Contacts of the helix formed by residues 403 - 426 (chain D) in PDB entry 7REQ
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 TYR 403 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 5.2 7.8 - + - -
61C LEU* 3.6 42.6 + - + +
72C HIS* 5.8 0.2 - + - -
404C SER* 3.1 34.9 + - - +
405C GLY* 3.5 20.6 - - - -
76D TYR* 3.8 23.6 - - + -
77D ARG 3.5 24.2 - - - +
78D PRO* 3.6 33.6 - - + +
80D ASP* 3.9 4.9 - - - +
81D ALA* 3.9 16.2 - - + -
401D GLY 3.1 9.6 + - - -
402D SER* 1.3 70.1 - - - +
404D TYR* 1.3 62.0 + - - +
406D GLU* 4.1 0.2 - - - -
407D SER* 3.0 26.7 + - - -
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Residues in contact with TYR 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLY 4.5 1.1 + - - -
398C ARG* 2.9 39.6 + - + +
399C VAL* 3.5 30.2 - - + +
402C PRO* 3.6 33.1 + - + +
404C SER 4.8 0.2 + - - -
72D ILE* 4.0 11.4 - - + -
76D TYR* 3.4 37.9 - + + +
291D PHE* 3.5 39.4 - + + +
402D SER* 3.4 0.6 + - - -
403D TYR* 1.3 79.8 - - - +
405D VAL* 1.3 56.6 + - + +
407D SER* 3.6 1.4 - - - -
408D LEU* 2.9 43.3 + - + +
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Residues in contact with VAL 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C TRP* 5.4 0.4 - - + -
291D PHE* 3.7 35.9 - - + +
294D ILE* 3.8 25.1 - - + -
295D ALA* 4.7 5.8 - - + +
298D ARG* 3.9 13.0 - - - +
399D ALA* 4.1 17.5 - - + +
402D SER* 3.2 25.5 + - - +
404D TYR* 1.3 73.9 - - + +
406D GLU* 1.3 61.3 + - - +
408D LEU* 4.1 5.3 - - - +
409D THR* 2.7 43.6 + - - +
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Residues in contact with GLU 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ASP 4.2 1.3 - - - -
81D ALA* 3.9 10.3 - - + -
82D PRO* 3.9 35.6 - - + +
85D LEU* 4.2 8.0 - - - +
94D THR* 4.6 4.3 - - - +
298D ARG* 2.8 41.5 + - - +
399D ALA 5.0 0.4 - - - -
400D GLY* 3.6 1.1 - - - -
401D GLY* 2.8 33.9 + - - -
402D SER 2.9 25.0 + - - +
403D TYR 4.1 0.4 - - - +
405D VAL* 1.3 70.7 - - - +
407D SER* 1.3 64.1 + - - +
409D THR* 3.5 2.6 + - - -
410D ARG* 3.3 21.1 + - - +
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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
----------------------------------------------------------
76D TYR* 3.3 31.4 - - - -
80D ASP* 3.6 20.3 + - - +
403D TYR 3.0 19.5 + - - -
404D TYR 3.6 0.7 - - - -
406D GLU* 1.3 76.2 - - - +
408D LEU* 1.3 56.2 + - - +
410D ARG* 3.3 6.2 + - - +
411D SER* 3.0 32.8 + - - -
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Residues in contact with LEU 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C ARG* 4.7 0.7 - - - +
70D ILE* 3.9 27.6 - - + -
71D ASP 5.5 0.4 - - - +
72D ILE* 4.0 15.0 - - + -
76D TYR* 5.3 3.3 - - - +
291D PHE* 3.9 25.4 - - + +
292D LEU* 3.7 29.6 - - + +
295D ALA* 3.8 10.8 - - + -
404D TYR* 2.9 45.9 + - + +
405D VAL* 4.1 2.7 - - - +
407D SER* 1.3 72.5 - - - +
409D THR* 1.3 54.9 + - - +
411D SER* 3.8 5.9 - - - -
412D LEU* 2.9 31.2 + - + +
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Residues in contact with THR 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D THR* 4.0 10.1 - - + -
295D ALA* 3.6 23.9 - - - +
298D ARG* 2.9 32.0 + - + +
299D ALA* 3.3 33.8 - - - +
302D GLU* 4.2 7.2 - - - +
405D VAL 2.7 22.4 + - - -
406D GLU* 3.6 4.7 - - - +
408D LEU* 1.3 73.3 - - - +
410D ARG* 1.3 56.9 + - - +
412D LEU* 4.7 0.2 - - - -
413D ALA* 2.9 25.3 + - - +
