Contacts of the helix formed by residues 2360 - 2373 (chain A) in PDB entry 5DZZ
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 GLU2360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2354A MET* 4.7 0.3 - - - +
2359A ILE* 1.3 79.3 - - - +
2361A LYS* 1.3 79.4 + - - +
2362A GLY 3.4 4.7 + - - +
2363A HIS* 3.5 12.6 + - + +
2364A GLY* 3.0 24.4 + - - -
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Residues in contact with LYS2361 (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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2354A MET* 3.3 46.4 + - + +
2355A ASN* 5.0 8.4 + - - +
2357A GLU* 4.9 13.2 - - - -
2359A ILE 4.7 1.8 - - - +
2360A GLU* 1.3 84.3 + - - +
2362A GLY* 1.3 61.4 + - - +
2364A GLY* 3.1 1.3 + - - +
2365A ILE* 2.8 47.2 + - + +
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Residues in contact with GLY2362 (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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2360A GLU* 3.4 3.4 + - - +
2361A LYS* 1.3 79.4 - - - +
2363A HIS* 1.3 60.8 + - - +
2365A ILE* 3.7 7.8 + - - +
2366A ARG* 3.3 34.7 + - - +
2411A ASP 6.1 1.1 - - - -
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Residues in contact with HIS2363 (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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2293A GLU* 3.3 39.0 + - - +
2328A LYS* 5.1 2.9 + - - +
2331A SER* 5.0 9.2 - - - -
2332A ALA* 4.6 13.1 - - + +
2339A TYR* 5.1 1.8 - - - -
2359A ILE* 4.3 16.2 - - + +
2360A GLU* 3.5 18.7 + - + +
2361A LYS 3.2 0.6 - - - -
2362A GLY* 1.3 75.8 - - - +
2364A GLY* 1.3 61.2 + - - +
2366A ARG* 3.2 18.5 - - - +
2367A LEU* 3.1 50.4 - - + +
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Residues in contact with GLY2364 (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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2350A LEU* 4.2 6.1 - - - +
2354A MET* 4.2 13.9 - - - -
2359A ILE* 3.8 19.5 - - - +
2360A GLU 3.0 15.3 + - - -
2361A LYS 3.1 3.1 + - - -
2363A HIS* 1.3 77.2 - - - +
2365A ILE* 1.3 64.0 + - - +
2367A LEU* 3.4 2.9 + - - +
2368A LEU* 3.1 26.9 + - - +
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Residues in contact with ILE2365 (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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2354A MET* 4.5 11.4 - - + -
2361A LYS* 2.8 29.4 + - + +
2362A GLY* 4.1 7.2 - - - +
2364A GLY* 1.3 76.8 - - - +
2366A ARG* 1.3 63.3 + - - +
2368A LEU* 3.2 10.9 + - + +
2369A GLU* 3.1 29.6 + - - +
2401A LEU* 5.9 7.0 - - + -
2405A LEU* 3.7 26.4 - - + +
2411A ASP* 4.5 21.8 - - + +
2412A THR* 4.4 16.6 - - + +
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Residues in contact with ARG2366 (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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2290A GLU* 3.6 21.8 + - - +
2293A GLU* 3.5 26.4 + - - -
2362A GLY* 3.3 23.3 + - - +
2363A HIS* 3.2 24.3 - - - +
2365A ILE* 1.3 80.3 - - - +
2367A LEU* 1.3 66.1 + - + +
2369A GLU* 3.4 16.9 - - - +
2370A ALA* 3.3 21.3 + - - +
2414A GLY* 4.0 28.4 + - - -
2415A PHE* 3.4 30.9 - - + -
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Residues in contact with LEU2367 (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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2293A GLU* 3.7 31.0 - - + +
2294A ALA* 4.5 4.5 - - + -
2297A ALA* 3.6 27.6 - - + +
2332A ALA* 4.5 6.3 - - + -
2335A ALA* 4.6 1.1 - - + -
2339A TYR* 4.1 16.8 - - - +
2350A LEU* 3.7 22.9 - - + -
2359A ILE* 4.9 0.2 - - + -
2363A HIS* 3.1 42.6 - - + +
2364A GLY 3.4 2.4 + - - +
2365A ILE 3.2 0.8 - - - -
