Contacts of the helix formed by residues 490 - 511 (chain E) in PDB entry 1R4N
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 PRO 490 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E THR* 4.1 3.1 - - + +
157E GLY 3.0 25.8 - - - +
158E LEU* 4.5 3.6 - - + -
488E ALA 2.9 22.4 - - - +
489E GLU* 1.3 77.3 - - - +
491E HIS* 1.3 65.9 + - - +
492E THR* 4.7 5.8 - - - +
493E ILE* 3.2 14.0 + - + +
494E ALA* 3.0 19.1 + - - +
19F HIS* 4.2 14.8 - - + +
23F PHE* 3.3 33.7 - - + -
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Residues in contact with HIS 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E ALA* 4.3 5.6 - - + +
43E THR* 5.8 0.2 - - + -
44E GLU* 3.2 29.5 + - + -
72E ASN* 2.8 33.7 + - + +
73E ASN* 4.8 0.4 - - - -
74E PHE* 4.3 6.3 - - + -
489E GLU 3.3 4.5 + - - -
490E PRO* 1.3 66.5 - - - +
492E THR* 1.3 57.8 + - + +
493E ILE 2.8 5.5 + - - -
494E ALA* 3.0 5.4 + - - -
495E ALA* 2.6 36.7 + - + +
19F HIS* 5.4 0.6 - - - +
65F LYS* 2.6 24.6 + - - +
66F ASN* 3.4 27.4 - - - -
69F LEU* 3.6 39.8 - - + +
70F SER* 5.4 1.1 - - - +
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Residues in contact with THR 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E LEU* 5.3 1.6 - - - +
490E PRO* 4.7 5.4 - - - +
491E HIS* 1.3 76.5 - - - +
493E ILE* 1.3 66.0 + - - +
495E ALA* 3.9 6.5 - - - -
496E PHE* 3.4 16.1 + - - +
522E TYR* 5.4 0.7 + - - -
66F ASN* 4.1 6.5 - - + +
70F SER* 3.4 24.9 + - - +
301F ALA* 3.4 17.6 - - - +
304F ALA* 3.5 27.6 - - + -
305F THR* 2.8 34.2 + - - +
308F PHE* 5.6 2.4 - - + +
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Residues in contact with ILE 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E THR* 3.4 22.0 - - + +
157E GLY 3.5 12.3 - - - +
158E LEU* 3.4 45.3 - - + +
159E VAL 4.1 16.2 - - - +
160E GLY* 4.6 6.3 - - - -
490E PRO* 3.2 12.3 + - + +
491E HIS 2.8 1.2 + - - -
492E THR* 1.3 78.9 + - - +
494E ALA* 1.3 67.6 + - - +
495E ALA 2.9 2.5 + - - -
496E PHE* 2.9 14.4 + - - +
497E LEU* 3.0 11.8 + - + +
522E TYR* 3.7 27.6 - - + +
524E GLY* 4.1 5.4 - - - -
305F THR* 4.8 5.6 - - - +
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Residues in contact with ALA 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E ALA* 3.6 17.7 - - + -
41E THR* 3.4 36.9 - - - +
44E GLU* 3.9 6.7 - - + +
155E THR* 3.5 14.3 + - - +
489E GLU* 4.1 2.7 - - + +
490E PRO 3.0 8.5 + - - +
491E HIS* 3.0 7.1 + - - +
493E ILE* 1.3 79.0 - - - +
495E ALA* 1.3 57.2 + - - +
497E LEU* 3.7 1.4 - - - +
498E GLY* 2.8 27.2 + - - -
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Residues in contact with ALA 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLU* 3.9 14.6 - - - +
48E ASN* 4.8 0.2 + - - -
491E HIS* 2.6 21.4 + - + +
492E THR 3.8 1.6 - - - +
493E ILE 2.9 0.4 + - - -
494E ALA* 1.3 70.3 - - - +
496E PHE* 1.3 66.3 + - - +
498E GLY* 2.9 3.3 + - - -
499E GLY* 2.9 19.8 + - - -
62F GLU* 5.6 1.8 - - - +
65F LYS* 4.2 10.8 - - - +
66F ASN* 3.7 18.4 - - - +
297F ALA* 4.6 8.4 - - + +
301F ALA* 3.5 20.2 - - + -
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Residues in contact with PHE 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492E THR 3.4 9.2 + - - +
493E ILE 2.9 8.4 + - - +
495E ALA* 1.3 78.2 - - - +
497E LEU* 1.3 70.5 + - + +
499E GLY* 2.9 12.3 + - - -
500E ALA* 3.1 16.2 + - + -
520E TYR* 3.8 25.1 - + - -
522E TYR* 3.3 66.6 - + + +
529E SER* 5.2 0.2 - - - -
298F VAL* 3.4 37.7 - - + +
301F ALA* 3.3 11.8 - - + +
302F VAL* 3.8 18.2 - - + -
322F LEU* 5.8 2.7 - - + -
