Contacts of the helix formed by residues 490 - 511 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR* 4.1 3.1 - - + -
157A GLY 3.0 25.4 - - - +
158A LEU* 4.4 4.3 - - + -
488A ALA 2.9 22.9 - - - +
489A GLU* 1.3 77.4 - - - +
491A HIS* 1.3 60.7 + - - +
492A THR* 4.7 5.2 - - - +
493A ILE* 3.2 14.0 + - + +
494A ALA* 3.0 23.4 + - - +
19B HIS* 4.2 14.6 - - + +
23B PHE* 3.4 33.4 - - + -
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Residues in contact with HIS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 4.2 6.5 - - + +
43A THR* 5.8 0.2 - - + -
44A GLU* 3.2 29.0 + - + -
72A ASN* 2.8 31.7 + - + +
73A ASN* 4.8 0.4 - - - -
74A PHE 4.3 6.5 - - - -
489A GLU 3.3 4.8 + - - -
490A PRO* 1.3 66.5 - - - +
492A THR* 1.3 56.5 + - + +
493A ILE 2.9 5.5 + - - -
494A ALA* 3.0 5.5 + - - +
495A ALA* 2.6 37.2 + - + +
19B HIS* 5.4 0.6 - - - +
65B LYS* 2.6 26.7 + - + +
66B ASN* 3.4 28.9 - - - +
69B LEU* 3.5 40.2 + - + +
70B SER* 5.4 0.4 - - - +
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Residues in contact with THR 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.3 1.4 - - - +
490A PRO* 4.7 5.7 - - - +
491A HIS* 1.3 74.8 - - - +
493A ILE* 1.3 64.6 + - - +
495A ALA* 3.9 6.7 - - - -
496A PHE* 3.4 4.7 + - - +
522A TYR* 5.4 0.2 + - - -
66B ASN* 4.0 9.9 - - + +
70B SER* 3.3 25.7 + - - +
301B ALA* 3.4 29.7 - - - +
304B ALA* 3.4 27.8 - - + -
305B THR* 2.8 33.5 + - - +
308B PHE* 5.7 1.4 - - + +
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Residues in contact with ILE 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A THR* 3.4 24.2 - - + +
157A GLY 3.5 11.0 - - - +
158A LEU* 3.4 44.6 - - + +
159A VAL 4.2 15.3 - - - +
160A GLY* 4.6 5.6 - - - -
490A PRO* 3.2 12.7 + - + +
491A HIS 2.9 0.6 - - - -
492A THR* 1.3 78.5 + - - +
494A ALA* 1.3 69.7 + - - +
495A ALA 2.9 2.7 + - - -
496A PHE* 2.9 14.6 + - - +
497A LEU* 3.0 11.7 + - + +
522A TYR* 3.6 27.4 - - + +
524A GLY* 4.1 5.8 - - - -
305B THR* 4.7 5.8 - - - +
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Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 3.5 18.2 - - + -
41A THR* 3.5 35.9 - - - +
44A GLU* 4.0 6.6 - - + +
155A THR* 3.5 14.6 + - - +
489A GLU* 4.1 2.5 - - + +
490A PRO 3.0 8.9 + - - +
491A HIS* 3.0 7.1 + - - +
493A ILE* 1.3 80.0 - - - +
495A ALA* 1.3 57.3 - - - +
497A LEU* 3.7 1.6 - - - +
498A GLY* 2.8 27.2 + - - -
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Residues in contact with ALA 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLU* 3.9 15.0 - - + +
48A ASN* 4.8 0.3 + - - -
491A HIS* 2.6 21.6 + - + +
492A THR 3.9 1.3 - - - +
493A ILE 2.9 0.8 + - - -
494A ALA* 1.3 70.1 - - - +
496A PHE* 1.3 66.3 + - - +
498A GLY* 3.0 3.3 + - - -
499A GLY* 2.9 19.6 + - - -
62B GLU* 5.5 2.2 - - - +
65B LYS* 4.1 11.9 - - - +
66B ASN* 3.6 20.0 - - - +
297B ALA* 4.5 8.2 - - + +
301B ALA* 3.6 18.2 - - + -
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Residues in contact with PHE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A THR 3.4 8.7 + - - +
493A ILE 2.9 11.3 + - - +
495A ALA* 1.3 74.2 - - - +
497A LEU* 1.3 69.5 + - + +
499A GLY* 3.0 12.0 + - - -
500A ALA* 3.1 16.4 + - + -
520A TYR* 3.8 25.8 - + - -
522A TYR* 3.4 61.7 - + + +
298B VAL* 3.2 40.8 - - + +
301B ALA* 3.3 13.5 - - + +
302B VAL* 3.8 21.5 - - + -
322B LEU* 5.8 2.9 - - + -
324B PHE* 4.4 10.1 - + - -
