Contacts of the helix formed by residues 25 - 39 (chain D) in PDB entry 1JPL
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 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D LYS 4.9 0.4 - - - +
16D ALA* 5.5 1.0 + - - -
21D ASN* 4.3 20.4 + - - +
22D ARG* 5.5 7.4 + - - +
23D GLN* 3.4 5.9 + - - +
24D GLU* 1.3 67.6 - - - +
26D TRP* 1.3 58.8 + - - +
27D GLU* 3.0 21.2 + - - +
28D TYR* 3.0 47.5 + - + +
29D ILE* 3.0 27.5 + - - +
64D GLN* 5.1 0.6 - - - +
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Residues in contact with TRP 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLU* 3.0 55.9 + - + +
25D ASP* 1.3 69.8 + - - +
27D GLU* 1.3 60.5 + - - +
28D TYR 3.3 0.2 - - - -
29D ILE* 3.5 31.9 - - + -
30D ILE* 3.0 46.2 + - + +
67D THR* 5.1 14.8 - - - -
71D ALA* 4.3 11.9 - - + -
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TRP* 4.6 2.1 - - - -
25D ASP* 3.0 10.3 + - - +
26D TRP* 1.3 77.4 - - - +
28D TYR* 1.3 68.0 + - + +
30D ILE* 4.0 2.7 - - - +
31D GLY* 2.9 25.6 + - - -
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Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TRP* 4.1 23.4 - + - +
15D LYS* 3.6 58.4 + - + +
16D ALA* 3.7 21.8 - - + +
21D ASN* 5.4 4.3 - - - -
25D ASP* 3.0 40.6 + - + +
27D GLU* 1.3 81.4 - - + +
29D ILE* 1.3 60.5 + - - +
31D GLY 4.5 0.2 - - - +
32D PHE* 3.0 30.0 + - - +
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Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA* 3.7 19.5 - - + +
24D GLU* 5.2 4.9 - - + -
25D ASP 3.0 23.9 + - - +
26D TRP* 3.5 33.4 - - + +
27D GLU 3.2 0.4 - - - -
28D TYR* 1.3 76.8 - - - +
30D ILE* 1.3 64.8 + - + +
32D PHE* 3.2 8.1 + - - +
33D CYS* 3.1 23.3 + - - -
64D GLN* 5.2 0.9 - - + +
67D THR* 4.8 8.3 - - - +
68D VAL* 3.3 36.8 - - + -
71D ALA* 3.5 30.3 - - + -
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TRP* 3.0 34.1 + - + +
27D GLU* 4.3 3.1 - - - +
29D ILE* 1.3 80.3 - - + +
31D GLY* 1.3 57.2 + - - +
33D CYS* 2.9 9.7 + - + +
34D ASP* 2.7 37.3 + - + +
71D ALA* 5.1 1.6 - - + -
75D ASN* 4.3 28.9 - - - +
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Residues in contact with GLY 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TRP* 3.7 24.8 - - - -
27D GLU 2.9 19.4 + - - -
30D ILE* 1.3 76.1 - - - +
32D PHE* 1.3 52.8 + - - +
34D ASP* 3.0 10.1 + - - +
35D GLN* 2.6 36.7 + - - +
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Residues in contact with PHE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.6 41.5 - - + -
12D TRP* 3.9 11.3 - - + -
13D LEU* 3.9 31.0 - - + -
16D ALA* 4.9 4.3 - - + -
28D TYR 3.0 20.2 + - - +
29D ILE* 3.3 5.6 - - - +
31D GLY* 1.3 73.9 - - - +
33D CYS* 1.3 58.8 + - - +
35D GLN* 3.2 7.8 + - - +
36D ILE* 2.9 57.7 + - + +
46D ALA* 3.9 15.5 - - + -
49D LEU* 4.8 1.8 - - + -
50D LEU* 4.0 11.4 - - + -
68D VAL* 3.5 26.7 - - + -
72D CYS* 3.7 11.7 - - - -
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Residues in contact with CYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE* 3.1 18.9 + - - -
30D ILE* 2.9 12.9 + - + +
32D PHE* 1.3 73.8 - - - +
34D ASP* 1.3 65.5 + - - +
36D ILE* 3.1 7.2 + - - +
37D ASN* 3.0 28.9 + - - -
68D VAL 4.7 0.2 - - - -
71D ALA* 3.9 18.4 - - - -
72D CYS* 3.7 38.8 - - - -
75D ASN* 4.0 20.9 - - + -
76D CYS* 3.8 8.5 - - - -
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Residues in contact with ASP 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 2.7 19.9 + - + +
31D GLY* 3.4 11.8 - - - +
33D CYS* 1.3 72.4 - - - +
35D GLN* 1.3 66.7 + - - +
37D ASN* 3.1 20.3 + - - +
38D LYS* 3.0 47.2 + - - +
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Residues in contact with GLN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLU 4.7 0.2 - - - +
8D SER* 3.1 28.6 + - - -
9D LEU* 3.3 25.2 - - + +
12D TRP* 4.0 26.9 - - + +
31D GLY 2.6 17.0 + - - +
32D PHE* 3.2 13.9 - - - +
34D ASP* 1.3 75.7 + - - +
36D ILE* 1.3 62.7 + - - +
38D LYS* 3.1 18.6 + - - +
39D GLU* 3.2 39.0 + - - +
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Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.9 13.9 - - + -
32D PHE* 2.9 45.6 + - + +
33D CYS 3.1 6.7 + - - +
35D GLN* 1.3 77.9 - - - +
37D ASN* 1.3 60.0 + - - +
38D LYS 3.3 1.0 + - - -
39D GLU 3.5 10.0 + - - +
42D GLY* 3.8 6.3 - - - +
43D PRO* 3.8 31.4 - - + -
46D ALA* 3.4 22.2 - - + -
72D CYS* 3.5 20.2 - - - -
76D CYS* 4.1 15.5 - - + -
79D ARG* 3.1 16.8 + - - -
80D PHE* 4.2 6.7 - - + -
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Residues in contact with ASN 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D CYS 3.0 16.2 + - - +
34D ASP* 3.1 13.9 + - - +
36D ILE* 1.3 77.2 - - - +
38D LYS* 1.3 62.3 + - + +
75D ASN* 2.8 20.1 - - - +
76D CYS* 3.3 38.6 + - - +
79D ARG* 3.7 18.1 + - - +
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Residues in contact with LYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASP* 3.0 43.6 + - - +
35D GLN* 3.1 12.9 + - - +
37D ASN* 1.3 82.8 - - + +
39D GLU* 1.3 67.0 + - - +
40D LEU* 3.6 2.3 + - - -
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Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLU* 3.4 35.0 - - + +
8D SER* 5.7 0.7 - - - -
9D LEU* 4.3 13.5 - - + -
35D GLN* 3.2 40.5 + - - +
36D ILE 3.5 4.4 + - - +
38D LYS* 1.3 81.5 - - + +
40D LEU* 1.3 69.0 + - - +
41D GLU 4.4 0.7 - - - +
42D GLY* 3.0 30.3 + - - +
45D ILE* 6.2 0.4 - - + -
79D ARG* 3.2 12.9 + - - -
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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