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Residues in contact with ARG 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 15.9 - - - +
13C GLY 2.8 32.3 + - - +
14C ASN* 4.2 11.8 - - - +
15C ALA* 4.4 1.4 - - - +
302D GLU* 2.9 30.1 + - - +
406D GLU 3.3 10.0 + - - +
407D SER* 3.7 9.6 - - - +
409D THR* 1.3 76.7 - - - +
411D SER* 1.3 57.5 + - - +
413D ALA* 3.3 3.5 + - - -
414D ASP* 2.9 62.0 + - - +
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Residues in contact with SER 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE* 4.2 23.5 - - - +
71D ASP 5.5 2.2 + - - -
407D SER* 3.0 24.1 + - - -
408D LEU* 3.4 9.1 + - - -
410D ARG* 1.3 75.8 - - - +
412D LEU* 1.3 55.8 + - - +
414D ASP* 4.0 5.6 - - - +
415D ALA* 3.1 30.1 + - - +
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE* 4.0 25.6 - - + -
248D ASP* 4.2 18.4 - - + -
249D VAL* 4.3 8.4 - - + +
252D LEU* 4.1 6.7 - - + -
292D LEU* 3.7 29.8 - - + +
295D ALA* 3.7 14.4 - - + -
296D ARG* 3.5 35.7 - - + +
299D ALA* 4.2 7.4 - - + -
408D LEU* 2.9 16.7 + - + +
409D THR 3.9 3.1 - - - +
411D SER* 1.3 70.7 - - - +
413D ALA* 1.3 65.1 + - - +
415D ALA* 4.8 2.9 - - - -
416D ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 20.1 - - + +
252D LEU* 4.6 3.6 - - - -
256D LEU* 5.8 0.2 - - - +
299D ALA* 3.8 23.3 - - + +
302D GLU* 4.4 12.8 - - + +
303D ALA* 5.3 5.9 - - + +
409D THR 2.9 22.7 + - - +
410D ARG* 3.3 6.9 + - - +
412D LEU* 1.3 72.6 - - - +
414D ASP* 1.3 56.1 + - - +
416D ALA* 3.7 0.9 - - - +
417D TRP* 2.8 32.2 + - - +
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Residues in contact with ASP 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.3 9.2 - - - +
410D ARG* 2.9 63.0 + - - +
411D SER* 4.0 4.7 - - - +
413D ALA* 1.3 71.4 - - - +
415D ALA* 1.4 61.7 + - - +
417D TRP* 3.4 6.7 + - - +
418D LYS* 3.1 24.1 + - - +
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Residues in contact with ALA 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASP 6.1 0.2 - - - +
70D ILE* 3.9 21.8 - - + -
249D VAL* 3.6 21.2 - - + +
411D SER 3.1 18.3 + - - +
412D LEU 4.2 1.3 - - - +
414D ASP* 1.4 76.4 - - - +
416D ALA* 1.3 61.6 + - - +
418D LYS* 3.7 8.4 + - - +
419D GLU* 3.3 17.7 + - - +
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Residues in contact with ALA 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D VAL* 3.8 12.3 - - + +
252D LEU* 3.5 31.0 - - + -
253D ALA* 3.3 25.7 - - - +
256D LEU* 4.8 4.5 - - + -
412D LEU 2.9 18.8 + - - +
413D ALA* 4.0 1.6 - - - +
415D ALA* 1.3 73.9 - - - +
417D TRP* 1.3 57.8 + - - +
419D GLU 3.3 0.7 + - - -
420D PHE* 2.9 28.4 + - - +
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Residues in contact with TRP 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 4.2 10.8 - + - -
10C VAL* 2.9 36.4 + - + -
11C ASP* 4.0 12.6 - - - -
12C LEU* 3.5 39.3 - - + +
256D LEU* 4.5 2.8 - - + +
303D ALA* 3.7 32.8 - - + -
306D ARG* 3.8 17.5 - - + -
307D ILE* 4.0 11.2 - - + -
413D ALA 2.8 23.0 + - - +
414D ASP* 3.4 9.4 + - - +
416D ALA* 1.3 68.8 - - - +
418D LYS* 1.3 55.4 + - - +
420D PHE* 3.1 36.1 + + - +
421D GLN* 2.9 52.2 + - + +
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Residues in contact with LYS 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D ASP 3.1 16.7 + - - +
415D ALA* 3.7 8.7 - - - +
416D ALA 3.4 0.2 - - - -
417D TRP* 1.3 74.6 - - - +
419D GLU* 1.3 61.3 + - - +
421D GLN* 3.4 17.4 + - - +
422D GLU* 3.2 26.2 + - + +
