Contacts of the helix formed by residues 387 - 407 (chain D) in PDB entry 1Y8Q
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 ILE 387 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C GLN* 3.6 23.1 - - + +
25C LEU* 3.7 19.7 - - + -
26C TRP* 3.8 17.9 - - + -
312C GLN* 3.8 7.2 - - + +
58D ASN* 4.2 6.7 - - - +
59D ARG* 3.8 6.1 - - - -
143D GLY 4.0 5.3 + - - +
144D TYR* 3.9 21.8 - - + -
386D ALA* 1.3 80.3 - - - +
388D ALA* 1.3 62.2 + - - +
389D THR* 3.2 23.3 - - - +
390D THR* 3.4 25.9 - - - +
391D ASN* 2.9 23.9 + - - +
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Residues in contact with ALA 388 (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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22C GLN* 5.2 1.2 + - - -
54C ASN* 4.2 16.2 - - - +
57C LEU* 4.0 22.0 - - + -
58C ALA* 5.8 0.7 - - + +
31D GLU* 4.7 4.3 - - - +
58D ASN* 3.7 19.9 + - - +
59D ARG* 3.6 18.9 - - - +
387D ILE* 1.3 72.0 - - - +
389D THR* 1.3 66.9 + - - +
391D ASN* 3.2 6.1 + - - +
392D ALA* 2.9 22.3 + - - +
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Residues in contact with THR 389 (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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54C ASN* 3.9 14.6 - - + +
308C GLY* 3.3 26.8 - - - +
311C ALA* 3.7 15.3 - - + -
312C GLN* 2.9 43.8 + - - +
315C VAL* 5.6 4.0 - - + -
387D ILE* 3.2 14.1 - - - +
388D ALA* 1.3 76.6 - - + +
390D THR* 1.3 60.9 + - - +
392D ALA* 3.3 8.4 + - - +
393D VAL* 3.0 27.0 + - - +
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Residues in contact with THR 390 (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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312C GLN* 3.3 18.9 + - - +
141D THR* 3.8 14.1 - - + -
143D GLY 2.7 28.7 + - - +
144D TYR* 3.6 12.5 - - - +
145D LEU 3.5 21.3 - - - +
387D ILE* 3.4 14.0 - - - +
388D ALA 3.3 0.6 - - - -
389D THR* 1.3 77.8 + - - +
391D ASN* 1.3 62.5 + - - +
393D VAL* 3.2 3.0 + - - +
394D ILE* 3.2 29.6 + - - +
418D LEU* 3.9 13.0 - - + -
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Residues in contact with ASN 391 (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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27D GLY* 3.8 30.6 - - - +
28D ILE* 3.4 15.7 + - - +
31D GLU* 4.0 5.0 - - + +
59D ARG* 3.7 23.7 - - - +
141D THR* 2.7 32.8 + - - -
386D ALA* 4.7 3.8 - - - +
387D ILE 2.9 22.6 + - - +
388D ALA* 3.2 7.1 + - - +
390D THR* 1.3 78.8 - - - +
392D ALA* 1.3 62.9 + - - +
394D ILE* 3.6 1.6 + - - +
395D ALA* 3.0 25.6 + - - +
801D ATP 5.2 2.5 + - - -
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Residues in contact with ALA 392 (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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50C GLU* 4.8 2.7 - - - +
53C LYS* 4.0 9.4 - - - +
54C ASN* 4.2 9.9 - - - +
304C ALA* 3.8 23.0 - - + +
308C GLY* 4.7 0.2 - - - -
31D GLU* 3.7 30.2 - - - +
388D ALA 2.9 16.3 + - - +
389D THR* 3.6 6.3 - - - +
390D THR 3.2 0.2 - - - -
391D ASN* 1.3 79.6 - - - +
393D VAL* 1.3 62.2 + - - +
395D ALA* 3.5 2.1 + - - +
396D GLY 3.1 17.7 + - - -
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Residues in contact with VAL 393 (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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305C VAL* 3.6 42.8 - - + +
308C GLY* 3.9 10.5 - - - -
309C ILE* 3.9 19.3 - - + -
312C GLN* 5.7 2.0 - - - +
389D THR 3.0 15.9 + - - +
390D THR* 3.2 7.2 + - - +
392D ALA* 1.3 75.7 - - - +
394D ILE* 1.3 64.1 + - - +
396D GLY 3.1 2.4 + - - -
397D LEU* 3.1 33.1 + - + +
418D LEU* 4.0 28.0 - - + -
429D LEU* 4.6 3.8 - - + -
