Contacts of the helix formed by residues 301 - 326 (chain D) in PDB entry 6E7P
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 PHE 301 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D VAL* 4.0 40.6 - - + -
78D VAL* 4.2 20.2 - - + -
79D GLN* 3.9 26.2 - - - -
297D PHE 4.0 13.2 - - - +
298D ARG* 3.1 16.4 + - + +
300D LEU* 1.3 79.4 - - - +
302D ASP* 1.3 60.3 + - - +
303D VAL 3.1 1.8 - - - -
304D VAL* 3.0 36.6 + - + +
305D VAL* 3.5 4.6 + - + -
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Residues in contact with ASP 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLN* 3.9 19.2 + - - +
298D ARG 4.0 4.1 + - - -
299D LEU* 2.9 28.2 - - - +
301D PHE* 1.3 76.5 - - - +
303D VAL* 1.3 60.4 + - - +
305D VAL* 3.0 14.0 + - - +
306D ILE* 2.7 40.7 + - + +
369D THR* 4.6 14.3 + - - +
372D LYS* 4.8 12.3 + - + +
373D ILE* 3.6 26.9 - - - +
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Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LEU 4.6 0.7 - - - +
300D LEU* 3.3 50.7 - - + +
302D ASP* 1.3 90.1 + - - +
304D VAL* 1.3 62.3 + - + +
306D ILE* 3.4 20.3 - - + +
307D LEU* 2.8 35.5 + - + +
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Residues in contact with VAL 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D VAL* 4.5 17.9 - - + -
300D LEU 4.2 13.0 - - - +
301D PHE* 3.0 27.1 + - + +
303D VAL* 1.3 79.5 - - + +
305D VAL* 1.3 59.9 + - - +
307D LEU* 3.1 12.3 + - + +
308D THR* 2.8 45.9 + - + +
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Residues in contact with VAL 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D VAL* 3.7 21.5 - - + -
76D VAL* 4.7 7.6 - - + -
79D GLN* 3.9 24.5 - - + +
301D PHE* 3.9 13.2 - - + +
302D ASP* 3.0 14.5 + - - +
304D VAL* 1.3 75.0 - - - +
306D ILE* 1.3 62.3 + - - +
308D THR* 4.0 5.8 - - - -
309D CYS* 3.4 30.0 + - - +
365D THR* 4.0 19.5 - - + -
366D ILE* 4.9 2.0 - - - +
369D THR* 3.8 27.4 - - + +
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Residues in contact with ILE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ASP* 2.7 24.4 + - + +
303D VAL* 3.4 26.2 - - + +
304D VAL 3.2 0.2 - - - -
305D VAL* 1.3 75.2 - - - +
307D LEU* 1.3 54.1 + - + +
310D SER* 2.6 33.7 + - - -
366D ILE* 3.5 25.3 - - + +
369D THR* 4.4 13.5 - - - +
370D ILE* 5.8 7.9 - - + +
373D ILE* 4.5 21.8 - - + -
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D VAL* 2.8 22.5 + - + +
304D VAL* 3.1 15.7 + - + +
306D ILE* 1.3 79.1 - - + +
308D THR* 1.3 57.8 + - + +
310D SER* 2.6 20.7 + - - +
311D LEU* 2.7 40.1 + - + +
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Residues in contact with THR 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LEU* 4.5 19.2 - - + +
71D VAL* 4.6 22.9 - - + -
72D LYS* 4.8 10.1 - - - +
75D VAL* 4.5 9.6 - - + +
76D VAL* 5.9 0.5 - - - +
304D VAL* 2.8 37.0 + - + +
305D VAL* 3.9 7.3 + - - -
307D LEU* 1.3 76.8 - - + +
309D CYS* 1.3 66.8 + - - +
311D LEU* 3.9 8.2 - - + +
312D SER* 3.0 28.6 + - - -
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Residues in contact with CYS 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS* 4.5 10.3 - - - +
76D VAL* 4.0 18.2 - - - -
