Contacts of the helix formed by residues 393 - 416 (chain A) in PDB entry 5L26
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 LEU 393 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU* 4.3 20.4 - - + +
173A LEU* 4.5 14.8 - - + -
174A PHE* 3.8 35.2 - - + -
177A MET* 3.8 7.4 - - - -
221A VAL* 5.1 6.1 - - + -
389A ASP 3.2 16.8 + - - +
390A VAL 3.3 5.3 + - - +
392A ARG* 1.3 101.2 - - + +
394A GLY* 1.3 63.0 + - - +
395A ILE 3.5 1.3 - - - -
396A LYS* 4.1 32.5 - - + +
397A ALA* 3.0 26.3 + - - +
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Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MET* 3.9 7.6 - - - -
181A LEU* 4.4 0.9 - - - +
372A ILE* 3.6 30.3 - - - +
390A VAL 3.3 10.5 + - - -
391A ALA 3.6 4.5 + - - -
392A ARG 3.1 4.0 - - - -
393A LEU* 1.3 78.9 - - - +
395A ILE* 1.3 61.7 + - - +
397A ALA* 3.4 2.4 + - - +
398A VAL* 3.2 27.4 + - - +
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 5.6 9.4 - - + -
372A ILE* 3.8 16.1 - - + +
391A ALA 5.1 0.4 + - - -
392A ARG 4.6 4.2 + - - +
394A GLY* 1.3 71.6 - - - +
396A LYS* 1.3 69.6 + - + +
398A VAL* 3.2 6.6 + - + +
399A VAL* 3.1 30.0 + - + +
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Residues in contact with LYS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU 5.8 4.5 - - - +
22A THR* 4.1 23.0 - - + +
174A PHE* 3.4 23.6 - - + -
220A LEU* 3.7 8.0 - - + +
221A VAL* 5.1 6.3 - - + -
392A ARG* 5.1 8.9 - - - +
393A LEU* 3.6 31.7 + - + +
394A GLY 3.4 0.4 - - - -
395A ILE* 1.3 79.5 - - + +
397A ALA* 1.3 57.7 + - - +
399A VAL* 3.3 11.5 + - - +
400A ALA* 2.9 22.7 + - - +
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 3.3 16.4 - - + -
177A MET* 3.9 24.0 - - + -
178A SER* 4.1 7.7 + - - +
181A LEU* 3.4 24.0 - - + +
393A LEU 3.0 19.8 + - - +
394A GLY 3.7 2.0 - - - +
396A LYS* 1.3 74.8 - - - +
398A VAL* 1.3 61.7 + - - +
400A ALA* 3.2 3.9 + - - +
401A GLY* 2.8 24.1 + - - -
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 3.6 15.0 - - + -
328A VAL* 4.7 12.3 - - + -
367A ALA* 3.8 23.6 - - - +
368A ASN* 3.4 27.8 - - - +
369A LEU* 5.0 6.3 - - + -
372A ILE* 3.5 18.2 - - + -
394A GLY 3.2 16.3 + - - +
395A ILE* 3.2 9.2 + - + +
397A ALA* 1.3 72.0 - - - +
399A VAL* 1.3 55.0 + - + +
401A GLY* 3.2 1.6 + - - +
402A SER* 2.7 45.3 + - - +
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 5.6 1.3 - - + -
20A LEU* 4.2 22.7 - - + -
220A LEU* 4.8 5.8 - - + -
395A ILE* 3.1 24.8 + - + +
396A LYS* 3.4 10.1 - - - +
398A VAL* 1.3 78.6 - - + +
400A ALA* 1.3 55.6 + - - +
402A SER* 3.2 7.4 + - - -
403A LEU* 2.8 51.0 + - + +
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 3.9 3.8 - - + -
178A SER* 3.4 26.7 - - - +
213A GLY* 5.4 1.2 - - - +
216A PHE* 3.8 20.2 - - + +
220A LEU* 3.7 20.2 - - + +
396A LYS 2.9 14.3 + - - +
397A ALA 3.3 8.7 - - - +
399A VAL* 1.3 77.4 - - - +
401A GLY* 1.3 56.9 + - - +
403A LEU* 4.7 0.9 - - - -
404A SER* 3.1 28.1 + - - -
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Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER 4.4 1.7 + - - -
181A LEU* 4.2 1.3 - - - -
182A ALA* 3.8 27.3 - - - +
367A ALA* 3.8 6.1 - - - -
