Contacts of the helix formed by residues 490 - 511 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C THR* 4.1 3.0 - - + +
157C GLY 3.0 25.4 - - - +
158C LEU* 4.5 4.3 - - + -
488C ALA 2.9 23.1 - - - +
489C GLU* 1.3 76.8 - - - +
491C HIS* 1.3 65.2 + - - +
492C THR* 4.7 5.2 - - - +
493C ILE* 3.2 13.9 + - + +
494C ALA* 3.0 19.1 + - - +
19D HIS* 4.2 15.7 - - + +
23D PHE* 3.4 32.5 - - + -
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Residues in contact with HIS 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA* 4.3 6.0 - - + +
43C THR* 5.8 0.2 - - + -
44C GLU* 3.2 29.4 + - + -
72C ASN* 2.8 31.9 + - + +
73C ASN* 4.8 0.4 - - - -
74C PHE 4.3 6.3 - - - -
489C GLU 3.3 4.2 + - - -
490C PRO* 1.3 67.1 - - - +
492C THR* 1.3 57.3 + - + +
493C ILE 2.8 5.0 + - - -
494C ALA* 2.9 4.8 + - - -
495C ALA* 2.6 36.7 + - + +
19D HIS* 5.4 0.8 - - - +
65D LYS* 2.7 32.1 + - + -
66D ASN* 3.4 20.0 - - - -
69D LEU* 3.5 44.1 + - + +
70D SER* 5.4 1.1 - - - +
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Residues in contact with THR 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 5.3 1.6 - - - +
490C PRO* 4.7 5.5 - - - +
491C HIS* 1.3 77.0 - - - +
493C ILE* 1.3 65.6 + - - +
495C ALA* 3.9 6.5 - - - -
496C PHE* 3.4 15.8 + - - +
522C TYR* 5.4 0.5 + - - -
66D ASN* 4.1 8.1 - - + +
70D SER* 3.4 25.1 + - - +
301D ALA* 3.5 16.9 - - - +
304D ALA* 3.5 28.0 - - + -
305D THR* 2.8 34.8 + - - +
308D PHE* 5.7 1.2 - - + +
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Residues in contact with ILE 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C THR* 3.4 22.4 - - + +
157C GLY 3.5 12.3 - - - +
158C LEU* 3.4 44.4 - - + +
159C VAL 4.2 15.7 - - - +
160C GLY* 4.6 5.8 - - - -
490C PRO* 3.2 12.9 + - + +
491C HIS 2.8 1.2 + - - -
492C THR* 1.3 78.7 + - - +
494C ALA* 1.3 68.2 + - - +
495C ALA 2.9 1.1 - - - -
496C PHE* 2.8 16.1 + - - +
497C LEU* 3.0 12.3 + - + +
522C TYR* 3.6 27.8 - - + +
524C GLY* 4.1 5.6 - - - -
305D THR* 4.8 5.6 - - + +
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Residues in contact with ALA 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA* 3.6 16.8 - - + -
41C THR* 3.4 36.2 - - - +
44C GLU* 4.0 6.5 - - + +
155C THR* 3.5 13.9 - - - +
489C GLU* 4.1 2.5 - - + +
490C PRO 3.0 9.1 + - - +
491C HIS* 2.9 6.9 + - - +
493C ILE* 1.3 78.3 - - - +
495C ALA* 1.3 57.3 + - - +
497C LEU* 3.4 2.2 + - - +
498C GLY* 2.8 27.5 + - - -
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Residues in contact with ALA 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 3.9 14.6 - - + +
48C ASN* 4.8 0.2 + - - -
491C HIS* 2.6 21.6 + - + +
492C THR 3.8 1.3 - - - +
493C ILE 2.8 0.6 + - - -
494C ALA* 1.3 70.3 - - - +
496C PHE* 1.3 65.8 + - - +
498C GLY* 3.0 2.9 + - - -
499C GLY* 2.9 20.1 + - - -
62D GLU* 5.6 2.0 - - - +
65D LYS* 4.1 11.0 - - - +
66D ASN* 3.7 19.7 - - - +
297D ALA* 4.5 9.0 - - + +
301D ALA* 3.6 18.8 - - + -
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Residues in contact with PHE 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C THR 3.4 9.6 + - - +
493C ILE 2.8 11.3 + - - +
495C ALA* 1.3 73.8 - - - +
497C LEU* 1.3 69.3 + - + +
499C GLY* 3.0 11.4 + - - -
500C ALA* 3.1 16.9 + - + -
520C TYR* 3.8 26.2 - + - -
522C TYR* 3.4 66.4 - + + +
298D VAL* 3.3 38.6 - - + +
301D ALA* 3.4 12.4 - - + +
302D VAL* 3.8 18.2 - - + -
322D LEU* 5.8 2.5 - - + -
324D PHE* 4.4 10.8 - + - -