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Residues in contact with ILE 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 3.9 12.8 - - + -
139D SER* 3.9 11.9 - - - -
141D THR* 3.8 20.6 - - + -
146D GLY* 4.0 8.3 - - - -
147D GLN* 4.0 16.6 - - - +
148D VAL* 3.7 14.8 - - + -
390D THR* 3.2 18.2 + - + +
391D ASN 4.1 1.8 - - - +
393D VAL* 1.3 75.6 - - + +
395D ALA* 1.3 58.4 + - - +
397D LEU* 3.1 12.8 + - + +
398D ILE* 2.9 46.5 + - + +
418D LEU* 3.5 29.8 - - + -
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Residues in contact with ALA 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 4.0 7.2 - - + +
31D GLU* 3.3 26.5 - - + -
32D LEU* 3.6 13.1 - - + +
35D ASN* 3.5 15.1 + - - +
391D ASN 3.0 19.8 + - - +
392D ALA 3.8 1.8 - - - +
394D ILE* 1.3 77.7 - - - +
396D GLY* 1.3 62.6 + - - +
398D ILE* 3.3 20.6 + - - +
399D VAL* 3.4 15.6 + - - +
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Residues in contact with GLY 396 (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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301C PRO* 3.6 32.6 - - - +
304C ALA* 4.2 1.6 - - - -
305C VAL* 4.0 7.6 - - - -
35D ASN* 3.5 11.8 - - - +
392D ALA 3.1 13.6 + - - -
393D VAL 3.1 4.2 + - - -
395D ALA* 1.3 76.1 - - - +
397D LEU* 1.3 61.6 + - - +
399D VAL* 3.3 3.2 + - - +
400D LEU* 3.2 18.3 + - - +
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Residues in contact with LEU 397 (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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305C VAL* 3.9 6.0 - - + +
331C PHE* 3.8 33.4 - - + -
336C GLY* 5.4 0.9 - - - -
147D GLN* 6.3 0.2 - - - -
148D VAL* 4.0 16.8 - - + -
393D VAL* 3.1 22.6 + - + +
394D ILE* 3.1 18.7 + - + +
396D GLY* 1.3 74.3 - - - +
398D ILE* 1.3 64.7 + - - +
400D LEU* 3.3 9.0 + - + +
401D GLU* 3.0 28.4 + - - +
416D ILE* 3.9 43.0 - - + +
418D LEU* 5.6 1.1 - - + -
429D LEU* 4.2 17.7 - - + -
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Residues in contact with ILE 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 3.7 20.2 - - + -
32D LEU* 4.2 12.8 - - + -
113D MET* 3.9 30.9 - - + +
114D ASN 4.8 3.8 - - - +
137D ILE* 3.4 21.5 - - + +
139D SER* 3.1 35.2 - - - +
148D VAL* 4.0 14.8 - - + -
394D ILE* 2.9 25.7 + - + +
395D ALA* 3.6 9.6 - - - +
396D GLY 3.2 0.6 - - - -
397D LEU* 1.3 76.6 - - - +
399D VAL* 1.3 57.2 + - - +
401D GLU* 3.3 2.0 + - - +
402D GLY* 2.9 22.0 + - - -
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Residues in contact with VAL 399 (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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301C PRO* 3.5 23.8 - - + -
32D LEU* 3.7 17.7 - - + -
35D ASN* 3.7 23.1 - - + -
36D LEU* 4.0 11.4 - - + -
39D THR* 3.8 21.3 - - + +
41D PHE* 4.4 11.4 - - + -
113D MET* 5.8 1.3 - - - -
395D ALA 3.4 13.2 + - - +
396D GLY 3.3 7.0 + - - +
397D LEU 3.3 0.4 - - - -
398D ILE* 1.3 75.0 - - - +
400D LEU* 1.3 65.6 + - - +
402D GLY* 3.1 2.6 + - - +
403D LEU* 2.9 27.1 + - + +
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Residues in contact with LEU 400 (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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161C TYR* 4.2 28.9 - - + -
299C MET* 4.9 3.4 - - + -
301C PRO* 3.8 22.4 - - + +
302C VAL* 4.7 9.2 - - + -
305C VAL* 4.8 2.5 - - + -
331C PHE* 3.9 33.7 - - + -
333C GLY* 4.0 15.9 - - - +
396D GLY 3.2 15.7 + - - +
397D LEU* 3.3 14.3 + - + +
399D VAL* 1.3 78.6 - - - +
401D GLU* 1.3 67.6 + - - +
403D LEU* 3.3 18.1 + - + +
404D LYS* 3.2 21.7 + - - +
