Contacts of the helix formed by residues 246 - 269 (chain A) in PDB entry 4GV1
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A PHE* 1.3 76.7 - - - +
247A GLU* 1.3 58.1 + - - +
248A ASP* 3.7 7.9 + - - +
249A ARG* 3.1 25.5 + - - +
250A ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 247 (chain A).
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 3.8 0.4 + - - -
246A SER* 1.3 72.7 - - - +
248A ASP* 1.3 59.6 + - - +
250A ALA* 3.4 1.2 + - - +
251A ARG* 2.8 40.4 + - - +
343A MET* 3.8 25.6 - - + -
371A THR 4.5 2.1 - - - +
372A LEU* 3.5 11.1 - - + +
373A GLY* 2.9 32.1 + - - -
375A GLU* 5.3 2.9 - - - +
376A ALA* 3.8 19.5 + - - +
407A PHE* 4.0 11.6 - - + -
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Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 3.3 8.4 + - - +
247A GLU* 1.3 79.2 - - - +
249A ARG* 1.3 56.6 + - - +
251A ARG* 2.8 35.4 + - - +
252A PHE* 3.1 27.4 + - - +
424A PRO* 5.5 2.5 - - + -
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A HIS* 4.4 7.5 - - - +
242A GLU* 2.7 38.2 + - - -
245A PHE* 3.6 33.9 - - + +
246A SER* 3.1 22.3 + - - +
248A ASP* 1.3 72.3 - - - +
250A ALA* 1.3 66.0 + - - +
252A PHE* 3.3 4.9 + - - +
253A TYR* 3.1 57.5 + - + -
282A LEU* 4.7 1.0 - - - +
424A PRO* 3.6 31.6 - - + +
425A PHE* 3.5 34.7 - - - +
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 4.3 2.8 - - + +
246A SER 2.9 13.1 + - - +
247A GLU 3.7 2.5 - - - +
249A ARG* 1.3 75.5 - - - +
251A ARG* 1.3 53.4 + - - +
253A TYR* 3.5 1.7 + - - +
254A GLY* 2.8 33.8 + - - -
339A MET* 3.9 8.1 - - + +
342A MET* 4.0 29.8 - - + +
343A MET* 3.4 38.6 - - + -
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Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLU* 2.8 27.7 + - - +
248A ASP* 2.8 39.9 + - - +
250A ALA* 1.3 70.6 - - - +
252A PHE* 1.3 60.0 + - - +
254A GLY 3.5 0.2 + - - -
255A ALA* 2.9 30.2 + - - +
375A GLU* 5.5 2.4 - - - +
407A PHE* 2.8 69.2 + - + +
408A PHE* 3.6 13.6 - - + +
409A ALA 5.6 2.4 + - - -
411A ILE* 4.2 24.0 - - + -
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Residues in contact with PHE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ASP 3.1 12.6 + - - +
249A ARG 3.3 6.9 + - - +
251A ARG* 1.3 74.9 - - - +
253A TYR* 1.3 84.6 + + - +
255A ALA* 3.3 6.1 + - - +
256A GLU* 3.2 55.5 + - + +
286A GLY 3.6 18.6 - - - -
287A HIS* 3.6 11.0 - - - -
411A ILE* 6.1 0.9 - - - -
421A LEU* 3.8 39.9 - - + -
422A SER 4.2 3.8 - - - -
423A PRO* 3.6 21.1 - - + -
424A PRO* 3.5 26.9 - - + -
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Residues in contact with TYR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LEU* 3.9 11.9 - - + -
245A PHE* 3.6 29.4 - + - -
249A ARG* 3.1 59.3 + - + -
250A ALA 3.9 4.0 - - - +
252A PHE* 1.3 105.8 - + - +
254A GLY* 1.3 56.1 + - - +
256A GLU* 3.2 4.0 + - - +
257A ILE* 2.9 34.9 + - + +
282A LEU* 3.6 27.0 - - + +
286A GLY 3.9 4.0 + - - -
288A ILE* 3.7 26.6 - - + +
342A MET* 4.1 17.3 - - + -
424A PRO* 4.8 2.9 - - + +
425A PHE* 4.0 8.1 + - - +
