Contacts of the helix formed by residues 2486 - 2507 (chain B) in PDB entry 2H7C
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 SER2486 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2451B TYR* 4.0 4.5 + - - -
2454B SER* 5.8 0.4 - - - -
2484B GLY 3.7 3.0 + - - -
2485B ALA* 1.3 76.0 - - - +
2487B GLU* 1.3 65.6 + - - +
2488B GLU* 3.6 10.5 + - - +
2489B GLU* 3.2 24.2 + - - +
2490B ILE* 2.9 22.9 + - - +
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Residues in contact with GLU2487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2486B SER* 1.3 73.6 - - - +
2488B GLU* 1.3 57.3 + - - +
2490B ILE* 3.3 23.1 + - - +
2491B ARG* 2.9 68.8 + - - +
2494B LYS* 5.5 2.9 + - - -
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Residues in contact with GLU2488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2451B TYR* 3.0 28.5 + - + +
2486B SER* 3.1 8.6 + - - +
2487B GLU* 1.3 79.4 - - - +
2489B GLU* 1.3 58.1 + - - +
2491B ARG* 3.3 9.3 + - - +
2492B LEU* 3.0 27.9 + - + +
2531B ALA* 3.6 30.4 - - + +
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Residues in contact with GLU2489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2451B TYR* 3.6 26.9 - - + +
2453B PRO* 3.0 17.8 - - + +
2454B SER* 2.7 49.0 + - - -
2455B PHE* 3.6 13.2 - - - -
2473B PHE* 5.5 0.2 - - - +
2474B SER* 5.3 2.5 + - - +
2479B PRO* 3.9 9.1 - - + +
2485B ALA* 3.5 14.6 - - + +
2486B SER* 3.2 15.3 + - - +
2488B GLU* 1.3 79.0 - - - +
2490B ILE* 1.3 62.6 + - - +
2492B LEU* 3.3 8.5 + - + +
2493B SER* 3.1 22.7 + - - -
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Residues in contact with ILE2490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2479B PRO* 4.1 17.0 - - + +
2480B PHE* 3.8 25.4 - - + -
2485B ALA* 3.8 26.0 - - + +
2486B SER 2.9 21.6 + - - +
2487B GLU* 3.5 26.2 - - - +
2489B GLU* 1.3 77.4 - - - +
2491B ARG* 1.3 63.1 + - + +
2493B SER* 3.3 4.7 + - - -
2494B LYS* 3.1 33.2 + - - +
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Residues in contact with ARG2491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2487B GLU* 2.9 51.2 + - - +
2488B GLU* 3.7 7.4 - - - +
2490B ILE* 1.3 79.1 - - + +
2492B LEU* 1.3 62.7 + - - +
2494B LYS* 3.3 15.3 + - + +
2495B MET* 3.0 24.3 + - - +
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Residues in contact with LEU2492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2449B PHE* 4.1 4.3 - - + -
2451B TYR* 3.5 50.5 - - + -
2474B SER* 3.7 18.4 - - - +
2488B GLU* 3.0 14.1 + - + +
2489B GLU* 3.5 9.6 - - + +
2490B ILE 3.2 0.2 - - - -
2491B ARG* 1.3 77.9 - - - +
2493B SER* 1.3 58.0 + - - +
2495B MET* 3.3 13.0 + - + +
2496B VAL* 2.9 35.9 + - + +
2529B ILE* 4.0 22.4 - - + -
2530B GLY* 3.4 26.9 - - - +
2531B ALA* 6.1 1.1 - - - -
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Residues in contact with SER2493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2474B SER* 2.9 33.6 + - - +
2477B GLY* 3.2 20.3 - - - -
2479B PRO* 3.9 18.4 - - - -
2480B PHE* 3.6 8.8 - - - -
2489B GLU 3.1 12.9 + - - -
2490B ILE 3.6 8.7 - - - -
2491B ARG 3.3 0.2 - - - -
2492B LEU* 1.3 74.7 - - - +
2494B LYS* 1.3 67.3 + - - +
2496B VAL* 3.2 1.4 + - - +
2497B MET* 2.9 27.5 + - - +
