Contacts of the helix formed by residues 292 - 313 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLN* 3.3 27.4 - - + +
19A LEU* 3.5 24.5 - - + -
20A TRP* 4.2 15.7 - - + -
52A PRO* 5.8 2.2 - - + -
89B ASN* 4.5 7.4 - - - +
90B ARG* 4.1 6.3 - - - +
182B THR* 5.9 0.3 - - - +
184B GLY 5.0 2.5 + - - +
185B PHE* 4.3 11.4 - - + -
291B ALA* 1.3 83.6 - - - +
293B ALA* 1.3 66.8 + - - +
294B SER* 3.4 27.6 - - - +
295B THR* 3.8 9.8 + - - +
296B ASN* 3.7 16.5 + - - -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 3.7 33.2 - - - +
51A LEU* 4.3 16.4 - - + -
52A PRO* 4.8 5.6 - - + +
62B GLU* 5.0 3.7 - - - +
89B ASN 4.4 4.9 + - - +
90B ARG* 3.8 24.4 - - + +
292B VAL* 1.3 70.5 - - - +
294B SER* 1.3 72.6 + - - +
296B ASN* 2.9 20.4 + - - +
297B ALA* 3.0 8.9 + - - -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 4.3 11.4 + - - +
52A PRO* 5.5 1.2 - - - +
499A GLY* 3.6 15.0 - - - -
502A ALA* 5.0 0.3 - - - +
503A GLN* 3.4 41.9 + - - +
506A ILE* 4.4 7.8 - - - +
185B PHE* 4.9 0.4 - - - -
292B VAL* 3.4 19.1 - - - +
293B ALA* 1.3 74.8 + - - +
295B THR* 1.3 66.1 + - - +
297B ALA* 3.1 17.4 - - - +
298B VAL* 3.3 10.7 + - - +
326B ASP* 4.8 2.2 - - - -
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR* 3.3 22.7 - - - +
184B GLY 3.0 26.9 + - - +
185B PHE* 3.5 23.7 + - - +
186B LYS 3.8 18.4 - - - +
187B GLY* 4.7 0.2 - - - -
292B VAL* 3.8 8.5 + - - +
293B ALA 2.9 2.8 + - - -
294B SER* 1.3 72.5 - - - +
296B ASN* 1.3 68.3 + - - +
298B VAL* 2.8 20.2 + - - +
299B ILE* 3.2 17.0 + - + -
324B PHE* 4.9 5.6 - - + -
326B ASP* 4.3 5.8 + - - -
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Residues in contact with ASN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY* 3.5 37.1 - - - +
59B LEU* 3.8 14.4 - - + +
62B GLU* 4.6 5.2 - - - +
90B ARG* 3.6 26.2 - - - +
182B THR* 3.0 36.5 + - - +
291B ALA* 4.9 1.2 - - - +
292B VAL 3.7 9.0 + - - -
293B ALA* 2.9 10.4 + - - +
295B THR* 1.3 76.1 - - - +
297B ALA* 1.3 64.4 + - - +
299B ILE 4.8 0.2 - - - +
300B ALA* 2.8 28.8 + - - +
176I GLY* 3.8 4.7 + - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 5.9 0.7 - - - +
48A ASN* 3.7 24.7 - - - +
495A ALA* 4.5 7.0 - - + +
499A GLY* 3.8 13.9 - - - +
62B GLU* 3.7 25.6 + - - +
293B ALA 3.0 6.9 + - - +
294B SER 3.1 12.8 - - - +
296B ASN* 1.3 76.3 - - - +
298B VAL* 1.3 53.5 + - - +
300B ALA* 3.8 1.2 - - - +
301B ALA* 2.8 38.5 + - - +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PHE* 3.2 41.6 - - + +
499A GLY 3.8 1.3 - - - -
500A ALA* 3.6 25.1 - - + +
294B SER 3.5 14.6 - - - +
295B THR 2.8 12.8 + - - +
297B ALA* 1.3 67.7 - - - +
299B ILE* 1.3 71.5 + - + +
301B ALA* 3.0 14.0 + - - +
302B VAL* 3.0 14.9 + - + +
324B PHE* 3.6 43.5 - - + -
326B ASP* 5.2 0.2 - - - +
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.8 17.9 - - + -