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Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ALA 2.8 21.0 + - - -
251A ARG 3.7 1.3 - - - -
253A TYR* 1.3 72.3 - - - +
255A ALA* 1.3 56.4 + - - +
257A ILE* 3.4 10.1 + - - +
258A VAL* 2.9 37.3 + - - +
335A LEU* 4.6 0.4 - - - -
339A MET* 3.9 24.9 - - - -
342A MET* 5.1 1.0 - - - +
408A PHE* 4.2 4.0 - - - -
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG 2.9 20.9 + - - +
252A PHE* 3.7 6.7 - - - +
253A TYR 3.3 0.2 - - - -
254A GLY* 1.3 72.9 - - - +
256A GLU* 1.3 58.2 + - + +
258A VAL 3.3 0.7 + - - -
259A SER* 2.9 26.3 + - - -
408A PHE* 3.8 8.6 - - + -
411A ILE* 4.6 8.7 - - + -
413A TRP* 3.4 35.4 - - + -
416A VAL* 3.8 18.1 - - + +
421A LEU* 5.4 2.2 - - + -
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 3.3 51.3 - - + -
252A PHE* 3.2 30.6 + - + +
253A TYR 3.2 8.1 + - - +
255A ALA* 1.3 76.0 - - + +
257A ILE* 1.3 61.8 + - - +
259A SER 3.3 1.0 + - - -
260A ALA* 3.1 19.9 + - - +
287A HIS* 2.6 33.6 + - - -
288A ILE* 2.9 41.9 + - + +
416A VAL* 4.1 9.5 - - + +
419A LYS* 5.1 0.2 - - - -
421A LEU* 5.5 1.9 - - + +
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A TYR* 2.9 29.3 + - + +
254A GLY* 3.7 6.3 - - - +
256A GLU* 1.3 73.4 - - - +
258A VAL* 1.3 60.0 + - - +
260A ALA* 3.2 6.2 + - - +
261A LEU* 2.9 50.1 + - + +
275A LEU* 4.0 15.5 - - + -
280A LEU* 3.8 38.8 - - + -
288A ILE* 4.3 13.7 - - + -
290A ILE* 4.7 4.5 - - + -
335A LEU* 3.7 18.6 - - + -
338A VAL* 4.6 1.8 - - + -
342A MET* 4.1 15.0 - - + -
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLY 2.9 23.7 + - - +
255A ALA 3.3 3.6 + - - +
257A ILE* 1.3 75.1 - - - +
259A SER* 1.3 54.5 + - - +
261A LEU* 4.0 0.6 - - - +
262A ASP* 2.8 36.9 + - - +
332A TRP* 4.5 11.0 - - + -
335A LEU* 3.5 30.1 - - + -
399A ALA* 4.5 12.6 - - + +
402A ILE* 4.0 14.6 - - + -
403A MET* 3.7 33.2 - - + -
408A PHE* 4.7 6.3 - - + -
413A TRP* 3.9 9.4 - - + -
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Residues in contact with SER 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A HIS* 3.3 22.8 + - - -
209A PHE* 4.1 7.1 - - - -
255A ALA 2.9 14.5 + - - -
256A GLU 3.4 10.1 - - - -
257A ILE 3.3 0.2 - - - -
258A VAL* 1.3 78.3 - - - +
260A ALA* 1.3 61.1 + - - +
262A ASP* 3.6 6.5 + - - +
263A TYR* 3.2 17.8 + - - +
403A MET* 6.3 0.7 - - - -
413A TRP* 5.0 8.4 + - - -
416A VAL* 4.0 15.3 - - - -
417A TYR* 4.2 14.7 - - - +
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A HIS* 3.5 19.4 - - + -
209A PHE* 4.1 8.3 - - + -
210A LEU* 4.0 14.3 - - + +
256A GLU 3.1 13.6 + - - +
257A ILE 3.6 7.4 - - - +
259A SER* 1.3 75.2 - - - +
261A LEU* 1.3 58.4 + - - +
263A TYR* 3.3 6.1 + - - +
264A LEU* 3.0 31.9 + - - +
290A ILE* 3.8 24.0 - - + -
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ILE* 2.9 39.1 + - + +
260A ALA* 1.3 73.6 - - - +
262A ASP* 1.3 60.7 + - - +
264A LEU* 3.3 8.8 + - + +
265A HIS* 2.9 38.0 + - + +
272A TYR* 3.9 30.5 - - + -
275A LEU* 4.4 15.7 - - + -
290A ILE* 4.9 5.6 - - + -
331A ASP* 3.9 26.7 - - + +