332D THR* 5.1 4.9 - - + -
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Residues in contact with LEU 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 4.0 9.9 - - + -
45C ILE* 4.9 0.7 - - - -
153C CYS* 4.6 6.3 - - + -
154C ARG 3.1 35.2 - - - +
155C THR* 3.5 14.8 - - - +
160C GLY* 3.8 27.8 - - - +
161C TYR 3.5 8.3 - - - +
162C MET* 4.0 26.2 - - + -
493C ILE* 3.0 7.9 + - + +
494C ALA 3.7 7.6 - - - +
496C PHE* 1.3 90.7 - - + +
498C GLY* 1.3 57.3 + - - +
499C GLY 3.1 0.2 + - - -
500C ALA* 3.3 2.3 + - + +
501C ALA* 2.9 33.8 + - - +
520C TYR* 5.0 5.8 - - + -
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Residues in contact with GLY 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 4.4 0.6 - - - +
44C GLU* 4.2 1.8 - - - -
45C ILE* 3.3 33.6 - - - +
48C ASN* 2.9 18.2 + - - -
494C ALA 2.8 19.8 + - - -
495C ALA 3.5 3.4 - - - -
497C LEU* 1.3 74.5 - - - +
499C GLY* 1.3 55.8 + - - +
502C ALA* 3.1 22.7 + - - +
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Residues in contact with GLY 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASN* 3.5 11.9 - - - +
495C ALA 2.9 9.3 + - - -
496C PHE 3.0 4.9 + - - -
498C GLY* 1.3 77.0 - - - +
500C ALA* 1.3 64.3 + - - +
502C ALA* 3.6 2.9 - - - +
503C GLN* 3.4 16.3 + - - +
294D SER* 3.6 25.8 - - - -
297D ALA* 3.8 7.4 - - - -
298D VAL* 3.8 8.3 - - - -
326D ASP* 5.2 0.2 - - - +
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Residues in contact with ALA 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C MET* 4.3 4.5 - - + -
496C PHE* 3.1 23.6 + - + +
497C LEU* 4.1 2.5 - - + +
499C GLY* 1.3 75.1 - - - +
501C ALA* 1.3 62.9 + - - +
503C GLN* 3.4 6.5 + - - +
504C GLU* 3.3 28.9 + - - +
520C TYR* 4.9 0.4 - - + -
298D VAL* 3.6 10.8 - - + +
324D PHE* 4.6 4.9 - - + -
326D ASP* 4.5 3.5 - - - +
330D LEU* 3.7 32.8 - - + -
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Residues in contact with ALA 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 4.0 14.6 - - + -
151C LEU* 3.9 5.2 - - + +
153C CYS* 3.7 20.6 - - - -
162C MET* 3.6 22.5 - - - -
497C LEU 2.9 17.7 + - - +
500C ALA* 1.3 75.3 - - - +
502C ALA* 1.3 67.0 + - - +
504C GLU* 2.9 17.0 + - - +
505C VAL* 3.0 17.4 + - - +
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Residues in contact with ALA 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.8 15.2 - - - +
48C ASN* 3.2 29.8 - - + +
49C LEU* 3.3 23.6 - - + +
498C GLY 3.1 19.4 + - - +
499C GLY 3.6 4.5 - - - +
501C ALA* 1.3 79.7 - - - +
503C GLN* 1.3 63.4 + - - +
505C VAL* 3.3 1.8 + - - -
506C ILE* 3.2 18.3 + - - +
294D SER* 5.0 2.5 - - - +
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Residues in contact with GLN 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TRP* 4.2 0.9 - - - -
499C GLY 3.4 4.1 + - - +
500C ALA 3.6 9.4 - - - +
501C ALA 3.1 0.6 - - - -
502C ALA* 1.3 77.7 - - - +
504C GLU* 1.3 60.6 + - - +
506C ILE* 3.0 28.0 + - - +
507C LYS* 2.8 50.4 + - - +
513C PHE* 4.6 6.5 - - - -
185D PHE* 3.0 43.6 - - + -
294D SER* 3.4 19.4 + - - -
326D ASP* 3.7 25.8 - - + +
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Residues in contact with GLU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU* 4.4 8.5 - - + -
162C MET* 4.6 1.6 - - + -
164C ILE* 5.3 3.4 - - + -
500C ALA 3.3 14.1 - - - +
501C ALA* 2.9 9.7 + - - +
503C GLN* 1.3 75.1 - - - +
505C VAL* 1.3 64.8 + - - +
507C LYS* 2.9 46.1 + - - +
508C ILE* 2.8 32.7 + - + +
