Contacts of the helix formed by residues 16 - 29 (chain R) in PDB entry 3J7Y
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 ASP 16 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2273A A 4.3 19.4 + - - +
2274A A 4.5 14.6 + - - +
14R VAL* 3.5 4.4 - - - +
15R THR* 1.3 83.9 + - - +
17R ARG* 1.3 62.0 + - - +
18R TYR 3.3 2.2 - - - -
19R PHE* 3.2 32.5 + - - +
20R ARG* 3.7 15.4 + - - +
36c ARG* 5.1 0.3 - - - +
37c ALA* 3.6 19.3 + - + -
40c ARG* 3.6 31.2 + - - +
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Residues in contact with ARG 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1864A A 4.1 35.2 + - - +
1865A C 2.5 40.4 + - - -
1866A U 5.9 1.4 + - - -
2295A C 3.0 51.4 + - - +
2296A U 5.9 2.5 - - - +
14R VAL* 3.4 35.2 + - + +
15R THR 3.4 4.2 + - - -
16R ASP* 1.3 75.2 - - - +
18R TYR* 1.3 65.2 + - - +
20R ARG* 3.0 24.3 + - + +
21R ILE* 3.1 26.6 + - + +
32c LYS* 5.1 3.8 - - - +
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Residues in contact with TYR 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813A C 4.2 21.1 + - - -
1814A A 6.1 0.9 - - - -
1864A A 5.8 0.6 + - - -
15R THR 4.9 0.2 + - - -
17R ARG* 1.3 77.9 - - - +
19R PHE* 1.3 79.0 + + + +
21R ILE* 3.2 13.4 + - + +
22R GLN* 2.9 59.3 + - + +
41c PHE* 3.8 22.7 - + - -
44c GLU* 3.1 36.0 + - - -
48c GLN* 4.7 8.8 + - - -
32i ILE* 5.2 5.4 - - + -
34i ILE* 4.1 28.5 - - + +
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Residues in contact with PHE 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R ASP* 3.2 32.8 + - - +
17R ARG 3.1 1.0 - - - -
18R TYR* 1.3 85.6 - + - +
20R ARG* 1.3 58.2 + - + +
22R GLN* 3.2 5.7 + - + +
23R GLU* 2.9 32.3 + - - +
37c ALA 3.9 1.8 - - - -
40c ARG* 3.3 57.2 - - + +
41c PHE* 3.4 15.9 - - - -
44c GLU* 2.7 38.6 - - + -
34i ILE* 3.5 28.9 - - + -
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Residues in contact with ARG 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2273A A 3.7 40.1 + - - +
2274A A 4.8 1.2 + - - -
2294A A 3.4 43.0 + - - -
2295A C 3.8 8.2 + - - -
14R VAL* 3.2 29.9 - - - +
16R ASP* 4.0 16.4 + - - +
17R ARG* 3.0 15.3 + - + +
19R PHE* 1.3 77.0 - - + +
21R ILE* 1.3 64.2 + - + +
23R GLU* 3.2 29.1 + - - +
24R VAL* 3.5 10.9 + - - +
39R TYR* 4.1 7.3 + - - +
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Residues in contact with ILE 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1863A A 4.6 21.5 - - - +
2296A U 4.6 5.8 - - - +
17R ARG* 3.1 29.2 + - + +
18R TYR* 3.4 13.2 - - + +
20R ARG* 1.3 78.0 - - + +
22R GLN* 1.3 59.6 + - - +
24R VAL 3.4 2.6 + - - -
25R LEU* 3.0 47.0 + - + +
39R TYR* 3.3 52.5 - - + -
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Residues in contact with GLN 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R TYR* 2.9 47.1 + - + +
19R PHE* 3.5 11.9 - - - +
21R ILE* 1.3 74.8 - - - +
23R GLU* 1.3 57.4 + - - +
25R LEU* 4.0 17.1 - - - +
26R LYS* 2.7 40.9 + - + +
29R ARG* 5.0 14.8 - - - +
44c GLU* 4.9 7.9 - - - +
48c GLN* 5.9 2.2 - - - +
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Residues in contact with GLU 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19R PHE* 2.9 14.7 + - + +
20R ARG* 3.2 20.4 + - - +
22R GLN* 1.3 75.9 - - - +
24R VAL* 1.3 60.3 + - + +
26R LYS* 3.1 53.8 + - + +
27R HIS* 3.8 6.0 - - - -
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Residues in contact with VAL 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R ARG 4.1 4.5 - - - +
21R ILE 3.4 1.4 + - - -
23R GLU* 1.3 75.4 - - + +
25R LEU* 1.3 67.3 + - - +
27R HIS* 3.1 19.6 + - - +
28R ALA 3.1 8.1 + - - -
39R TYR* 3.6 32.1 - - + +
42R ALA* 4.2 4.9 - - + -
43R VAL* 3.6 39.5 - - + +
46R VAL* 3.6 20.3 - - + +
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Residues in contact with LEU 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R ILE* 3.0 43.2 + - + +
22R GLN* 3.9 19.5 - - - +
24R VAL* 1.3 76.7 - - - +
26R LYS* 1.3 63.6 + - - +
28R ALA* 3.0 12.4 + - + +
29R ARG* 3.1 31.8 + - - +
36R ASN 3.5 22.2 - - - +
37R ARG 3.6 24.5 - - - +
39R TYR* 4.2 9.9 - - + -
42R ALA* 3.9 21.1 - - + -
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Residues in contact with LYS 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R GLN* 2.7 21.9 + - + +
23R GLU* 3.1 40.0 + - + +
24R VAL 3.2 0.2 - - - -
25R LEU* 1.3 72.1 - - - +
27R HIS* 1.3 98.0 + - + +
29R ARG* 3.2 27.4 + - - +
30R HIS* 5.7 1.0 - - - -
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Residues in contact with HIS 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1830A G 5.3 0.3 + - - -
23R GLU 3.8 8.3 - - - -
24R VAL* 3.1 8.7 + - - +
26R LYS* 1.3 110.7 + - + +
28R ALA* 1.3 59.3 + - - +
29R ARG 3.4 0.6 + - - -
30R HIS* 4.0 10.0 + - - -
31R PHE* 3.5 17.5 - - - -
46R VAL* 3.9 19.7 - - + -
50R PHE* 3.3 34.8 - + + -
170S ILE* 4.9 9.9 - - + +
183S LYS* 5.4 5.9 + - - -
2b THR 5.0 8.1 + - - -
5b GLY* 5.9 0.3 - - - -
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Residues in contact with ALA 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R VAL 3.1 8.2 + - - +
25R LEU* 3.0 9.2 + - - +
27R HIS* 1.3 78.7 - - - +
29R ARG* 1.3 63.1 + - - +
30R HIS 3.1 3.6 + - - -
31R PHE* 3.2 20.8 + - + -
35R LYS 3.6 20.0 - - - +
36R ASN* 2.9 18.6 - - - +
42R ALA* 3.8 9.6 - - + -
46R VAL* 3.5 19.5 - - + -
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Residues in contact with ARG 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1815A A 5.7 1.4 + - - -
22R GLN* 5.0 11.1 - - - +
25R LEU* 3.1 31.6 + - - +
26R LYS* 3.2 23.8 - - - +
27R HIS 3.4 3.2 - - - -
28R ALA* 1.3 75.7 - - - +
30R HIS* 1.3 60.4 + - + +
31R PHE 3.4 0.6 - - - +
36R ASN* 2.6 61.0 + - - +
37R ARG* 4.6 2.8 - - - +
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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