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Residues in contact with GLU 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D VAL* 4.8 6.7 - - + -
250D ALA* 5.0 6.3 - - + -
253D ALA* 3.5 23.8 - - + -
254D TRP* 2.8 26.9 + - + +
415D ALA 3.3 12.5 + - - +
416D ALA* 3.3 0.6 + - - -
418D LYS* 1.3 77.7 - - - +
420D PHE* 1.3 59.9 + - - +
422D GLU* 3.3 8.8 + - - +
423D VAL* 3.2 22.7 + - - +
437D HIS* 2.7 36.5 + - - -
441D VAL* 4.1 10.5 - - + +
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Residues in contact with PHE 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.5 40.2 - + + -
253D ALA* 3.9 14.0 - - - +
256D LEU* 3.9 9.2 - - + -
257D ALA* 3.5 36.6 - - + -
260D ALA* 3.8 11.0 - - + -
307D ILE* 3.7 27.4 - - + -
416D ALA 2.9 17.9 + - - +
417D TRP* 3.3 36.6 - + - +
419D GLU* 1.3 70.5 - - - +
421D GLN* 1.3 61.6 + - + +
423D VAL* 3.2 7.6 + - - +
424D GLU* 3.1 32.0 + - + +
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Residues in contact with GLN 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE 3.4 15.9 + - - +
8C ASP* 3.4 34.5 + - - +
9C SER* 4.3 1.6 - - - +
10C VAL 2.6 30.7 + - - +
11C ASP* 4.7 4.2 + - - +
417D TRP* 2.9 32.7 + - + +
418D LYS* 3.5 21.7 - - - +
420D PHE* 1.3 72.2 - - + +
422D GLU* 1.3 58.5 + - - +
424D GLU* 3.3 3.5 + - - -
425D LYS* 3.0 24.8 + - - +
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Residues in contact with GLU 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D LYS* 3.2 19.5 + - + +
419D GLU* 3.3 19.5 + - - +
421D GLN* 1.3 74.6 - - - +
423D VAL* 1.3 64.2 + - - +
425D LYS* 3.6 16.4 + - - +
426D LEU* 3.2 30.4 + - + +
437D HIS* 4.8 9.2 - - + -
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Residues in contact with VAL 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D TRP* 3.8 18.4 - - + +
257D ALA* 3.6 21.3 - - + -
419D GLU* 3.2 31.0 + - - +
420D PHE 3.2 8.3 + - - +
422D GLU* 1.3 73.7 - - - +
424D GLU* 1.3 60.4 + - + +
426D LEU* 3.4 18.8 + - - +
427D GLY 3.5 0.7 + - - -
428D GLY* 2.9 20.9 + - - +
429D MET* 3.6 33.2 - - - +
432D ALA* 4.2 6.0 - - + +
437D HIS* 3.9 12.6 - - + +
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Residues in contact with GLU 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 3.7 11.4 + - - -
7C PHE* 2.7 32.3 + - + -
8C ASP* 3.7 23.2 - - + +
257D ALA* 5.0 3.1 - - - +
260D ALA* 4.3 2.4 - - - +
264D ARG* 2.7 46.7 + - - -
420D PHE* 3.1 36.5 + - + +
421D GLN 3.5 9.2 - - - +
423D VAL* 1.3 75.3 - - + +
425D LYS* 1.3 58.0 + - - +
427D GLY* 3.3 11.8 + - - -
428D GLY* 3.7 13.0 + - - +
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Residues in contact with LYS 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASP* 3.8 21.0 - - + +
421D GLN 3.0 17.4 + - - +
422D GLU* 3.8 22.2 - - - +
423D VAL 3.4 0.4 - - - -
424D GLU* 1.3 72.3 - - - +
426D LEU* 1.3 59.2 + - + +
427D GLY 3.4 0.9 + - - -
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Residues in contact with LEU 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D GLU* 3.2 17.0 - - + +
423D VAL* 3.4 10.5 + - - +
424D GLU 3.4 0.6 - - - -
425D LYS* 1.3 74.5 - - + +
427D GLY* 1.3 56.6 + - - +
428D GLY 5.0 1.8 - - - +
431D LYS* 3.9 17.4 - - + +
432D ALA* 4.9 6.7 - - + +
435D THR* 5.5 2.2 - - - +
437D HIS* 3.6 44.4 - - + +
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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