397A ALA 2.8 14.5 + - - -
398A VAL 3.6 3.4 - - - -
400A ALA* 1.3 73.3 - - - +
402A SER* 1.3 60.2 + - - +
404A SER* 3.4 1.7 + - - -
405A ASN* 2.9 39.8 + - - +
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LYS* 4.4 4.4 + - - +
328A VAL* 4.1 19.1 - - - +
367A ALA* 3.8 9.8 - - - +
398A VAL* 2.7 33.9 + - - +
399A VAL* 3.5 8.2 - - - -
401A GLY* 1.3 73.6 - - - +
403A LEU* 1.3 59.8 + - - +
405A ASN* 3.3 8.9 + - - +
406A LEU* 2.9 41.2 + - - +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.8 32.6 - - + +
16A ILE* 4.7 17.5 - - + -
17A ALA* 4.0 21.3 - - + +
20A LEU* 5.5 0.2 - - + -
216A PHE* 3.3 46.9 - - + -
220A LEU* 5.1 3.8 - - + -
399A VAL* 2.8 40.1 + - + +
400A ALA* 4.0 1.6 - - - +
402A SER* 1.3 74.6 - - - +
404A SER* 1.3 57.5 + - - +
406A LEU* 3.8 10.1 - - + +
407A MET* 2.9 24.1 + - - +
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 3.6 0.9 - - - +
182A ALA* 3.5 18.0 - - - +
208A MET 4.7 0.3 + - - -
209A ALA* 4.1 5.9 + - - -
212A GLY* 3.0 34.7 - - - -
213A GLY* 3.3 3.0 + - - -
216A PHE* 3.6 10.0 - - - -
400A ALA 3.1 19.9 + - - -
401A GLY 3.6 5.2 - - - -
402A SER 3.2 0.2 - - - -
403A LEU* 1.3 75.0 - - - +
405A ASN* 1.3 65.1 + - - +
407A MET* 3.3 3.9 + - - +
408A SER* 3.2 25.5 + - - -
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Residues in contact with ASN 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU 4.1 2.2 + - - -
182A ALA 3.1 18.0 - - - +
327A LYS* 3.4 28.0 - - - +
361A PHE 3.7 12.6 - - - +
362A ALA* 3.6 19.2 - - - +
364A CYS 3.0 20.4 - - - +
365A GLY* 3.7 10.7 - - - -
367A ALA* 3.9 3.2 - - - +
401A GLY 2.9 21.4 + - - +
402A SER* 3.7 4.2 - - - +
404A SER* 1.3 76.2 + - - +
406A LEU* 1.3 63.7 + - + +
408A SER* 3.4 5.5 + - - -
409A ALA* 3.1 21.3 + - - +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.8 27.4 - - + -
306A LEU* 3.7 30.1 - - + -
310A ILE* 4.1 19.5 - - + +
324A ILE* 4.0 34.1 - - + -
362A ALA* 4.3 9.4 - - + +
402A SER* 2.9 29.6 + - - +
403A LEU* 3.8 10.8 - - + +
405A ASN* 1.3 75.3 - - + +
407A MET* 1.3 60.6 + - - +
409A ALA* 3.1 6.2 + - - +
410A VAL* 2.9 31.0 + - - +
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Residues in contact with MET 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 3.8 38.8 - - - +
13A LEU* 3.6 18.8 - - + +
14A ILE* 4.0 10.5 - - + -
36A PHE* 3.8 22.9 - - + -
39A GLN* 3.4 28.3 - - - +
215A LEU* 4.6 2.0 - - + -
216A PHE* 3.8 26.0 - - + -
403A LEU 2.9 17.8 + - - +
404A SER 3.5 5.6 - - - +
406A LEU* 1.3 77.0 - - - +
408A SER* 1.3 61.2 + - - +
410A VAL* 3.2 5.4 + - - +
411A ILE* 3.1 31.6 + - + +
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 2.8 21.0 + - - -
205A ALA* 5.2 4.1 + - - -
208A MET* 3.6 32.5 + - - +
209A ALA* 5.6 0.5 - - - -
361A PHE* 4.1 17.8 - - - -
404A SER* 3.2 9.1 + - - -
405A ASN* 3.8 9.3 - - - -
406A LEU 3.3 0.2 - - - -
407A MET* 1.3 78.1 - - - +
409A ALA* 1.3 57.1 + - - +
411A ILE* 3.4 10.5 + - - +
412A ALA* 2.8 27.5 + - - +
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Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 4.6 4.9 - - + -
358A ILE* 3.4 40.7 - - + +
361A PHE* 3.7 9.6 - - - +
