Contacts of the helix formed by residues 2410 - 2428 (chain B) in PDB entry 5NUG
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 SER2410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2386B PRO* 5.7 5.9 - - - +
2388B ASP* 5.2 6.8 + - - +
2409B ALA* 1.3 82.8 + - - +
2411B PRO* 1.4 74.5 - - - +
2412B MET* 3.3 15.6 + - - +
2413B LEU* 3.6 22.0 + - - +
2414B GLN* 3.1 23.1 + - - +
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Residues in contact with PRO2411 (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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2409B ALA 4.2 3.1 - - - +
2410B SER* 1.4 87.8 - - - +
2412B MET* 1.3 61.4 + - + +
2414B GLN* 3.2 13.6 + - + +
2415B ILE* 2.9 40.0 + - + +
2473B ASN* 5.9 2.7 - - - +
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Residues in contact with MET2412 (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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2386B PRO* 5.6 1.6 - - + -
2387B LEU* 4.0 27.1 - - + +
2388B ASP* 3.7 31.4 - - + +
2410B SER* 3.3 9.5 + - - +
2411B PRO* 1.3 82.8 - - + +
2413B LEU* 1.3 57.7 + - - +
2415B ILE* 3.2 13.6 + - + +
2416B GLN* 2.9 39.8 + - + +
2466B CYS* 4.4 5.8 - - + +
2467B ARG* 3.9 39.9 - - + +
2470B ALA* 4.3 17.9 - - + -
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Residues in contact with LEU2413 (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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2382B LEU 4.7 2.9 - - - +
2383B ARG 3.2 30.5 - - - +
2384B SER* 4.4 2.0 - - - +
2386B PRO* 4.1 36.9 - - + +
2409B ALA* 4.2 21.8 - - + +
2410B SER* 3.5 23.0 + - - +
2412B MET* 1.3 79.0 - - - +
2414B GLN* 1.3 58.8 + - - +
2416B GLN* 3.2 7.2 + - + +
2417B ARG* 2.9 51.9 + - - +
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Residues in contact with GLN2414 (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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2409B ALA 6.1 0.9 - - - +
2410B SER 3.1 11.1 + - - +
2411B PRO* 3.3 15.5 - - - +
2413B LEU* 1.3 78.3 - - - +
2415B ILE* 1.3 59.0 + - + +
2417B ARG* 3.2 13.4 + - - +
2418B ASP* 2.9 49.7 + - - +
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Residues in contact with ILE2415 (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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2411B PRO* 2.9 26.9 + - + +
2412B MET* 3.3 13.7 - - + +
2414B GLN* 1.3 76.3 - - + +
2416B GLN* 1.3 59.1 + - - +
2418B ASP* 3.2 10.6 + - - +
2419B ALA* 2.9 29.0 + - + +
2466B CYS* 4.5 13.0 - - + +
2469B VAL* 3.5 35.0 - - + -
2470B ALA* 4.3 13.0 - - + -
2473B ASN* 3.6 32.3 - - + +
2481B MET* 6.2 0.7 - - + -
2486B LEU* 4.4 6.9 - - + +
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Residues in contact with GLN2416 (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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2381B ARG 4.4 1.0 + - - -
2382B LEU* 2.6 54.9 + - + +
2384B SER 4.1 0.8 + - - -
2385B ILE 4.8 0.4 + - - -
2386B PRO* 3.7 19.1 - - - +
2387B LEU* 3.1 40.7 + - - +
2412B MET* 2.9 24.7 + - + +
2413B LEU* 3.4 9.8 - - - +
2415B ILE* 1.3 77.4 - - - +
2417B ARG* 1.3 56.5 + - - +
2419B ALA* 3.2 8.5 + - - +
2420B ALA* 2.9 28.9 + - - +
2463B HIS* 5.1 0.8 + - - -
2466B CYS* 3.9 24.7 - - + -
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Residues in contact with ARG2417 (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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2383B ARG* 3.6 43.0 + - + +
2384B SER* 5.6 1.4 - - - +
2413B LEU* 2.9 39.5 + - - +
2414B GLN* 3.4 12.6 - - - +
2416B GLN* 1.3 77.1 - - - +
2418B ASP* 1.3 64.8 + - - +
2420B ALA* 3.2 9.1 + - - +
2421B THR* 3.0 27.4 + - - -
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Residues in contact with ASP2418 (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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2414B GLN* 2.9 36.7 + - - +
2415B ILE* 3.4 11.0 - - - +
2417B ARG* 1.3 77.5 - - - +
2419B ALA* 1.3 62.5 + - - +
2421B THR* 3.4 7.9 + - - -
2422B ILE* 3.3 26.9 + - - +
2483B ILE* 4.1 21.1 - - + +
2486B LEU* 4.0 16.4 - - + +
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Residues in contact with ALA2419 (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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2382B LEU* 4.7 1.6 - - + -
2415B ILE* 2.9 14.6 + - + +
2416B GLN* 3.2 12.8 + - - +
2418B ASP* 1.3 77.8 - - - +
2420B ALA* 1.3 62.0 + - - +
2422B ILE* 3.0 27.4 - - - +
2423B MET* 3.0 23.4 + - - +
2466B CYS* 4.7 12.1 - - - -
2486B LEU* 4.0 5.8 - - + +
2490B ILE* 3.8 23.3 - - + -
