Contacts of the helix formed by residues 25 - 39 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LYS 4.9 0.9 - - - +
16C ALA* 5.1 2.1 + - - -
21C ASN* 4.1 24.4 + - - +
23C GLN 3.4 2.8 + - - +
24C GLU* 1.3 71.3 - - - +
26C TRP* 1.3 62.9 + - - +
27C GLU* 3.0 25.2 + - - +
28C TYR* 3.0 39.2 + - + +
29C ILE* 3.0 27.3 + - - +
64C GLN* 4.8 2.0 - - - +
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Residues in contact with TRP 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLN* 6.1 1.1 - - - -
24C GLU* 3.7 26.8 + - + +
25C ASP* 1.3 67.6 + - - +
27C GLU* 1.3 64.9 + - - +
29C ILE* 3.6 39.0 - - + -
30C ILE* 3.0 48.3 + - + +
67C THR* 3.6 29.6 - - + -
70C GLU* 6.4 0.9 - - + -
71C ALA* 4.2 13.5 - - + -
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Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP* 4.4 3.9 - - + -
25C ASP* 3.0 19.3 + - - +
26C TRP* 1.3 79.9 - - - +
28C TYR* 1.3 88.2 + - + +
30C ILE* 4.3 1.8 - - - +
31C GLY* 3.2 18.2 + - - -
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Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP* 3.8 27.5 - + + +
15C LYS* 3.7 54.1 + - + +
16C ALA* 3.8 22.5 - - + +
21C ASN* 6.0 1.3 - - - -
25C ASP* 3.0 35.7 + - - +
27C GLU* 1.3 105.2 + - + +
29C ILE* 1.3 66.1 + - - +
31C GLY* 3.6 0.5 - - - -
32C PHE* 2.9 24.3 + - - +
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Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 4.1 16.2 - - - +
24C GLU* 3.9 19.1 - - + -
25C ASP 3.0 25.1 + - - +
26C TRP* 3.6 49.8 - - + -
28C TYR* 1.3 76.1 - - - +
30C ILE* 1.3 65.3 + - + +
32C PHE* 3.4 5.9 + - - +
33C CYS* 3.3 19.6 + - - -
64C GLN* 5.8 0.9 - - + +
67C THR* 4.2 9.9 - - + -
68C VAL* 4.1 25.6 - - + +
71C ALA* 3.8 19.1 - - + -
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 3.0 46.3 + - + +
27C GLU 4.3 1.8 - - - +
29C ILE* 1.3 76.3 - - + +
31C GLY* 1.3 66.1 + - - +
33C CYS* 3.0 8.2 + - + +
34C ASP* 2.8 41.2 + - - +
71C ALA* 5.1 2.0 - - + -
75C ASN* 4.0 20.6 - - + +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP* 3.5 32.7 - - - -
27C GLU 3.2 10.2 + - - -
28C TYR 3.2 3.4 + - - -
30C ILE* 1.3 76.9 - - - +
32C PHE* 1.3 49.2 + - - +
34C ASP* 3.0 11.1 + - - +
35C GLN* 2.8 37.4 + - - +
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Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.1 46.4 - - + -
12C TRP* 3.9 18.4 - - + -
13C LEU* 3.6 34.5 - - + -
16C ALA* 5.0 4.0 - - + -
28C TYR 2.9 12.0 + - - +
29C ILE* 3.5 10.3 - - - +
31C GLY* 1.3 75.3 - - - +
33C CYS* 1.3 63.3 + - - +
35C GLN* 3.1 6.2 + - - +
36C ILE* 2.9 50.9 + - + +
46C ALA* 3.9 22.2 - - + -
49C LEU* 4.7 1.3 - - + -
50C LEU* 4.1 9.2 - - + -
68C VAL* 3.5 24.2 - - + -
72C CYS* 3.9 8.1 - - - -
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Residues in contact with CYS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 3.5 14.4 - - - -
30C ILE* 3.0 12.4 + - + +
32C PHE* 1.3 77.6 - - - +
34C ASP* 1.3 67.2 + - - +
36C ILE* 3.1 9.1 + - - +
37C ASN* 3.0 25.8 + - - -
68C VAL* 4.8 0.7 - - - -
71C ALA* 3.8 18.4 - - - -
72C CYS* 3.8 38.4 - - - -
75C ASN* 4.1 16.4 - - + +
76C CYS* 4.0 13.7 - - - -
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Residues in contact with ASP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 2.8 34.0 + - - +
31C GLY* 3.4 10.5 - - - +
33C CYS* 1.3 75.9 - - - +
35C GLN* 1.3 67.8 + - - +
37C ASN* 3.1 16.1 + - - +
38C LYS* 3.1 27.7 + - + +
75C ASN* 6.0 1.2 - - - +
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C SER* 3.4 15.2 + - - -
9C LEU* 3.5 19.7 - - + +
12C TRP* 2.7 49.4 - - + +
31C GLY 2.8 22.4 + - - +
32C PHE* 3.1 7.2 + - - +
34C ASP* 1.3 72.1 - - - +
36C ILE* 1.3 64.8 + - - +
38C LYS* 2.9 10.0 + - - +
39C GLU* 2.9 30.6 + - + +
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.3 12.3 - - + -
32C PHE* 2.9 45.8 + - + +
33C CYS* 3.3 8.7 - - - +
35C GLN* 1.3 77.5 - - - +
37C ASN* 1.3 55.1 + - - +
39C GLU 3.4 10.2 - - - +
42C GLY* 3.9 9.8 - - - +
43C PRO* 3.9 28.7 - - + -
46C ALA* 3.5 18.8 - - + -
72C CYS* 3.6 20.9 - - - -
76C CYS* 4.1 13.7 - - + -
79C ARG* 2.7 26.6 + - - +
80C PHE* 4.1 9.2 - - + -
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Residues in contact with ASN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C CYS 3.0 14.6 + - - +
34C ASP* 3.1 18.6 + - - +
36C ILE* 1.3 78.2 - - - +
38C LYS* 1.3 67.1 + - + +
75C ASN* 3.0 19.7 - - - +
76C CYS* 3.3 38.8 + - - +
79C ARG* 3.8 14.8 + - - +
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ASP* 3.1 12.7 + - + +
35C GLN* 2.9 12.6 + - - +
37C ASN* 1.3 87.0 - - + +
39C GLU* 1.3 65.2 + - + +
40C LEU 3.8 1.4 + - - -
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Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLU* 3.4 43.7 - - + +
8C SER* 5.8 2.1 - - - -
9C LEU* 5.0 12.3 - - + -
35C GLN* 2.9 23.2 + - + +
36C ILE 3.4 4.4 + - - +
38C LYS* 1.3 81.2 - - + +
40C LEU* 1.3 61.8 + - - +
41C GLU 3.4 1.6 - - - +
42C GLY* 3.2 21.9 + - - +
79C ARG* 2.6 31.2 + - - -
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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