305D VAL* 3.4 19.7 + - - +
308D THR* 1.3 86.6 + - - +
310D SER* 1.3 58.3 + - - +
312D SER* 3.5 2.6 + - - -
313D PHE* 2.8 27.6 + - - +
362D ASP* 3.4 31.8 - - + +
365D THR* 3.7 29.4 - - + -
366D ILE* 5.1 9.4 - - + -
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Residues in contact with SER 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D ILE 2.6 19.5 + - - -
307D LEU* 2.6 23.2 + - - +
309D CYS* 1.3 76.6 - - - +
311D LEU* 1.3 62.7 + - - +
313D PHE* 3.0 12.0 + - - +
314D LEU* 2.8 27.7 + - - +
366D ILE* 4.0 15.3 - - - +
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Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LEU* 4.3 17.8 - - + +
307D LEU* 2.7 41.1 + - + +
308D THR* 4.1 7.0 - - + +
310D SER* 1.3 77.5 + - - +
312D SER* 1.3 56.7 + - - +
314D LEU* 3.6 13.5 + - + +
315D LEU* 3.2 24.4 + - - +
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Residues in contact with SER 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LEU* 4.2 16.1 - - - +
69D GLN* 3.7 5.5 + - - -
72D LYS* 3.4 32.6 + - - -
308D THR 3.0 20.1 + - - -
309D CYS 3.8 1.6 - - - -
311D LEU* 1.3 74.3 - - - +
313D PHE* 1.3 59.3 + - - +
314D LEU 3.2 1.6 - - - -
315D LEU* 3.7 5.8 - - - +
316D CYS* 3.1 43.0 + - - +
362D ASP* 3.7 2.2 + - - +
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Residues in contact with PHE 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D CYS 2.8 18.8 + - - +
310D SER* 3.0 11.8 + - - +
312D SER* 1.3 76.0 - - - +
314D LEU* 1.3 63.6 + - - +
316D CYS* 5.4 0.9 - - - -
317D ALA* 3.5 27.5 + - + +
359D VAL* 3.6 35.4 - - + -
362D ASP* 3.9 23.5 + - + +
363D VAL* 4.1 17.7 - - + -
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D SER 2.8 15.0 + - - +
311D LEU* 3.7 14.1 - - + +
312D SER 3.2 0.2 - - - -
313D PHE* 1.3 80.6 - - - +
315D LEU* 1.3 69.9 + - + +
317D ALA* 4.4 1.8 - - - +
318D ARG* 3.6 23.6 + - - +
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LYS* 3.5 60.3 - - + +
68D LEU* 5.5 6.5 - - + -
311D LEU 3.2 16.1 + - - +
312D SER* 3.4 6.4 + - - +
314D LEU* 1.3 86.1 - - + +
316D CYS* 1.3 77.1 + - - +
318D ARG* 3.3 27.2 + - + +
319D SER* 3.8 4.3 + - - -
355D TYR* 6.1 1.8 - - + -
801D HZ7 4.2 16.6 - - - +
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Residues in contact with CYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LYS 5.8 0.9 - - - -
69D GLN* 4.4 13.5 - - - -
312D SER* 3.1 33.1 + - - +
313D PHE* 5.2 0.9 - - - +
315D LEU* 1.3 90.6 - - - +
317D ALA* 1.3 61.4 - - - +
319D SER* 3.2 15.8 + - - -
320D LEU* 3.3 15.0 + - - +
355D TYR* 3.9 33.8 - - + +
358D LEU* 4.7 9.4 - - + -
359D VAL* 4.6 13.7 - - + +
362D ASP* 5.6 0.9 - - - +
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D PHE* 3.5 27.5 + - + +
314D LEU* 4.4 2.0 - - - +
315D LEU 3.3 0.8 - - - -
316D CYS* 1.3 76.9 - - - +
318D ARG* 1.3 55.5 + - - +
319D SER 3.2 0.2 - - - -
320D LEU* 3.1 22.4 + - + +
321D LEU* 2.7 40.6 + - + +
359D VAL* 4.8 5.8 - - + +
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Residues in contact with ARG 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D LEU* 3.6 18.2 + - + +
315D LEU* 3.3 20.1 + - + +
