Contacts of the helix formed by residues 277 - 301 (chain 2) in PDB entry 4BOG
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 277 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1352 PHE* 3.8 24.2 - + - -
1362 PRO* 3.3 28.3 - - + +
1372 PHE* 3.3 38.8 - + - -
1382 ASP* 4.7 1.1 + - - -
2102 ILE* 4.1 0.8 - - + +
2732 LEU* 4.5 11.9 - - + -
2742 ILE* 2.9 48.4 + - + +
2752 GLY 2.4 6.7 + - - -
2762 LYS* 1.3 71.0 - - + +
2782 MET* 1.3 53.1 + - - +
2792 LEU 2.9 4.5 - - - -
2802 PHE* 2.7 66.6 + + - +
2812 THR* 4.0 0.5 + - - -
4312 ILE* 4.8 9.7 - - + +
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Residues in contact with MET 278 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2311 ASN* 4.9 4.9 - - - +
2612 VAL* 5.0 9.6 - - + -
2642 ILE* 3.6 39.7 - - + -
2682 SER* 6.2 0.9 - - - +
2732 LEU* 5.5 9.4 - - + +
2752 GLY* 2.9 13.6 + - - +
2772 TYR* 1.3 74.4 - - - +
2792 LEU* 1.3 50.8 + - + +
2802 PHE 3.0 0.2 - - - -
2812 THR* 2.6 50.0 + - - -
2822 MET* 2.8 63.0 + - + +
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Residues in contact with LEU 279 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2752 GLY 3.7 8.5 - - - +
2762 LYS* 3.2 35.2 - - + +
2772 TYR 2.8 0.2 + - - -
2782 MET* 1.3 78.8 - - + +
2802 PHE* 1.3 69.1 + - + +
2822 MET* 3.2 25.0 - - + +
2832 ILE* 3.5 14.8 + - - +
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Residues in contact with PHE 280 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2762 LYS* 2.6 29.2 - - + -
2772 TYR* 2.7 49.8 + + - +
2792 LEU* 1.3 76.1 - - + +
2812 THR* 1.3 58.4 + - - +
2832 ILE* 5.1 0.2 - - - -
2842 PHE* 2.6 63.7 + + + -
4242 SER 5.8 1.1 - - - -
4272 ALA* 5.6 6.7 - - + -
4282 GLY* 5.4 12.3 - - - -
4312 ILE* 4.0 25.1 - - + -
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Residues in contact with THR 281 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2182 VAL* 4.0 27.4 - - + -
2222 CYS* 6.2 4.3 - - - -
2602 ILE* 6.5 0.4 - - + -
2612 VAL* 6.3 0.4 - - - -
2642 ILE* 5.5 7.4 - - + -
2772 TYR 4.3 0.5 + - - -
2782 MET* 2.6 45.0 + - - -
2802 PHE* 1.3 76.0 - - + +
2822 MET* 1.3 68.5 + - - +
2842 PHE* 4.1 9.6 - - + -
2852 VAL* 2.7 31.3 + - + +
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Residues in contact with MET 282 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2311 ASN* 3.9 26.9 - - - +
2341 THR* 5.3 11.0 - - + -
2612 VAL* 5.5 6.7 - - + -
2782 MET* 2.8 36.7 + - + +
2792 LEU* 3.2 23.6 - - + +
2802 PHE 3.2 0.2 - - - -
2812 THR* 1.3 78.7 - - - +
2832 ILE* 1.3 56.0 + - + +
2852 VAL* 3.9 6.9 - - + +
2862 ILE* 2.7 67.4 + - + +
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Residues in contact with ILE 283 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2792 LEU 3.6 14.1 - - - +
2802 PHE* 3.9 2.9 - - - +
2822 MET* 1.3 80.0 - - + +
2842 PHE* 1.3 71.0 + - + +
2862 ILE* 3.1 17.0 - - + +
2872 SER* 2.5 38.3 + - - -
2902 ILE* 4.8 1.2 - - - +
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Residues in contact with PHE 284 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2252 PHE* 5.9 1.7 - - + -
2802 PHE* 2.6 57.6 + + + +
2812 THR* 3.8 9.2 - - + +
2832 ILE* 1.3 86.8 - - + +
2852 VAL* 1.3 58.8 + - + +
2872 SER* 2.6 27.6 + - - -
2882 SER* 3.3 4.7 + - - -
4202 ILE* 4.6 13.6 - - + +
4232 VAL* 5.3 5.4 - - + -
4242 SER* 2.9 53.2 - - - +
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Residues in contact with VAL 285 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2222 CYS* 5.3 0.7 - - - -