180B GLY* 3.9 8.1 - - - -
181B GLY 3.5 22.0 - - - +
182B THR* 4.2 5.2 - - - +
187B GLY* 3.5 12.3 - - - -
188B ASN* 3.3 43.1 - - - +
189B ALA* 4.1 6.3 - - + +
295B THR* 3.2 11.0 + - + +
296B ASN 4.0 4.0 - - - +
298B VAL* 1.3 80.1 - - + +
300B ALA* 1.3 56.5 + - - +
302B VAL* 2.7 29.5 + - + +
303B CYS* 3.0 16.7 + - - -
322B LEU* 5.3 3.4 - - + +
324B PHE* 4.3 13.0 - - + -
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.8 18.1 - - + +
62B GLU* 3.5 30.1 - - + -
63B LEU* 3.8 18.4 - - + +
66B ASN* 3.6 5.3 + - - +
296B ASN 2.8 21.3 + - - +
299B ILE* 1.3 75.0 - - - +
301B ALA* 1.3 57.1 + - - +
302B VAL 3.0 0.2 + - - -
303B CYS* 3.3 3.0 + - - -
304B ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A THR 3.4 13.8 - - - +
495A ALA* 3.6 9.4 - - + -
496A PHE* 3.3 32.8 - - + +
522A TYR* 5.0 1.1 + - - -
66B ASN* 3.5 11.4 - - - +
297B ALA 2.8 23.9 + - - +
298B VAL 3.0 4.5 + - - +
300B ALA* 1.3 73.1 - - - +
302B VAL* 1.3 61.1 + - - +
304B ALA* 3.6 2.9 - - - +
305B THR* 3.2 23.9 + - - -
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PHE* 3.8 24.5 - - + -
522A TYR* 4.0 3.6 - - - +
527A GLN* 2.9 32.5 - - + +
189B ALA* 3.9 20.2 - - + -
298B VAL* 3.0 17.9 + - + +
299B ILE* 2.7 18.0 + - + +
301B ALA* 1.3 69.7 - - - +
303B CYS* 1.3 68.7 + - - +
304B ALA 3.0 0.9 - - - -
305B THR* 3.0 15.2 + - - -
306B GLU* 3.1 15.5 + - + +
318B LEU* 4.9 4.5 - - + -
322B LEU* 4.2 16.4 - - + -
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Residues in contact with CYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 5.8 0.4 - - - -
63B LEU* 4.2 13.0 - - + -
142B VAL* 4.2 3.6 - - + -
143B CYS 5.4 2.0 - - - -
178B ILE* 3.3 23.3 - - + +
179B ASP 3.8 23.6 - - - -
180B GLY* 4.0 5.8 - - - -
189B ALA* 3.9 12.8 - - - -
299B ILE* 3.0 24.0 + - - -
300B ALA* 3.8 6.1 - - - +
302B VAL* 1.3 80.5 - - - +
304B ALA* 1.3 65.6 + - - +
306B GLU* 3.1 6.9 + - - +
307B VAL* 2.9 24.7 + - - +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A THR* 3.4 23.3 - - + -
63B LEU* 4.1 10.0 - - + +
66B ASN* 3.4 22.9 - - + +
67B LEU* 4.7 8.8 - - + +
70B SER* 5.6 0.8 - - - -
300B ALA 2.9 18.4 + - - +
301B ALA 3.6 4.3 - - - +
303B CYS* 1.3 78.9 - - - +
305B THR* 1.3 66.2 + - - +
307B VAL* 2.9 15.5 + - - +
308B PHE* 3.1 11.3 + - - +
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.0 14.8 - - + -
492A THR* 2.8 35.5 + - - +
493A ILE* 4.7 4.7 + - - +
522A TYR* 4.9 0.7 + - - -
524A GLY* 4.8 2.2 - - - +
527A GLN* 3.8 15.9 + - - +
301B ALA 3.2 6.8 + - - -
302B VAL 3.0 9.0 + - - -
304B ALA* 1.3 78.3 - - - +
306B GLU* 1.3 52.5 + - - +
308B PHE* 2.9 13.9 + - + +
309B LYS* 2.7 59.2 + - + +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A GLN* 3.1 29.8 + - - +
178B ILE* 4.3 5.2 - - + -
191B VAL* 3.2 34.3 - - + -
