13.1 - - - +
35F PHE* 3.1 23.0 - - - +
309F LYS 2.4 27.2 + - - -
310F ILE* 3.7 11.4 + - - +
311F ALA 4.6 1.2 + - - -
312F THR* 1.3 72.5 - - - +
314F ALA* 1.3 57.2 + - - +
315F TYR 3.2 10.3 - - - +
317F PRO* 6.3 0.4 - - - -
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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