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Residues in contact with ALA2420 (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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2379B LEU* 4.1 8.4 - - + +
2382B LEU* 3.9 20.4 - - + +
2383B ARG* 3.5 36.5 + - + +
2416B GLN 2.9 13.4 + - - +
2417B ARG 3.4 8.7 - - - +
2419B ALA* 1.3 76.7 - - - +
2421B THR* 1.3 57.2 + - - +
2423B MET* 3.2 3.7 + - - +
2424B GLN* 2.9 32.7 + - - +
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Residues in contact with THR2421 (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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2383B ARG* 4.6 9.8 + - - +
2417B ARG 3.0 14.6 + - - -
2418B ASP* 3.6 10.3 + - - -
2420B ALA* 1.3 79.2 - - - +
2422B ILE* 1.3 64.0 + - + +
2423B MET 3.4 0.2 + - - -
2424B GLN* 3.6 4.4 + - - +
2425B PRO* 3.5 16.5 - - - +
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Residues in contact with ILE2422 (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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2418B ASP* 3.3 13.4 + - + +
2419B ALA* 3.0 26.7 - - - +
2421B THR* 1.3 81.0 - - + +
2423B MET* 1.3 60.8 + - + +
2425B PRO* 3.9 7.6 - - - +
2426B TYR* 3.8 17.0 - - - -
2486B LEU* 3.6 34.5 - - + +
2487B GLU* 3.6 39.3 - - + +
2490B ILE* 4.0 17.9 - - + -
2491B GLN* 4.8 11.5 + - + +
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Residues in contact with MET2423 (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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2378B PHE* 4.0 3.6 - - + -
2379B LEU* 4.8 1.1 - - + -
2382B LEU* 4.0 21.3 - - + -
2419B ALA* 3.0 33.6 + - - +
2420B ALA* 3.7 3.6 - - - +
2422B ILE* 1.3 77.8 - - - +
2424B GLN* 1.3 65.5 + - - +
2425B PRO* 3.2 3.1 - - - -
2426B TYR* 2.9 28.9 + - + +
2427B PHE* 3.5 37.7 + - + -
2462B LEU* 3.8 26.2 - - + +
2466B CYS* 6.2 0.9 - - - -
2490B ILE* 3.9 30.5 - - + -
2494B LEU* 4.0 10.5 - - + -
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Residues in contact with GLN2424 (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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2376B ASN* 5.2 5.5 + - - -
2379B LEU* 3.9 25.4 - - + +
2383B ARG* 2.9 29.5 + - - +
2420B ALA 2.9 17.1 + - - +
2421B THR* 4.0 5.8 - - - +
2423B MET* 1.3 74.6 - - - +
2425B PRO* 1.4 69.6 - - + +
2426B TYR 3.2 0.9 + - - -
2427B PHE* 3.4 11.3 + - - +
2428B THR* 3.5 23.2 + - + +
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Residues in contact with PRO2425 (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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2421B THR 3.5 12.6 - - - +
2422B ILE 3.9 8.1 - - - +
2423B MET 3.3 4.5 - - - -
2424B GLN* 1.4 94.9 - - + +
2426B TYR* 1.3 67.5 + - + +
2428B THR* 4.1 16.5 - - + +
2431B GLY* 4.5 5.7 - - - -
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Residues in contact with TYR2426 (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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2422B ILE 3.8 18.2 - - - -
2423B MET* 2.9 30.9 + - + +
2425B PRO* 1.3 77.0 - - + +
2427B PHE* 1.3 64.5 + - + +
2431B GLY* 3.5 3.1 - - - -
2432B LEU* 2.8 60.3 + - + +
2433B VAL* 3.6 7.3 + - + -
2491B GLN* 3.2 46.7 + - + +
2494B LEU* 4.3 17.0 - - + -
2523B THR 4.7 6.0 + - - -
2524B VAL* 4.0 25.3 - - + +
2525B PRO* 5.5 0.2 - - - +
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Residues in contact with PHE2427 (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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2372B ASP* 4.6 0.3 - - - +
2375B PHE* 3.3 51.3 - + + -
2378B PHE* 3.6 15.7 - + - -
2379B LEU* 3.8 32.8 - - + -
2423B MET* 3.5 49.4 - - + -
2424B GLN* 3.4 4.7 + - - +
2426B TYR* 1.3 77.8 - - + +
2428B THR* 1.3 68.6 + - - +
2429B SER 3.6 0.9 - - - +
2430B ASN 4.2 0.9 - - - +
2433B VAL* 3.9 23.6 - - + -
2434B THR* 3.1 22.9 + - - -
2458B LEU* 4.5 4.3 - - + -
2459B PHE* 4.7 0.2 - + - -
2462B LEU* 3.6 13.9 - - + -
2494B LEU* 4.3 8.1 - - + -
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Residues in contact with THR2428 (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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2372B ASP* 4.7 11.4 + - - +
2375B PHE* 5.6 2.9 - - - -
2376B ASN* 4.8 12.3 + - - -
2379B LEU* 6.2 1.6 - - - -
2424B GLN* 3.5 26.4 + - + +
2425B PRO* 4.1 11.6 - - + +
2426B TYR 4.0 0.3 - - - +
2427B PHE* 1.3 85.7 - - - +
2429B SER* 1.3 76.8 + - - +
2431B GLY* 3.7 12.8 + - - -
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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