Contacts of the helix formed by residues 18 - 40 (chain 9) in PDB entry 6B8H
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 18 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160 THR 4.5 3.5 + - - -
170 ILE* 4.5 6.9 - - - +
190 LEU 5.0 0.7 - - - -
200 LEU* 3.8 24.3 - - - +
159 SER 4.1 4.2 + - - -
169 THR 3.2 1.2 - - - -
179 ILE* 1.3 78.0 - - - +
199 LEU* 1.3 62.0 + - - +
209 LEU 3.2 0.7 - - - -
219 GLY* 3.2 15.6 + - - -
229 ALA 4.1 2.1 + - - -
619 THR 5.5 0.2 - - - +
629 GLY* 4.9 5.2 - - - -
659 CYS* 4.1 23.8 - - - -
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Residues in contact with LEU 19 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188 GLY 4.8 1.8 - - - -
618 THR* 4.2 13.0 - - - +
648 PHE* 3.9 35.0 - - + -
658 CYS* 3.6 28.5 - - - +
169 THR* 3.6 22.0 - - - +
179 ILE 3.0 1.6 + - - -
189 GLY* 1.3 74.6 - - - +
209 LEU* 1.3 59.6 + - - +
229 ALA* 3.2 10.1 + - + +
239 GLY* 3.0 22.5 + - - -
629 GLY* 3.3 37.2 - - - +
659 CYS* 5.0 3.6 - - + +
669 LEU* 4.3 19.1 - - + -
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Residues in contact with LEU 20 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200 LEU* 4.2 24.2 - - + -
240 ILE* 5.0 1.6 - - + -
178 ILE* 4.4 6.7 - - + +
188 GLY* 3.8 21.5 + - - +
208 LEU* 4.4 22.2 - - + -
218 GLY* 3.8 22.4 - - - +
179 ILE* 3.2 32.9 + - + +
189 GLY 3.2 1.0 - - - -
199 LEU* 1.3 75.4 - - - +
219 GLY* 1.3 64.0 + - - +
239 GLY* 4.2 0.4 - - - +
249 ILE* 2.9 51.3 + - + +
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Residues in contact with GLY 21 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200 LEU* 3.8 16.3 - - - +
230 GLY* 3.7 9.7 - - - +
240 ILE* 3.6 28.6 - - - +
189 GLY 3.2 10.1 + - - -
199 LEU 3.1 1.4 - - - -
209 LEU* 1.3 81.9 - - - +
229 ALA* 1.3 56.4 + - - +
249 ILE 3.5 0.2 + - - -
259 GLY* 2.9 24.6 + - - -
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Residues in contact with ALA 22 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230 GLY* 4.7 6.7 - - - -
618 THR* 4.8 8.1 - - + -
189 GLY 4.1 2.4 + - - -
199 LEU* 3.2 11.1 + - + +
219 GLY* 1.3 74.9 - - - +
239 GLY* 1.3 59.8 + - - +
259 GLY 4.4 0.2 - - - +
269 ILE* 3.0 51.7 + - + +
589 SER* 3.6 25.1 - - - +
599 GLU* 4.9 2.5 - - - +
619 THR* 4.9 0.2 - - - +
629 GLY* 4.3 14.6 - - - +
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Residues in contact with GLY 23 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218 GLY* 3.1 26.5 - - - +
228 ALA 4.5 1.6 - - - -
258 GLY* 3.6 6.6 - - - -
588 SER* 3.3 16.7 + - - -
618 THR* 3.7 21.7 + - - -
199 LEU 3.0 13.7 + - - -
209 LEU* 3.3 3.9 + - - -
229 ALA* 1.3 75.8 - - - +
249 ILE* 1.3 58.4 + - - +
269 ILE* 4.8 0.7 - - - -
279 ALA* 4.2 3.5 + - - +
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Residues in contact with ILE 24 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240 ILE* 4.6 18.2 - - + -
208 LEU* 5.0 1.8 - - + -
218 GLY* 3.7 21.8 - - - +
248 ILE* 4.5 23.1 - - + -
258 GLY* 4.7 3.4 - - - -
288 ILE* 4.4 14.1 - - + +
209 LEU* 2.9 38.6 + - + +
219 GLY 4.1 2.0 - - - +
239 GLY* 1.3 78.8 - - - +
259 GLY* 1.3 64.4 + - - +
269 ILE 3.4 0.7 - - - -
279 ALA* 3.2 7.8 + - - +
289 ILE* 3.0 39.0 + - + +
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Residues in contact with GLY 25 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230 GLY 4.2 4.3 - - - -
240 ILE* 4.5 4.2 - - - +
270 ALA* 3.2 29.8 - - - +
219 GLY 2.9 17.2 + - - -
229 ALA 3.9 0.2 - - - -
249 ILE* 1.3 75.0 - - - +