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Residues in contact with GLU 401 (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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137D ILE* 4.1 11.0 - - + -
148D VAL* 4.1 18.2 - - + -
149D THR 6.2 0.2 - - - -
150D THR* 4.0 9.2 + - - +
397D LEU 3.0 16.3 + - - +
398D ILE* 3.5 9.2 - - - +
400D LEU* 1.3 80.1 - - - +
402D GLY* 1.3 62.2 + - - +
404D LYS* 2.7 42.0 + - - +
405D ILE* 3.2 16.6 + - - +
413D CYS* 3.1 16.1 - - - +
414D ARG* 3.0 36.4 + - - +
416D ILE* 4.0 18.1 - - + +
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Residues in contact with GLY 402 (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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41D PHE* 5.4 3.1 - - - -
111D LEU* 3.8 23.3 - - - -
137D ILE* 3.7 6.0 - - - +
398D ILE 2.9 14.1 + - - -
399D VAL* 3.1 6.2 + - - -
401D GLU* 1.3 78.5 - - - +
403D LEU* 1.3 55.4 + - - +
405D ILE* 3.4 5.2 + - - +
406D LEU* 3.0 37.1 + - - +
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Residues in contact with LEU 403 (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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161C TYR* 4.8 6.7 - - + +
299C MET* 4.5 11.9 - - + -
301C PRO* 5.1 1.1 - - + -
7D LEU* 4.4 20.2 - - + -
11D LEU* 3.7 26.0 - - + +
15D VAL* 3.8 22.9 - - + -
39D THR* 4.2 26.7 - - + -
41D PHE* 4.3 7.8 - - + -
399D VAL* 2.9 22.2 + - + +
400D LEU* 3.6 18.4 - - + +
401D GLU 3.2 0.4 - - - -
402D GLY* 1.3 72.9 - - - +
404D LYS* 1.3 66.8 + - - +
406D LEU* 3.5 0.8 + - - +
407D SER* 3.0 27.4 + - - -
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Residues in contact with LYS 404 (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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333C GLY 4.5 8.2 + - - -
334C MET* 3.9 37.9 + - + -
335C LYS 6.0 1.0 - - - -
336C GLY 6.1 0.2 - - - +
400D LEU* 3.2 17.5 - - - +
401D GLU* 2.7 39.8 + - - +
403D LEU* 1.3 76.9 - - - +
405D ILE* 1.3 55.9 + - - +
407D SER* 2.7 27.4 + - - -
408D GLY 3.1 0.2 + - - -
409D LYS* 3.0 29.0 + - + +
412D GLN* 3.0 45.8 + - + +
413D CYS* 3.6 12.6 - - - -
414D ARG* 4.6 3.2 - - - +
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Residues in contact with ILE 405 (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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111D LEU* 4.0 22.2 - - + -
135D PRO* 3.8 28.9 - - + -
137D ILE* 4.1 10.5 - - + -
150D THR* 3.6 30.7 - - + +
401D GLU 3.2 12.9 + - - +
402D GLY* 3.6 7.4 - - - +
404D LYS* 1.3 80.6 - - - +
406D LEU* 1.3 62.8 + - + +
408D GLY* 3.1 17.0 + - - -
410D ILE* 3.3 32.1 - - + +
413D CYS* 3.6 9.0 - - - -
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Residues in contact with LEU 406 (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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11D LEU* 3.7 20.3 - - + +
14D ALA* 4.3 16.3 - - + +
15D VAL* 4.0 16.2 - - + +
41D PHE* 3.7 36.1 - - + -
110D ILE* 3.6 45.8 - - + +
111D LEU* 4.6 8.7 - - + -
402D GLY 3.0 20.5 + - - +
403D LEU* 3.8 0.7 - - - -
404D LYS 3.2 0.2 - - - -
405D ILE* 1.3 83.8 - - + +
407D SER* 1.3 57.2 + - - +
408D GLY 3.2 1.5 + - - -
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Residues in contact with SER 407 (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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11D LEU* 3.5 27.0 - - - +
403D LEU 3.0 14.6 + - - -
404D LYS* 2.7 12.0 + - - -
406D LEU* 1.3 76.4 - - - +
408D GLY* 1.3 62.8 + - - +
409D LYS* 3.4 30.2 + - - +
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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
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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