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Residues in contact with LYS2494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2160B HIS* 4.8 10.8 - - - +
2161B GLU* 4.4 2.6 - - - +
2480B PHE* 3.4 36.8 - - + -
2487B GLU* 5.5 2.8 + - - -
2490B ILE* 3.1 24.3 + - + +
2491B ARG* 3.3 16.1 + - + +
2493B SER* 1.3 75.7 - - - +
2495B MET* 1.3 58.8 + - - +
2497B MET* 4.0 9.9 - - - +
2498B LYS* 3.0 35.8 + - - +
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Residues in contact with MET2495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2491B ARG 3.0 16.8 + - - +
2492B LEU* 3.6 14.6 - - + +
2494B LYS* 1.3 75.0 - - - +
2496B VAL* 1.3 65.1 + - + +
2498B LYS* 3.3 3.3 + - - +
2499B PHE* 2.9 49.3 + - + +
2514B LEU* 3.6 27.0 - - + +
2515B PRO* 4.0 23.3 - - + -
2529B ILE* 3.8 22.7 - - + -
2533B THR* 3.4 29.2 - - + +
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Residues in contact with VAL2496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2449B PHE* 4.7 4.7 - - + -
2471B GLU* 6.2 0.7 - - + -
2474B SER* 3.9 17.3 - - - -
2475B VAL* 3.7 37.7 - - + +
2492B LEU* 2.9 25.2 + - + +
2493B SER 3.8 2.9 - - - +
2495B MET* 1.3 77.2 - - + +
2497B MET* 1.3 65.2 + - - +
2499B PHE* 3.2 7.3 + - - -
2500B TRP* 2.9 39.4 + - + +
2529B ILE* 4.1 29.2 - - + -
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Residues in contact with MET2497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2156B ALA 4.3 0.2 - - - +
2157B LEU* 3.8 38.7 - - + +
2160B HIS* 3.8 27.1 - - + +
2161B GLU* 3.4 8.4 - - + +
2474B SER 3.4 5.4 - - - +
2475B VAL* 3.4 19.5 - - - +
2477B GLY* 3.8 18.8 - - - -
2480B PHE* 3.7 31.9 - - + -
2493B SER* 2.9 21.7 + - - +
2494B LYS* 4.0 8.1 - - - +
2496B VAL* 1.3 76.9 - - - +
2498B LYS* 1.3 58.3 + - - +
2500B TRP* 3.8 4.4 - - - +
2501B ALA* 2.9 32.9 + - - +
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Residues in contact with LYS2498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2160B HIS 5.2 2.0 + - - -
2161B GLU* 3.2 33.5 + - - +
2494B LYS* 3.0 22.2 + - - +
2495B MET* 3.7 4.5 - - - +
2497B MET* 1.3 77.2 - - - +
2499B PHE* 1.3 56.5 + - - +
2501B ALA 3.7 0.5 - - - -
2502B ASN* 2.8 45.4 + - - +
2505B ARG* 4.9 0.4 - - - +
2512B GLU 4.7 8.7 - - - +
2514B LEU* 3.8 32.5 - - + -
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Residues in contact with PHE2499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2495B MET* 2.9 47.0 + - + -
2496B VAL* 3.5 9.2 - - - +
2498B LYS* 1.3 75.5 - - - +
2500B TRP* 1.3 74.9 + + + +
2502B ASN 3.3 0.7 + - - -
2503B PHE* 3.0 22.9 + - - +
2509B PRO* 3.4 36.9 - - + +
2510B ASN* 4.6 2.5 - - - -
2514B LEU* 3.5 18.8 - - + -
2515B PRO* 3.3 36.8 - - + -
2517B TRP* 3.9 23.3 - + + -
2527B LEU* 3.4 27.4 - - + -
2529B ILE* 5.0 3.8 - - + -
2533B THR* 4.8 0.2 - - + -
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Residues in contact with TRP2500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2136B MET* 3.9 15.0 - - + +
2157B LEU* 5.6 2.9 - - + -
2218B PHE* 4.0 8.5 - + - -
2244B ILE* 3.7 21.7 - - + +
2246B GLU* 3.0 25.5 + - + -
2347B MET* 3.8 19.7 - - - -
2447B TYR* 3.5 44.2 - + - -
2449B PHE* 6.5 0.7 - + - -
2471B GLU* 5.3 2.5 - - + -
2475B VAL* 3.7 35.7 - - + +
2496B VAL* 2.9 36.5 + - + +