269 ILE* 1.3 65.0 + - - +
289 ILE* 3.0 21.4 + - - -
299 VAL* 3.0 10.6 + - - +
589 SER* 5.0 0.2 - - - -
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Residues in contact with ILE 26 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270 ALA* 5.2 0.2 - - - -
578 LEU* 4.8 5.8 - - + -
588 SER* 5.0 10.8 - - - +
618 THR* 3.7 24.7 - - + +
229 ALA* 3.0 26.9 + - + +
239 GLY 5.3 1.6 - - - +
259 GLY* 1.3 73.9 - - - +
279 ALA* 1.3 57.6 + - - +
299 VAL* 3.3 8.6 + - - +
309 PHE* 2.9 47.3 + - + -
559 PHE* 3.6 50.3 - - + +
589 SER* 4.1 17.0 - - - -
599 GLU* 4.0 7.0 - - - +
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Residues in contact with ALA 27 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 GLY* 3.2 41.1 - - - +
288 ILE* 4.0 8.4 - - + +
298 VAL* 3.7 16.3 - - + +
588 SER* 5.0 3.5 + - - +
239 GLY 4.2 3.0 + - - +
249 ILE 3.2 12.2 + - - +
259 GLY 3.1 0.6 - - - -
269 ILE* 1.3 79.6 - - - +
289 ILE* 1.3 60.0 + - - +
309 PHE* 3.7 1.1 - - - +
319 ALA* 2.8 31.4 + - - +
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Residues in contact with ILE 28 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240 ILE* 4.6 13.5 - - + -
270 ALA 4.5 4.9 - - - +
280 ILE* 4.7 15.7 - - + -
310 ALA* 3.6 18.1 - - + +
288 ILE* 4.6 13.5 - - + -
249 ILE* 3.0 47.5 + - + +
259 GLY* 3.0 11.7 + - - +
279 ALA* 1.3 76.5 - - - +
299 VAL* 1.3 57.9 + - - +
319 ALA* 3.3 6.5 + - + +
329 ALA* 3.0 28.8 + - - +
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Residues in contact with VAL 29 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270 ALA* 3.4 33.9 - - + +
300 PHE* 4.3 11.9 - - + -
310 ALA* 4.1 6.7 - - - +
340 ILE* 3.9 10.7 - - + +
259 GLY 3.0 14.5 + - - +
269 ILE* 3.6 10.8 - - - +
279 ALA 3.2 0.2 - - - -
289 ILE* 1.3 76.0 - - - +
309 PHE* 1.3 62.0 + - + +
329 ALA* 3.3 3.8 + - - +
339 LEU* 2.9 25.6 + - - +
509 MET 5.0 0.2 - - - +
519 ALA* 3.9 36.8 - - + +
549 GLY* 4.9 10.3 - - - -
559 PHE* 4.9 4.7 - - + +
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Residues in contact with PHE 30 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298 VAL* 4.4 14.4 - - + -
508 MET* 5.1 7.2 - - + +
538 LEU* 4.8 12.6 - - + -
548 GLY* 3.5 32.1 - - - -
578 LEU* 3.8 23.6 - - + -
269 ILE* 2.9 41.1 + - + +
279 ALA* 4.1 4.0 - - - +
299 VAL* 1.3 79.7 - - + +
319 ALA* 1.3 57.7 + - - +
339 LEU* 3.3 21.9 - - + +
349 ILE* 2.9 36.9 + - + +
489 PHE* 5.8 1.1 - + - -
519 ALA* 4.2 25.1 - - + -
529 ILE* 5.3 6.3 - - + -
559 PHE* 4.2 14.6 - + + -
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Residues in contact with ALA 31 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288 ILE* 3.7 25.1 - - + +
298 VAL* 5.1 1.7 - - - +
328 ALA* 3.7 23.3 - - + +
279 ALA 2.8 18.7 + - - +
289 ILE* 3.6 6.1 - - + +
299 VAL 3.2 0.2 - - - -
309 PHE* 1.3 76.0 - - - +
329 ALA* 1.3 59.2 + - - +
349 ILE* 3.3 1.8 + - - -
359 ASN* 2.9 37.2 + - - +
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Residues in contact with ALA 32 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310 ALA* 3.3 35.9 - - + +
340 ILE* 3.3 14.6 - - + +
350 ASN* 3.4 23.6 - - - +
289 ILE 3.0 16.3 + - - +
299 VAL 3.7 3.4 - - - +
319 ALA* 1.3 75.8 - - - +
339 LEU* 1.3 58.4 + - - +
359 ASN* 4.5 2.2 - - - +
369 GLY 2.9 23.4 + - - -
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Residues in contact with LEU 33 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340 ILE* 3.7 7.1 - - + +
508 MET* 3.7 33.0 - - + -
299 VAL 2.9 14.5 + - - +