362A ALA* 3.8 14.4 - - + +
405A ASN 3.1 14.4 + - - +
406A LEU* 3.1 11.2 + - - +
408A SER* 1.3 76.0 - - - +
410A VAL* 1.3 59.1 + - - +
412A ALA* 3.3 4.2 - - - +
413A GLY 3.0 22.9 + - - -
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 3.3 36.5 + - - +
9A GLY* 4.5 6.1 - - - -
10A MET* 3.6 20.2 - - + +
13A LEU* 3.7 15.9 - - + -
310A ILE* 3.6 39.5 - - + +
406A LEU 2.9 19.9 + - - +
407A MET 3.2 6.7 + - - +
409A ALA* 1.3 73.8 - - - +
411A ILE* 1.3 64.3 + - - +
413A GLY* 3.4 2.1 + - - -
414A LEU* 3.0 22.2 + - - +
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Residues in contact with ILE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 4.1 18.2 - - + -
36A PHE* 5.4 1.6 - - + +
39A GLN* 3.5 42.2 - - + +
40A VAL* 3.7 16.2 - - + +
43A GLY* 3.8 22.7 - - - -
44A ALA 4.3 0.2 - - - +
47A LEU* 4.2 0.8 - - + +
208A MET* 4.9 3.1 - - + -
407A MET* 3.1 20.4 + - + +
408A SER* 3.6 9.2 - - - +
410A VAL* 1.3 75.1 - - - +
412A ALA* 1.3 63.6 + - - +
414A LEU* 3.3 5.8 + - - +
415A PHE* 3.0 54.3 + - + +
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.8 11.7 - - + -
208A MET* 6.2 0.6 - - - +
357A ALA* 4.3 10.5 - - + +
361A PHE* 3.5 35.9 - - + -
408A SER 2.8 14.8 + - - +
409A ALA* 3.3 10.8 - - - +
411A ILE* 1.3 77.0 - - - +
413A GLY* 1.3 52.8 + - - +
414A LEU 3.1 0.3 + - - -
416A THR* 2.4 43.8 + - - +
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Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 4.0 9.9 - - - +
6A SER* 4.8 0.9 - - - -
310A ILE 5.3 0.9 - - - -
354A THR* 3.6 11.4 + - - -
358A ILE* 3.6 25.7 - - - +
409A ALA 3.0 8.5 + - - -
410A VAL 3.4 2.9 + - - -
412A ALA* 1.3 78.4 - - - +
414A LEU* 1.3 60.7 + - - +
416A THR* 3.2 8.3 + - - -
417A GLY* 3.2 17.2 + - - -
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 4.1 8.0 - - + +
3A VAL* 3.7 39.7 - - + +
6A SER* 3.5 23.9 + - - +
7A LEU* 5.9 3.8 - - + -
10A MET* 4.0 20.9 - - + -
40A VAL* 5.3 1.3 - - + -
410A VAL 3.0 16.9 + - - +
411A ILE 3.5 4.5 - - - +
412A ALA 3.1 0.2 - - - -
413A GLY* 1.3 77.0 - - - +
415A PHE* 1.3 88.9 + - + +
417A GLY* 3.1 18.4 + - - +
418A LEU* 5.8 0.9 - - - +
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Residues in contact with PHE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.9 15.0 - - + -
43A GLY 4.3 0.2 - - - -
44A ALA* 3.5 33.0 - - + -
47A LEU* 3.8 33.5 - - + +
48A TYR* 3.4 37.5 - + + -
411A ILE* 3.0 47.0 + - + +
414A LEU* 1.3 100.2 - - + +
416A THR* 1.3 59.6 + - - +
417A GLY 3.0 5.3 + - - -
418A LEU* 3.9 18.0 - - - +
420A GLY* 5.5 1.4 + - - -
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Residues in contact with THR 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.1 21.1 - - + -
201A TYR* 4.1 13.2 - - + +
353A ASP* 5.3 1.2 - - - +
354A THR* 3.8 20.0 + - - -
357A ALA* 3.8 27.6 - - + +
412A ALA* 2.4 39.2 + - + +
413A GLY* 3.2 10.2 + - - -
415A PHE* 1.3 71.9 - - - +
417A GLY* 1.3 54.2 + - - +
418A LEU 3.0 19.1 + - - +
420A GLY* 6.2 1.1 - - - +
421A ALA 6.0 5.4 - - - +
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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