2497B MET* 3.8 5.6 - - - +
2499B PHE* 1.3 82.7 - - + +
2501B ALA* 1.3 58.3 + - - +
2503B PHE* 3.3 9.0 + - - +
2504B ALA* 2.9 25.1 + - - +
2517B TRP* 4.0 15.5 - + - -
2529B ILE* 4.2 13.0 - - + -
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Residues in contact with ALA2501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2136B MET* 4.4 6.2 - - - -
2157B LEU* 5.1 1.1 - - + -
2161B GLU* 3.4 30.3 - - + -
2163B VAL* 3.9 8.8 - - + +
2497B MET 2.9 18.6 + - - +
2498B LYS 4.0 0.2 - - - +
2500B TRP* 1.3 74.4 - - - +
2502B ASN* 1.3 65.4 + - - +
2503B PHE 3.1 0.4 - - - -
2504B ALA* 3.2 9.9 + - - +
2505B ARG* 3.0 42.1 + - - +
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Residues in contact with ASN2502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2498B LYS* 2.8 24.7 + - - +
2499B PHE 3.6 0.9 - - - +
2501B ALA* 1.3 75.7 - - - +
2503B PHE* 1.3 57.1 + - - +
2505B ARG* 3.0 29.7 + - - +
2506B ASN* 2.8 35.1 + - - +
2508B ASN 3.1 9.3 - - - +
2509B PRO 2.9 31.6 + - - +
2510B ASN 3.6 11.7 + - - +
2511B GLY* 3.7 6.8 - - - -
2514B LEU* 3.3 24.5 - - - +
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Residues in contact with PHE2503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2216B THR* 4.7 1.8 - - + -
2242B ARG* 3.6 22.6 - - + +
2243B ALA 3.4 18.6 - - - -
2244B ILE* 3.7 23.6 - - + -
2345B PRO* 3.6 28.9 - - + -
2347B MET* 3.7 29.2 - - + -
2445B TYR* 3.8 18.4 - + - -
2499B PHE 3.0 13.5 + - - +
2500B TRP* 3.3 9.6 - - - +
2502B ASN* 1.3 78.0 - - - +
2504B ALA* 1.3 58.4 + - - +
2507B GLY* 2.7 54.9 + - - -
2508B ASN 3.5 8.6 + - - -
2509B PRO* 3.9 13.2 - - + -
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Residues in contact with ALA2504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2134B PRO* 4.3 13.4 - - + +
2135B VAL 5.2 0.7 - - - +
2136B MET* 3.8 27.4 - - + -
2214B SER* 3.4 10.9 + - - +
2216B THR* 3.2 25.3 + - - +
2242B ARG* 2.8 21.8 + - - -
2500B TRP 2.9 14.4 + - - +
2501B ALA* 3.2 9.4 + - + +
2503B PHE* 1.3 77.6 - - - +
2505B ARG* 1.3 57.6 + - - +
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Residues in contact with ARG2505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2134B PRO* 4.3 22.8 - - + +
2161B GLU* 2.8 50.3 + - - -
2162B ASN* 4.7 2.0 + - - +
2163B VAL* 3.9 7.1 - - - +
2214B SER* 4.5 3.6 + - - -
2242B ARG* 3.1 13.0 + - - -
2498B LYS* 4.9 1.2 - - - +
2501B ALA* 3.0 27.2 + - - +
2502B ASN* 3.0 32.1 + - - +
2504B ALA* 1.3 79.8 - - - +
2506B ASN* 1.3 73.9 + - - +
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Residues in contact with ASN2506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2242B ARG* 3.5 9.9 + - - +
2502B ASN* 2.8 23.5 + - - +
2505B ARG* 1.3 97.8 - - - +
2507B GLY* 1.3 58.2 + - - +
2508B ASN* 3.0 20.3 + - + +
2510B ASN 5.1 4.9 + - - -
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Residues in contact with GLY2507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2242B ARG* 3.7 9.3 - - - +
2345B PRO* 3.7 32.9 - - - +
2443B PRO* 4.6 4.3 - - - +
2445B TYR* 3.6 15.6 + - - -
2503B PHE* 2.7 33.6 + - - -
2506B ASN* 1.3 73.2 - - - +
2508B ASN* 1.3 58.1 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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