332B THR* 5.0 5.2 - - + -
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.0 9.9 - - + -
45A ILE* 4.9 0.4 - - - -
153A CYS* 4.7 6.3 - - + -
154A ARG 3.1 35.0 - - - +
155A THR* 3.5 14.4 - - - +
160A GLY* 3.8 23.6 - - - +
161A TYR 3.5 8.7 - - - +
162A MET* 4.0 30.1 - - + -
493A ILE 3.0 7.6 + - - +
494A ALA 3.7 8.1 - - - +
496A PHE* 1.3 89.1 - - + +
498A GLY* 1.3 58.9 + - - +
499A GLY 3.0 0.3 + - - -
500A ALA* 3.3 2.1 + - + +
501A ALA* 2.9 33.9 + - - +
520A TYR* 5.0 5.8 - - + -
522A TYR* 5.2 0.2 - - + -
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Residues in contact with GLY 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.4 0.4 - - - +
44A GLU* 4.2 2.0 - - - -
45A ILE* 3.4 34.1 - - - +
48A ASN* 2.9 18.4 + - - -
494A ALA 2.8 19.6 + - - -
495A ALA 3.0 3.6 + - - -
497A LEU* 1.3 72.9 - - - +
499A GLY* 1.3 56.7 + - - +
502A ALA* 3.1 22.4 + - - +
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Residues in contact with GLY 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN* 3.5 11.7 - - - -
495A ALA 2.9 9.1 + - - -
496A PHE 3.0 4.7 + - - -
498A GLY* 1.3 78.4 - - - +
500A ALA* 1.3 64.9 + - - +
502A ALA* 3.6 2.4 - - - +
503A GLN* 3.4 16.3 + - - +
294B SER* 3.6 26.3 - - - -
297B ALA* 3.8 8.1 - - - -
298B VAL* 3.8 7.4 - - - -
326B ASP* 5.1 0.2 - - - +
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Residues in contact with ALA 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A MET* 4.3 4.3 - - + -
496A PHE* 3.1 24.2 + - + +
497A LEU* 4.0 3.1 - - + +
499A GLY* 1.3 74.5 - - - +
501A ALA* 1.3 63.0 + - - +
503A GLN* 3.4 4.0 + - - +
504A GLU* 3.3 29.9 + - - +
520A TYR* 4.9 0.2 - - + -
298B VAL* 3.6 11.0 - - + +
324B PHE* 4.6 4.9 - - + -
326B ASP* 4.8 4.9 - - - -
330B LEU* 3.6 32.5 - - + -
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Residues in contact with ALA 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 4.0 14.8 - - + -
151A LEU* 3.9 5.0 - - + +
153A CYS* 3.7 21.3 - - - -
162A MET* 3.6 22.8 - - - -
497A LEU 2.9 18.7 + - - +
500A ALA* 1.3 74.9 - - - +
502A ALA* 1.3 66.4 + - - +
504A GLU* 2.9 16.3 + - - +
505A VAL* 3.0 17.0 + - - +
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Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.8 15.9 - - - +
48A ASN* 3.2 30.1 - - + +
49A LEU* 3.4 18.8 - - + +
498A GLY 3.1 19.8 + - - +
499A GLY 3.6 4.5 - - - +
501A ALA* 1.3 79.3 - - - +
503A GLN* 1.3 62.9 + - - +
505A VAL* 3.2 7.5 + - - +
506A ILE* 3.1 18.3 + - - +
294B SER* 5.0 2.5 - - - +
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Residues in contact with GLN 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TRP* 4.3 1.0 - - - -
499A GLY 3.4 3.3 + - - +
500A ALA 3.6 9.0 - - - +
501A ALA 3.1 0.6 - - - -
502A ALA* 1.3 77.2 - - - +
504A GLU* 1.3 60.1 + - - +
506A ILE* 2.9 28.0 + - - +
507A LYS* 2.8 50.6 + - - +
513A PHE* 4.6 6.9 - - - -
185B PHE* 3.1 42.7 - - + -
294B SER* 3.4 17.1 + - - -
326B ASP* 3.7 28.5 - - + +
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Residues in contact with GLU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.4 8.5 - - + -
162A MET* 4.6 1.6 - - + -
164A ILE* 5.3 2.7 - - + -
500A ALA 3.3 13.6 - - - +
501A ALA* 2.9 10.1 + - - +
503A GLN* 1.3 76.3 - - - +
505A VAL* 1.3 65.5 + - - +
507A LYS* 2.9 45.1 + - - +
508A ILE* 2.8 32.7 + - + +
515A ILE* 3.6 2.6 - - + +