324F PHE* 4.5 9.6 - + - -
332F THR* 5.0 5.6 - - + -
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Residues in contact with LEU 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E THR* 4.1 9.6 - - + -
45E ILE* 4.8 0.7 - - - -
153E CYS* 4.6 6.3 - - + -
154E ARG 3.1 35.2 - - - +
155E THR* 3.5 14.8 - - - +
160E GLY* 3.8 27.6 - - - +
161E TYR 3.5 8.1 - - - +
162E MET* 4.0 25.4 - - + -
493E ILE* 3.0 12.1 + - + +
494E ALA 3.7 4.0 - - - +
496E PHE* 1.3 89.6 - - + +
498E GLY* 1.3 58.0 + - - +
499E GLY 3.0 0.2 + - - -
500E ALA* 3.3 1.6 + - + -
501E ALA* 2.9 34.5 + - - +
520E TYR* 5.0 5.4 - - + -
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Residues in contact with GLY 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E THR* 4.7 0.4 - - - +
44E GLU* 4.1 2.2 - - - -
45E ILE* 3.3 34.1 - - - +
48E ASN* 2.9 17.4 + - - -
494E ALA 2.8 19.8 + - - -
495E ALA 2.9 4.2 + - - -
497E LEU* 1.3 73.1 - - - +
499E GLY* 1.3 58.0 + - - +
502E ALA* 3.1 22.1 + - - +
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Residues in contact with GLY 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ASN* 3.5 11.4 - - - +
495E ALA 2.9 12.0 + - - -
496E PHE 2.9 4.2 + - - -
498E GLY* 1.3 77.6 - - - +
500E ALA* 1.3 65.1 + - - +
502E ALA* 3.4 4.2 + - - +
503E GLN* 3.4 16.8 + - - +
294F SER* 3.7 25.7 - - - -
297F ALA* 3.8 5.4 - - - -
298F VAL* 3.8 7.9 - - - -
326F ASP* 5.1 0.2 - - - +
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Residues in contact with ALA 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E MET* 4.3 4.7 - - + -
496E PHE* 3.1 24.4 + - + +
497E LEU* 4.1 3.4 - - + +
499E GLY* 1.3 73.1 - - - +
501E ALA* 1.3 63.6 + - - +
503E GLN* 3.4 6.1 + - - +
504E GLU* 3.2 28.9 + - - +
520E TYR* 4.9 0.2 - - + -
298F VAL* 3.6 11.8 - - + +
324F PHE* 4.6 4.7 - - + -
326F ASP* 4.8 3.8 - - - -
330F LEU* 3.6 33.0 - - + -
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Residues in contact with ALA 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ILE* 4.0 14.8 - - + -
151E LEU* 3.9 5.3 - - + +
153E CYS* 3.7 21.1 - - - -
162E MET* 3.6 23.5 - - - -
497E LEU 2.9 18.7 + - - +
500E ALA* 1.3 75.7 - - - +
502E ALA* 1.3 66.2 + - - +
504E GLU* 2.9 17.1 + - - +
505E VAL* 3.0 17.2 + - - +
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Residues in contact with ALA 502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ILE* 3.8 15.2 - - - +
48E ASN* 3.3 28.9 - - + +
49E LEU* 3.3 24.0 - - + +
498E GLY 3.1 19.6 + - - +
499E GLY 3.6 4.5 - - - +
500E ALA 3.4 0.4 - - - -
501E ALA* 1.3 80.1 - - - +
503E GLN* 1.3 62.9 + - - +
505E VAL* 3.3 2.6 + - - -
506E ILE* 3.2 18.7 + - - +
294F SER* 5.0 2.5 - - - +
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Residues in contact with GLN 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TRP* 4.3 0.5 - - - -
499E GLY 3.4 3.9 + - - +
500E ALA 3.6 8.3 - - - +
501E ALA 3.1 0.6 - - - -
502E ALA* 1.3 77.4 - - - +
504E GLU* 1.3 65.7 + - - +
506E ILE* 3.0 27.9 + - - +
507E LYS* 2.8 45.7 + - - +
513E PHE* 4.7 6.1 - - - -
185F PHE* 3.1 41.5 - - + -
294F SER* 3.3 19.7 + - - -
326F ASP* 3.7 28.9 - - + +
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Residues in contact with GLU 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E LEU* 4.5 8.3 - - + -
162E MET* 4.6 1.8 - - + -
164E ILE* 5.3 3.8 - - + -
500E ALA 3.3 14.2 - - - +
501E ALA* 2.9 9.3 + - - +
503E GLN* 1.3 75.2 - - - +
505E VAL* 1.3 65.4 + - - +
507E LYS* 2.9 43.6 + - - +
508E ILE* 2.8 32.2 + - + +
515E ILE* 3.6 3.0 - - + +