302B VAL* 3.1 11.4 + - + +
303B CYS* 3.3 13.5 - - - +
305B THR* 1.3 76.5 - - - +
307B VAL* 1.3 54.5 + - - +
309B LYS* 2.9 28.2 + - - +
310B ILE* 2.7 41.2 + - + +
317B PRO* 3.4 3.6 - - + +
318B LEU* 2.6 35.4 + - + +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.6 3.8 - - + -
67B LEU* 3.7 16.6 - - + -
72B PHE* 3.7 19.7 - - + -
140B ILE* 3.6 34.5 - - + -
142B VAL* 3.4 36.3 - - + -
178B ILE* 4.2 4.9 - - + +
303B CYS 2.9 12.4 + - - +
304B ALA* 2.9 9.2 + - - +
306B GLU* 1.3 74.9 - - - +
308B PHE* 1.3 56.6 + - - +
310B ILE* 3.0 7.1 + - - +
311B ALA* 2.7 33.6 + - - +
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A THR* 5.7 1.3 - - + +
20B VAL* 3.6 17.9 - - + -
23B PHE* 4.5 16.6 - + + -
24B LEU* 3.7 22.4 - - + -
45B LEU* 4.1 3.6 - - + -
70B SER* 3.6 35.9 - - - -
72B PHE* 3.9 23.1 - + + -
304B ALA 3.1 6.9 + - - +
305B THR* 2.9 16.9 + - + +
307B VAL* 1.3 79.9 - - - +
309B LYS* 1.3 62.9 + - + +
312B THR* 2.6 60.3 + - + +
314B ALA* 4.3 11.4 - - + -
315B TYR* 5.7 2.5 - + - -
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 5.0 2.7 - - + -
524A GLY 2.8 30.9 + - - -
525A MET* 3.0 16.4 + - - +
527A GLN* 3.7 8.5 - - - +
305B THR* 2.7 34.7 + - + +
306B GLU* 3.1 35.0 + - - +
308B PHE* 1.3 74.6 - - + +
310B ILE* 1.3 61.0 + - - +
312B THR* 4.1 3.4 - - - -
313B SER* 2.4 38.3 + - - +
314B ALA* 4.6 2.7 - - - +
315B TYR* 3.9 38.8 - - + +
316B ILE 3.7 13.8 + - - +
317B PRO* 4.7 4.9 - - + -
318B LEU 4.6 0.6 - - - +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 3.9 13.7 - - + -
176B PRO* 3.8 31.9 - - + -
178B ILE* 3.5 33.4 - - + -
191B VAL* 4.3 17.7 - - + -
193B LEU* 4.9 3.8 - - + -
306B GLU* 2.7 19.3 + - + +
307B VAL 3.4 6.5 - - - +
309B LYS* 1.3 74.9 - - - +
311B ALA* 1.3 63.1 + - - +
312B THR 3.5 0.2 + - - -
313B SER* 3.6 12.8 + - - +
317B PRO* 4.0 25.1 - - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.0 7.4 - - + +
49B CYS* 4.0 13.4 - - - -
72B PHE* 3.7 24.9 - - + -
140B ILE* 3.6 19.1 - - + -
307B VAL 2.7 19.2 + - - +
308B PHE 4.1 0.9 - - - +
310B ILE* 1.3 77.5 - - - +
312B THR* 1.3 59.8 + - - +
313B SER* 4.6 1.4 + - - -
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.4 30.7 - - + -
35B PHE* 4.1 9.5 - - - -
41B SER 6.1 0.2 - - - +
45B LEU* 3.9 21.1 - - + -
308B PHE* 2.6 45.8 + - + +
311B ALA* 1.3 77.9 - - - +
313B SER* 1.3 73.8 + - - +
314B ALA* 3.3 18.3 + - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 3.4 31.7 - - - +
34B ASP* 4.7 13.1 - - - +
35B PHE* 3.1 22.8 - - - +
309B LYS 2.4 27.4 + - - -
310B ILE 3.6 11.0 + - - -
311B ALA 4.6 1.2 + - - -
312B THR* 1.3 72.2 - - - +
314B ALA* 1.3 53.5 + - - +
315B TYR 3.2 10.3 - - - +
317B PRO* 6.3 0.9 - - - -
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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