516A PHE* 3.3 50.3 + - + -
326B ASP* 3.3 17.0 - - - +
330B LEU* 3.3 6.5 - - - +
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Residues in contact with VAL 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.9 18.2 - - + -
45A ILE* 4.8 2.0 - - + -
49A LEU* 4.0 14.8 - - + -
125A VAL* 4.3 13.5 - - + -
127A VAL* 3.6 26.9 - - + -
151A LEU* 3.7 11.9 - - + -
501A ALA 3.0 15.5 + - - +
502A ALA* 3.3 10.5 - - - +
504A GLU* 1.3 76.2 - - - +
506A ILE* 1.3 59.3 + - - +
508A ILE* 3.3 10.7 + - - +
509A ILE* 2.9 44.2 + - + +
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Residues in contact with ILE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TRP* 3.7 37.9 - - + -
28A LEU* 4.4 19.1 - - + -
48A ASN 4.8 0.9 - - - +
49A LEU* 3.8 16.4 - - + -
52A PRO* 4.7 8.7 - - + -
502A ALA 3.1 12.9 + - - +
503A GLN* 2.9 29.4 + - - +
505A VAL* 1.3 72.6 - - - +
507A LYS* 1.3 67.4 + - - +
508A ILE 2.9 1.8 - - - -
509A ILE* 2.8 7.7 + - + +
510A THR* 2.7 49.0 + - + +
513A PHE* 6.1 0.7 - - + -
294B SER* 4.4 8.1 - - - +
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Residues in contact with LYS 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A HIS* 3.8 5.8 + - - -
503A GLN* 2.8 39.3 + - - +
504A GLU* 3.1 45.5 + - - +
506A ILE* 1.3 73.2 - - - +
508A ILE* 1.3 56.7 + - - +
510A THR* 3.7 5.6 - - - -
511A LYS* 2.9 27.4 + - - -
512A GLN 3.3 2.8 + - - -
513A PHE* 3.8 27.4 + - + +
514A VAL 3.0 28.9 + - - +
515A ILE* 4.0 9.2 - - + -
326B ASP 2.6 32.2 + - - -
329B GLY 3.4 10.9 + - - +
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Residues in contact with ILE 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A THR* 5.8 1.1 - - + -
125A VAL* 3.6 31.9 - - + -
149A PRO* 4.3 8.5 - - + -
150A LEU 5.8 0.7 - - - +
151A LEU* 5.5 6.5 - - + -
164A ILE* 3.7 17.5 - - + -
166A ILE* 3.6 35.4 - - + -
169A HIS* 3.8 11.6 - - + +
504A GLU* 2.8 19.6 + - + +
505A VAL* 3.3 15.0 - - + +
507A LYS* 1.3 76.3 - - - +
509A ILE* 1.3 64.1 + - - +
511A LYS* 3.3 19.6 + - - +
515A ILE* 4.1 12.1 - - + -
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Residues in contact with ILE 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 3.6 23.3 - - - +
28A LEU* 3.7 26.5 - - + -
31A ALA* 3.5 33.2 - - + -
33A VAL* 4.1 13.2 - - + -
49A LEU* 5.8 0.7 - - + -
54A ILE* 4.7 2.2 - - + -
124A THR* 3.9 21.8 - - + -
125A VAL* 4.4 3.1 - - + -
505A VAL* 2.9 39.0 + - + +
506A ILE* 2.8 7.5 + - + +
508A ILE* 1.3 78.5 - - - +
510A THR* 1.3 60.2 + - + +
511A LYS* 3.5 5.4 + - - +
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Residues in contact with THR 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TRP* 4.9 6.7 - - + +
24A GLY* 3.7 31.5 - - - +
27A ALA* 4.3 8.1 - - - +
28A LEU* 4.5 10.8 - - + +
506A ILE* 2.7 47.5 + - + +
507A LYS* 3.7 2.4 + - - -
509A ILE* 1.3 73.0 - - + +
511A LYS* 1.3 70.2 + - - +
512A GLN* 2.9 36.7 + - + +
513A PHE* 4.7 1.2 - - - -
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Residues in contact with LYS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A HIS* 4.1 20.0 - - + -
170A PRO* 4.8 17.2 - - + +
171A VAL* 4.1 17.4 - - - +
172A ILE 4.7 2.6 + - - -
173A GLU* 4.2 5.5 + - - +
507A LYS 2.9 14.3 + - - -
508A ILE 3.3 12.5 + - - +
509A ILE 3.3 4.6 - - - +
510A THR* 1.3 80.1 - - - +
512A GLN* 1.3 60.0 + - - +
513A PHE 3.8 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