515C ILE* 3.6 3.2 - - + -
516C PHE* 3.4 49.9 + - + -
326D ASP* 3.3 16.5 - - - +
330D LEU* 3.3 7.1 - - - +
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Residues in contact with VAL 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 4.0 17.7 - - + -
45C ILE* 4.9 1.8 - - + -
49C LEU* 4.0 14.6 - - + -
125C VAL* 4.3 13.0 - - + -
127C VAL* 3.6 26.7 - - + -
151C LEU* 3.7 12.1 - - + +
501C ALA 3.0 15.6 + - - +
502C ALA* 3.4 10.3 - - - +
504C GLU* 1.3 76.6 - - - +
506C ILE* 1.3 57.3 + - - +
508C ILE* 3.3 10.7 - - - +
509C ILE* 2.9 45.2 + - + +
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Residues in contact with ILE 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TRP* 3.7 38.4 - - + -
28C LEU* 4.4 17.9 - - + -
48C ASN 4.9 0.4 - - - +
49C LEU* 3.8 17.0 - - + -
52C PRO* 4.7 9.0 - - + -
502C ALA 3.4 13.0 - - - +
503C GLN* 3.0 29.2 + - - +
505C VAL* 1.3 73.4 - - - +
507C LYS* 1.3 58.1 + - - +
508C ILE 2.9 2.1 + - - -
509C ILE* 2.9 6.4 + - - +
510C THR* 2.7 59.4 + - + +
513C PHE* 6.2 0.4 - - + -
294D SER* 4.3 8.3 - - - +
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Residues in contact with LYS 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C HIS* 3.8 6.6 + - - -
503C GLN* 2.8 39.1 + - - +
504C GLU* 3.0 45.5 + - - +
506C ILE* 1.3 72.5 - - - +
508C ILE* 1.3 57.4 + - - +
510C THR* 3.8 6.3 - - - -
511C LYS* 2.9 27.2 + - - -
512C GLN 3.4 2.6 + - - -
513C PHE* 3.8 26.6 + - + +
514C VAL 3.1 29.7 + - - +
515C ILE* 4.0 10.5 - - + -
326D ASP 2.6 32.3 + - - -
329D GLY* 3.4 10.9 + - - +
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Residues in contact with ILE 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C THR* 5.2 1.1 - - + +
125C VAL* 3.5 32.3 - - + -
149C PRO* 4.3 8.3 - - + -
150C LEU 5.8 0.7 - - - +
151C LEU* 5.5 6.1 - - + -
164C ILE* 3.8 17.5 - - + -
166C ILE* 3.6 35.9 - - + -
169C HIS* 3.8 12.0 - - + +
504C GLU* 2.8 20.0 + - + +
505C VAL* 3.3 15.7 - - + +
507C LYS* 1.3 75.5 - - - +
509C ILE* 1.3 65.4 + - - +
511C LYS* 3.3 19.8 + - - +
515C ILE* 4.1 11.9 - - + -
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Residues in contact with ILE 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ALA* 3.7 23.3 - - - +
28C LEU* 3.8 24.9 - - + -
31C ALA* 3.4 34.3 - - + -
33C VAL* 4.1 13.0 - - + -
49C LEU* 5.8 0.9 - - + -
54C ILE* 4.7 2.0 - - + -
124C THR* 3.8 22.7 - - + -
125C VAL* 4.4 3.6 - - + -
505C VAL* 2.9 37.9 + - + +
506C ILE* 2.9 7.0 + - + +
508C ILE* 1.3 77.2 - - - +
510C THR* 1.3 62.2 + - + +
511C LYS* 3.5 5.4 + - - +
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Residues in contact with THR 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TRP* 4.9 6.5 - - + -
24C GLY* 3.6 31.4 - - - +
27C ALA* 4.3 8.7 - - - +
28C LEU* 4.4 10.1 - - + +
506C ILE* 2.7 48.2 + - + +
507C LYS* 3.7 2.3 + - - -
509C ILE* 1.3 72.2 - - + +
511C LYS* 1.3 70.5 + - - +
512C GLN* 2.9 37.8 + - + +
513C PHE* 4.7 1.4 - - - -
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Residues in contact with LYS 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C HIS* 4.0 20.9 - - + -
170C PRO* 4.8 17.0 - - + +
171C VAL* 4.1 17.7 - - - +
172C ILE 4.7 2.4 + - - -
173C GLU* 4.2 5.5 + - - +
507C LYS 2.9 15.3 + - - -
508C ILE 3.6 12.3 - - - +
509C ILE 3.3 5.3 - - - +
510C THR* 1.3 78.9 - - - +
512C GLN* 1.3 60.1 + - - +
513C 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