309 PHE* 3.3 27.8 - - + +
329 ALA* 1.3 77.2 - - - +
349 ILE* 1.3 57.6 + - + +
369 GLY* 3.3 1.0 + - - -
379 VAL* 2.9 44.5 + - + +
449 LYS 5.5 0.4 - - - +
479 VAL* 3.7 25.9 - - + +
489 PHE* 4.3 18.8 - - + +
519 ALA* 3.7 27.1 - - + -
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Residues in contact with ILE 34 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298 VAL* 3.7 29.8 - - + +
328 ALA* 3.3 28.5 - - + +
338 LEU* 3.8 5.6 - - + +
368 GLY* 4.7 5.4 - - - -
478 VAL* 3.7 27.6 - - + +
508 MET* 4.9 13.9 - - + -
518 ALA* 4.2 24.9 - - + +
309 PHE* 2.9 24.1 + - + +
319 ALA 3.3 4.5 + - - +
339 LEU* 1.3 75.1 - - + +
359 ASN* 1.3 58.9 + - - +
379 VAL* 3.3 4.8 + - - +
389 SER* 2.9 31.0 + - - -
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Residues in contact with ASN 35 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350 ASN* 4.2 13.2 - - - +
328 ALA* 3.6 30.6 - - - +
358 ASN* 4.2 15.0 - - - +
368 GLY 4.4 1.2 + - - -
398 ARG* 5.3 7.0 + - - +
319 ALA* 2.9 26.1 + - - +
329 ALA* 3.7 3.3 - - - +
349 ILE* 1.3 75.5 - - - +
369 GLY* 1.3 57.1 + - - +
389 SER* 3.4 12.3 + - - -
399 ARG* 3.4 30.4 + - - +
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Residues in contact with GLY 36 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340 ILE* 5.1 3.8 - - - -
350 ASN* 4.7 2.2 - - - -
380 SER* 3.0 29.5 + - - -
329 ALA 2.9 17.1 + - - -
339 LEU 3.7 0.9 - - - -
349 ILE 3.2 0.2 - - - -
359 ASN* 1.3 78.0 - - - +
379 VAL* 1.3 60.4 + - - +
389 SER 3.3 0.2 - - - -
409 ASN 2.8 29.2 + - - +
439 ILE* 4.4 3.9 - - - +
479 VAL* 6.2 2.5 - - - -
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Residues in contact with VAL 37 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438 ILE* 4.2 9.0 - - + +
468 THR* 4.4 4.7 - - + -
478 VAL* 3.8 23.3 - - + -
508 MET* 4.4 9.2 - - - -
339 LEU* 2.9 35.8 + - + +
349 ILE* 4.0 3.8 - - - +
369 GLY* 1.3 76.4 - - - +
389 SER* 1.3 62.3 + - - +
409 ASN 3.1 23.1 - - - -
419 PRO* 3.1 16.8 - - + +
439 ILE* 5.5 0.9 - - + -
449 LYS* 4.1 41.1 - - + -
479 VAL* 5.7 2.9 - - + -
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Residues in contact with SER 38 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368 GLY* 3.6 36.3 - - - -
398 ARG* 4.3 13.2 - - - +
408 ASN* 3.6 24.7 + - - +
438 ILE* 4.2 16.6 - - - -
478 VAL* 4.7 3.1 - - - +
349 ILE* 2.9 20.4 + - - -
359 ASN* 3.4 14.0 + - - -
379 VAL* 1.3 77.1 - - - +
399 ARG* 1.3 63.9 + - - +
419 PRO* 4.7 0.2 - - - +
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Residues in contact with ARG 39 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350 ASN* 4.8 7.7 + - - +
380 SER* 3.9 23.6 + - - +
390 ARG* 3.1 46.3 - - - +
398 ARG* 4.2 41.0 - - - +
359 ASN* 3.4 21.7 + - - +
369 GLY 3.4 1.0 + - - -
389 SER* 1.3 84.8 + - - +
409 ASN* 1.3 58.0 + - - +
419 PRO* 4.1 4.1 - - - +
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Residues in contact with ASN 40 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370 VAL 5.4 0.2 + - - -
380 SER* 3.9 23.7 + - - +
410 PRO* 5.3 10.9 - - - +
369 GLY 2.8 21.2 + - - +
379 VAL* 3.1 8.7 - - - +
399 ARG* 1.3 78.4 - - + +
419 PRO* 1.3 65.7 - - - +
429 SER* 2.6 31.7 + - - -
439 ILE* 3.5 29.8 - - + +
449 LYS 4.7 0.2 + - - -
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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) + - + + + + + -
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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