2366A ARG* 1.3 84.7 - - + +
2368A LEU* 1.3 63.8 + - - +
2370A ALA* 3.4 5.2 + - - +
2371A GLN* 3.2 27.0 + - - +
2415A PHE* 6.0 0.2 - - + -
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Residues in contact with LEU2368 (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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2350A LEU* 3.7 23.6 - - + -
2351A PHE* 4.4 18.8 - - + +
2354A MET* 3.9 29.2 - - + -
2364A GLY 3.1 18.2 + - - +
2365A ILE* 3.2 11.2 + - + +
2367A LEU* 1.3 77.1 - - - +
2369A GLU* 1.3 62.4 + - - +
2371A GLN* 3.1 8.9 + - - +
2372A ILE* 3.1 26.9 + - - +
2377A ILE* 4.2 22.5 - - + +
2396A TYR 4.9 1.3 - - - +
2397A PHE* 4.2 6.5 - - + -
2401A LEU* 4.0 18.4 - - + -
2405A LEU* 4.1 11.4 - - + -
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Residues in contact with GLU2369 (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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2365A ILE* 3.1 15.8 + - - +
2366A ARG* 3.4 15.5 - - - +
2368A LEU* 1.3 78.4 - - - +
2370A ALA* 1.3 57.5 + - - +
2372A ILE* 3.9 12.4 - - - +
2373A ALA* 3.1 29.6 + - - +
2405A LEU* 4.1 25.3 - - + +
2412A THR* 3.1 37.0 - - - +
2414A GLY 4.4 0.3 + - - -
2415A PHE* 3.4 24.6 - - - -
2425A THR* 4.2 7.0 - - - +
2426A TYR* 3.6 20.6 + - + +
2427A LEU* 5.2 1.6 + - + +
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Residues in contact with ALA2370 (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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2294A ALA* 4.3 17.0 - - + +
2297A ALA* 5.4 0.9 - - + -
2298A THR* 3.7 11.0 - - + +
2366A ARG 3.3 20.3 + - - +
2367A LEU* 3.5 9.6 - - - +
2368A LEU 3.1 0.6 - - - -
2369A GLU* 1.3 78.6 - - - +
2371A GLN* 1.3 59.6 + - - +
2373A ALA* 3.6 1.2 + - - +
2374A THR* 2.8 31.7 + - - +
2426A TYR* 3.7 27.4 - - + -
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Residues in contact with GLN2371 (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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2297A ALA 3.0 29.3 + - - +
2298A THR* 4.3 1.1 - - + -
2335A ALA* 3.1 32.9 + - - +
2350A LEU* 4.0 14.4 - - - +
2367A LEU 3.2 12.7 + - - +
2368A LEU* 3.1 8.0 + - - +
2370A ALA* 1.3 77.1 - - - +
2372A ILE* 1.3 62.2 + - - +
2374A THR* 3.2 8.5 + - - -
2376A GLY 2.8 35.1 + - - +
2377A ILE* 3.8 11.4 - - + +
2378A ILE* 2.9 37.3 + - + +
2385A ARG* 3.1 8.9 + - - +
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Residues in contact with ILE2372 (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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2368A LEU 3.1 16.0 + - - +
2369A GLU* 4.0 7.0 - - - +
2370A ALA 3.4 0.2 - - - -
2371A GLN* 1.3 75.9 - - - +
2373A ALA* 1.3 60.8 + - - +
2374A THR 3.1 1.3 + - - -
2375A GLY 3.7 7.8 + - - -
2376A GLY* 3.8 11.9 + - - -
2377A ILE* 3.8 17.3 - - + +
2388A VAL* 6.2 3.4 - - + -
2397A PHE* 3.5 36.1 - - + -
2402A SER* 5.8 1.1 - - - -
2405A LEU* 3.9 19.7 - - + -
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Residues in contact with ALA2373 (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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2257A SER* 4.6 2.4 + - - -
2369A GLU 3.1 19.3 + - - +
2370A ALA 4.0 0.7 - - - +
2371A GLN 3.2 0.2 - - - -
2372A ILE* 1.3 76.4 - - - +
2374A THR* 1.3 58.6 + - - +
2375A GLY 3.6 1.6 + - - -
2426A TYR* 3.8 22.9 - - + -
2427A LEU* 4.1 32.7 - - + +
2430A LYS* 3.5 24.3 - - + +
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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
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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