2252 PHE* 3.1 42.2 - - + -
2572 LEU* 4.2 30.0 - - + +
2612 VAL* 5.6 8.7 - - + -
2812 THR* 2.7 26.3 + - + +
2822 MET* 4.0 9.0 - - + +
2842 PHE* 1.3 71.1 - - + +
2862 ILE* 1.3 68.6 + - + +
2872 SER 2.6 5.6 - - - -
2882 SER* 2.8 18.5 + - - +
2892 ILE* 3.0 14.1 + - + +
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Residues in contact with ILE 286 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2341 THR* 5.7 7.2 - - + -
2381 LEU* 4.0 30.3 - - + -
2822 MET* 2.7 75.7 + - + +
2832 ILE* 3.1 18.4 - - + +
2852 VAL* 1.3 76.8 - - + +
2872 SER* 1.3 51.7 + - - +
2892 ILE* 3.0 7.2 + - + -
2902 ILE* 2.4 55.3 + - + +
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Residues in contact with SER 287 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2832 ILE 2.5 12.5 + - - -
2842 PHE* 2.6 18.4 - - - -
2852 VAL 2.6 0.8 - - - -
2862 ILE* 1.3 77.1 - - - +
2882 SER* 1.3 55.2 + - - -
2902 ILE* 2.9 24.2 - - - +
2912 VAL* 2.7 47.8 + - - +
4172 ILE* 5.7 0.3 - - - +
4202 ILE* 3.1 29.1 - - - +
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Residues in contact with SER 288 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2252 PHE* 5.2 10.2 - - - -
2292 THR* 3.1 31.6 - - - +
2532 LEU* 4.8 7.7 - - - +
2572 LEU* 5.4 7.2 - - - +
2842 PHE 3.3 3.9 + - - -
2852 VAL* 2.8 22.8 + - - -
2872 SER* 1.3 74.7 - - - +
2892 ILE* 1.3 57.4 + - - +
2912 VAL* 3.9 4.2 - - - +
2922 THR* 2.7 31.1 + - - -
4172 ILE* 6.0 5.8 - - - -
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Residues in contact with ILE 289 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2381 LEU* 3.6 35.4 - - + -
2411 PHE* 4.6 4.0 - - + -
2532 LEU* 5.7 4.5 - - + -
2542 THR* 4.7 7.6 - - - +
2572 LEU* 4.8 17.9 - - + -
2582 LEU* 4.6 20.4 - - + -
2852 VAL* 3.0 12.2 + - + +
2862 ILE* 3.4 13.5 - - + +
2872 SER 3.0 0.6 - - - -
2882 SER* 1.3 76.0 - - - +
2902 ILE* 1.3 58.6 + - + +
2922 THR* 3.0 10.9 + - + +
2932 VAL* 2.5 50.9 + - + +
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Residues in contact with ILE 290 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2832 ILE 4.8 1.3 - - - +
2862 ILE* 2.4 51.2 + - + +
2872 SER* 2.7 51.1 - - - +
2892 ILE* 1.3 67.6 - - + +
2912 VAL* 1.3 67.5 + - + +
2932 VAL* 2.8 30.2 - - - +
2942 VAL* 3.0 13.3 + - - +
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Residues in contact with VAL 291 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2332 PHE* 3.7 9.0 - - + -
2872 SER* 2.7 41.2 + - - +
2882 SER* 3.9 4.9 - - - +
2902 ILE* 1.3 79.6 - - + +
2922 THR* 1.3 56.1 + - - +
2932 VAL 2.9 1.5 + - - -
2942 VAL* 3.0 3.6 + - + -
2952 VAL* 2.4 67.7 + - + +
4132 VAL* 3.4 35.2 - - + -
4172 ILE* 5.4 4.5 - - + -
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Residues in contact with THR 292 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2411 PHE* 6.1 0.7 - - + -
2292 THR* 6.5 0.7 - - - -
2322 VAL* 4.9 2.9 - - - +
2502 LEU* 2.5 39.3 - - + +
2532 LEU* 5.2 3.4 - - + -
2882 SER* 2.7 20.9 + - - +
2892 ILE* 3.2 19.5 - - + +
2912 VAL* 1.3 73.1 - - - +
2932 VAL* 1.3 68.5 - - + +
2952 VAL* 3.0 13.2 - - - +
2962 ILE* 2.7 50.8 + - + +
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Residues in contact with VAL 293 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2411 PHE* 2.9 46.4 - - + -
2451 LEU* 4.8 2.9 - - + -
2892 ILE* 2.5 39.7 + - + +
2902 ILE* 2.8 15.5 - - - +
2922 THR* 1.3 78.4 - - + +
2942 VAL* 1.3 62.3 + - + +
2972 ASN* 2.4 54.2 + - - +