316D CYS 3.2 0.6 - - - -
317D ALA* 1.3 79.1 - - - +
319D SER* 1.3 56.2 + - - +
321D LEU* 3.2 18.6 + - + +
322D ARG* 2.8 32.0 + - - +
801D HZ7 3.8 33.2 + - - -
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Residues in contact with SER 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D PHE* 4.6 14.2 - - - -
315D LEU 3.8 4.4 + - - -
316D CYS* 3.2 12.4 + - - -
317D ALA 3.2 0.4 - - - -
318D ARG* 1.3 76.5 - - - +
320D LEU* 1.3 61.2 + - - +
322D ARG* 3.1 10.6 + - - +
323D GLY* 2.8 25.6 + - - -
352D ASN* 4.9 2.1 + - - -
355D TYR* 4.6 16.2 - - - -
801D HZ7 3.6 32.1 + - - -
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D CYS 3.8 8.1 - - - +
317D ALA* 3.1 18.5 + - + +
319D SER* 1.3 77.3 - - - +
321D LEU* 1.3 61.0 + - - +
323D GLY* 4.0 1.1 - - - +
324D PHE* 3.2 25.5 + - - +
351D VAL* 3.8 32.5 - - + +
352D ASN 5.0 1.6 - - - +
355D TYR* 4.3 19.5 - - + +
356D ILE* 4.6 17.9 - - + +
359D VAL* 3.7 30.5 - - + -
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ALA* 2.7 24.8 + - + +
318D ARG* 3.4 21.1 - - + +
320D LEU* 1.3 72.5 - - + +
322D ARG* 1.3 61.1 + - - +
324D PHE* 4.6 2.7 - - - +
325D LEU* 3.2 28.0 + - + +
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Residues in contact with ARG 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ARG* 4.7 23.8 + - - +
47D TYR* 6.1 2.8 - - - +
48D PHE* 5.2 16.5 - - + +
318D ARG* 2.8 20.8 + - - +
319D SER* 3.1 10.7 + - - +
321D LEU* 1.3 76.8 - - - +
323D GLY* 1.3 65.1 + - - +
325D LEU* 3.4 6.0 + - + +
326D LEU* 3.1 41.8 + - + +
801D HZ7 2.9 64.4 + - - -
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Residues in contact with GLY 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D PHE* 4.5 21.1 - - - -
319D SER 2.8 15.8 + - - -
320D LEU* 3.4 2.2 + - - -
322D ARG* 1.3 78.4 - - - +
324D PHE* 1.3 61.7 + - - +
326D LEU* 3.5 11.5 + - - +
327D GLN* 3.3 20.0 + - - +
350D PHE* 4.8 7.8 - - - +
351D VAL* 5.3 7.6 - - - -
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Residues in contact with PHE 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D LEU 3.2 16.1 + - - +
321D LEU* 4.7 2.7 - - - +
323D GLY* 1.3 73.3 - - - +
325D LEU* 1.3 67.2 + - - +
327D GLN* 3.2 45.0 + - - +
328D ASN* 4.2 2.3 + - - +
351D VAL* 5.2 7.3 - - + +
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Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ARG* 5.7 2.0 - - - +
321D LEU* 3.2 22.3 + - + +
322D ARG* 3.4 6.7 + - + +
323D GLY 3.3 0.2 - - - -
324D PHE* 1.3 83.0 - - - +
326D LEU* 1.3 72.2 + - + +
327D GLN 3.3 2.1 + - - -
328D ASN* 3.7 8.5 + - - +
329D GLU* 3.0 23.7 - - - +
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Residues in contact with LEU 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ARG* 3.4 40.2 - - + +
45D LEU* 4.5 24.8 - - + +
48D PHE* 6.3 6.3 - - + -
322D ARG* 3.1 46.5 + - + +
323D GLY* 3.5 7.6 + - - +
324D PHE 3.3 0.4 - - - -
325D LEU* 1.3 92.8 - - + +
327D GLN* 1.3 59.8 + - - +
328D ASN 3.5 0.7 - - - -
329D GLU* 3.4 21.6 + - + +
330D PHE* 4.3 9.7 + - - +
350D PHE* 5.5 2.6 - - - -
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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