332A TRP* 3.5 39.0 - - + -
335A LEU* 4.8 1.6 - - + -
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A VAL 2.8 22.4 + - - +
259A SER* 3.6 7.3 - - - +
261A LEU* 1.3 73.1 - - - +
263A TYR* 1.3 52.6 + - - +
265A HIS* 4.7 2.9 - - - -
266A SER* 2.8 51.1 + - - -
332A TRP* 4.3 1.6 - - - -
398A ASP* 5.2 1.1 - - - +
399A ALA* 3.5 27.0 - - + +
400A LYS* 2.7 37.1 + - - -
403A MET* 4.2 13.1 - - - +
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Residues in contact with TYR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASN 4.1 0.2 + - - -
205A SER* 3.5 2.3 - - - -
206A ARG* 3.0 37.5 + - - +
207A HIS* 3.4 35.9 - + + +
210A LEU* 3.9 24.7 - - + -
259A SER 3.2 5.3 + - - +
260A ALA 3.4 7.6 - - - +
261A LEU 3.3 0.2 - - - -
262A ASP* 1.3 78.9 - - - +
264A LEU* 1.3 65.5 + - + +
266A SER* 5.0 0.2 - - - -
267A GLU* 2.8 73.1 + - + +
268A LYS* 3.3 40.0 + - + -
417A TYR* 5.8 2.0 - + - -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A VAL* 4.9 8.1 - - + -
205A SER* 4.9 6.1 - - - -
210A LEU* 3.9 35.4 - - + -
260A ALA 3.0 17.8 + - - +
261A LEU* 3.3 14.8 + - + +
263A TYR* 1.3 87.1 - - + +
265A HIS* 1.3 58.5 + - + +
268A LYS* 3.3 11.4 + - + -
269A ASN 2.9 12.0 + - - -
270A VAL* 2.9 54.1 + - + +
272A TYR* 4.4 30.3 - - + +
290A ILE* 5.8 0.7 - - + -
293A PHE* 4.6 4.3 - - + -
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Residues in contact with HIS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU* 2.9 23.5 + - - +
262A ASP 3.9 2.7 - - - +
264A LEU* 1.3 74.7 - - + +
266A SER* 1.3 63.1 + - - +
269A ASN* 3.3 24.6 + - - +
270A VAL 3.2 23.8 - - - +
271A VAL* 4.3 2.4 - - + -
300A ILE 4.5 2.9 - - - +
302A ASP 5.9 0.5 + - - -
328A ARG* 3.4 46.1 + - + +
331A ASP* 2.7 29.5 + - + +
332A TRP* 3.6 26.8 - + - -
398A ASP* 2.7 34.0 + - - +
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ASP* 2.8 40.3 + - - -
265A HIS* 1.3 76.9 - - - +
267A GLU* 1.3 66.0 + - - +
269A ASN* 4.4 6.3 - - - +
328A ARG* 5.9 2.3 + - - +
398A ASP* 4.8 4.7 + - - +
400A LYS* 3.3 12.9 + - - -
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A TYR* 2.8 51.4 + - + +
266A SER* 1.3 81.6 - - - +
268A LYS* 1.3 71.7 + - + +
269A ASN* 3.8 2.6 + - - -
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Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASN* 2.8 56.6 + - + +
205A SER* 4.8 2.2 - - - -
263A TYR* 3.3 40.5 + - + +
264A LEU* 3.3 19.6 + - + +
267A GLU* 1.3 90.1 + - - +
269A ASN* 1.3 72.1 + - - +
270A VAL* 3.3 20.1 + - + +
298A GLU* 5.8 0.3 - - - +
299A GLY 4.9 1.9 + - - -
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LEU 2.9 3.8 + - - -
265A HIS* 3.3 16.0 + - - +
266A SER 4.4 7.3 - - - +
267A GLU 5.4 2.1 + - - -
268A LYS* 1.3 79.1 - - - +
270A VAL* 1.3 58.3 + - - +
297A LYS 3.7 0.2 - - - +
298A GLU* 3.6 0.7 - - - -
299A GLY* 3.0 17.3 + - - -
300A ILE* 2.9 47.8 + - - +
301A LYS* 3.8 43.8 + - - +
302A ASP 5.0 0.5 + - - -
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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