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Residues in contact with VAL 294 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2902 ILE 3.0 9.7 + - - +
2912 VAL* 3.8 5.2 - - - +
2932 VAL* 1.3 86.9 - - + +
2952 VAL* 1.3 60.1 + - + +
2972 ASN* 4.1 2.9 - - - -
2982 THR* 2.3 60.5 + - + +
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Residues in contact with VAL 295 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2322 VAL* 4.0 24.7 - - + -
2332 PHE* 3.9 11.4 - - + -
2912 VAL* 2.4 66.5 + - + +
2922 THR* 3.0 17.3 - - - +
2942 VAL* 1.3 73.1 - - + +
2962 ILE* 1.3 62.3 + - - +
2982 THR* 3.1 7.9 - - - -
2992 HIS* 2.2 35.5 + - - +
4092 ILE* 4.4 20.7 - - + +
4132 VAL* 4.2 8.5 - - + -
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Residues in contact with ILE 296 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2322 VAL* 4.4 9.2 - - + -
2462 SER* 3.5 17.5 - - - +
2472 ILE* 4.4 15.3 - - + -
2502 LEU* 3.0 29.8 - - + -
2922 THR* 2.7 50.6 + - + +
2952 VAL* 1.3 77.2 - - - +
2972 ASN* 1.3 61.6 + - - +
2992 HIS* 2.9 29.6 - - + +
3002 HIS* 2.4 50.0 + - + +
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Residues in contact with ASN 297 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2411 PHE* 5.1 0.6 - - - -
2451 LEU* 3.0 45.0 - - - +
2491 LEU* 4.3 15.2 - - - +
2521 GLU* 5.1 2.3 - - - +
2922 THR 4.3 1.2 + - - -
2932 VAL* 2.4 41.7 + - - +
2942 VAL* 3.4 5.2 - - - +
2962 ILE* 1.3 78.1 - - - +
2982 THR* 1.3 52.1 + - - +
3002 HIS* 3.1 6.1 + - - +
3012 ARG* 2.7 31.4 + - - +
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Residues in contact with THR 298 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2942 VAL* 2.3 59.9 + - + +
2952 VAL* 3.4 7.4 - - - +
2972 ASN* 1.3 66.9 - - - +
2992 HIS* 1.3 61.8 + - - +
3012 ARG* 2.6 75.1 + - + +
4052 VAL* 5.7 2.0 - - + -
4092 ILE* 5.0 12.3 - - + -
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Residues in contact with HIS 299 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2322 VAL* 3.6 10.1 + - - +
2352 LEU* 5.4 0.4 - - + -
2362 PRO* 2.8 55.1 - - + +
2402 GLY* 5.0 0.2 - - - -
2432 MET* 4.4 19.5 - - + +
2462 SER* 3.9 18.3 + - - -
2952 VAL 2.2 29.8 + - - +
2962 ILE* 2.7 34.7 + - + +
2982 THR* 1.3 72.4 - - - +
3002 HIS* 1.3 53.9 + + - +
3012 ARG* 3.4 10.6 + - - +
3022 SER* 4.9 0.3 + - - -
3062 HIS 2.3 22.9 - - - +
4062 ILE* 4.5 7.2 - - + -
4092 ILE* 6.5 0.9 - - + -
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Residues in contact with HIS 300 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2491 LEU* 6.0 8.3 - - + -
2521 GLU* 3.1 17.7 - - + +
2531 SER* 4.8 3.1 - - - -
2561 LYS* 3.9 31.9 - - + +
2432 MET* 3.6 39.6 + - + +
2442 THR* 4.6 1.8 - - - -
2472 ILE* 3.9 22.4 - - + +
2962 ILE* 2.4 50.7 + - + +
2972 ASN* 3.5 4.9 - - - +
2992 HIS* 1.3 69.1 - + + -
3012 ARG* 1.3 49.3 + - - +
3022 SER 2.6 18.4 + - - +
3062 HIS* 2.6 42.7 + - + +
----------------------------------------------------------
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Residues in contact with ARG 301 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2521 GLU* 2.9 26.4 - - - +
2972 ASN 2.7 9.0 + - - +
2982 THR* 2.6 65.2 + - + +
2992 HIS* 4.1 6.4 + - - +
3002 HIS* 1.3 69.5 - - - +
3022 SER* 1.3 68.6 + - - +
3032 PRO* 4.0 3.1 - - - +
4002 LYS 5.5 3.8 + - - -
4012 TYR* 6.4 0.4 - - - +
4022 VAL* 5.9 3.8 - - - +
4052 VAL* 3.2 43.9 - - - +
4062 ILE* 3.9 23.4 - - - +
4092 ILE* 5.3 2.0 - - - +
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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