516E PHE* 3.3 50.3 + - + -
326F ASP* 3.3 16.5 - - - +
330F LEU* 3.4 8.2 - - - +
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Residues in contact with VAL 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.9 18.6 - - + -
45E ILE* 4.8 2.2 - - + -
49E LEU* 4.0 13.5 - - + -
125E VAL* 4.3 13.2 - - + -
127E VAL* 3.6 26.9 - - + -
151E LEU* 3.7 11.9 - - + -
501E ALA 3.0 15.3 + - - +
502E ALA* 3.4 10.8 - - - +
504E GLU* 1.3 77.3 - - - +
506E ILE* 1.3 56.3 + - - +
508E ILE* 3.3 11.8 - - + +
509E ILE* 2.9 44.6 + - + +
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Residues in contact with ILE 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TRP* 3.7 37.2 - - + -
28E LEU* 4.4 18.6 - - + -
48E ASN 4.8 0.7 - - - +
49E LEU* 3.9 16.4 - - + -
52E PRO* 4.7 9.2 - - + -
502E ALA 3.2 12.8 + - - +
503E GLN* 3.0 29.6 + - - +
505E VAL* 1.3 73.6 - - - +
507E LYS* 1.3 68.0 - - - +
508E ILE 2.9 1.6 - - - -
509E ILE* 2.8 8.1 + - + +
510E THR* 2.7 49.4 + - + +
513E PHE* 6.1 0.7 - - + -
294F SER* 4.3 7.9 - - - +
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Residues in contact with LYS 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E HIS* 3.8 7.3 + - - -
503E GLN* 2.8 39.1 + - - +
504E GLU* 3.0 45.9 + - - +
506E ILE* 1.3 71.5 - - - +
508E ILE* 1.3 57.0 + - - +
510E THR* 3.8 5.8 - - - -
511E LYS* 2.9 26.2 + - - -
512E GLN 3.4 2.9 + - - -
513E PHE* 3.8 26.7 + - + +
514E VAL 3.1 29.8 + - - +
515E ILE* 4.0 9.6 - - + -
185F PHE* 5.9 0.2 - - - -
326F ASP 2.6 31.3 + - - -
329F GLY* 3.4 11.3 + - - +
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Residues in contact with ILE 508 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E THR* 5.8 0.7 - - + -
125E VAL* 3.6 33.7 - - + -
149E PRO* 4.3 8.3 - - + -
150E LEU 5.8 0.4 - - - +
151E LEU* 5.5 6.3 - - + -
164E ILE* 3.8 16.2 - - + -
166E ILE* 3.7 35.2 - - + -
169E HIS* 3.8 11.7 - - + +
504E GLU* 2.8 20.3 + - + +
505E VAL* 3.3 15.9 - - + +
506E ILE 2.8 0.2 + - - -
507E LYS* 1.3 76.5 - - - +
509E ILE* 1.3 64.3 + - - +
511E LYS* 3.4 19.4 + - - +
515E ILE* 4.2 11.9 - - + -
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Residues in contact with ILE 509 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ALA* 3.7 22.9 - - - +
28E LEU* 3.8 26.7 - - + -
31E ALA* 3.4 33.4 - - + -
33E VAL* 4.1 13.5 - - + -
49E LEU* 5.8 0.7 - - + -
54E ILE* 4.7 2.2 - - + -
124E THR* 3.9 22.9 - - + -
125E VAL* 4.5 3.1 - - + -
505E VAL* 2.9 37.9 + - + +
506E ILE* 2.8 11.9 + - + +
508E ILE* 1.3 73.9 - - - +
510E THR* 1.3 60.4 + - + +
511E LYS* 4.4 5.4 - - - +
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Residues in contact with THR 510 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E TRP* 4.9 6.1 - - + -
24E GLY* 3.7 31.4 - - - +
27E ALA* 4.3 9.3 - - - +
28E LEU* 4.5 10.8 - - + +
506E ILE* 2.7 48.7 + - + +
507E LYS* 3.8 2.3 - - - -
509E ILE* 1.3 72.3 - - + +
511E LYS* 1.3 70.0 + - - +
512E GLN* 2.9 36.6 + - + +
513E PHE* 4.8 1.6 - - - -
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Residues in contact with LYS 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E HIS* 4.1 18.8 - - + -
170E PRO* 4.8 16.5 - - + +
171E VAL* 4.1 17.1 - - - +
172E ILE 4.7 2.9 + - - -
173E GLU* 4.2 5.2 + - - +
507E LYS 2.9 15.2 + - - -
508E ILE 3.6 13.0 - - - +
509E ILE 3.3 4.6 - - - +
510E THR* 1.3 79.8 - - - +
512E GLN* 1.3 60.5 + - - +
513E PHE 3.7 1.3 - - - -
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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