Contacts of the helix formed by residues 3 - 17 (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 GLU 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MSE 3.8 0.3 - - - +
2D ALA* 1.3 86.7 - - - +
4D ALA* 1.3 69.1 - - + +
5D GLU* 3.2 20.3 + - - +
6D GLY 3.4 1.9 + - - -
7D GLU* 2.8 29.0 + - - +
204D GLY 4.3 6.9 - - - +
205D SER* 2.9 15.8 + - - +
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Residues in contact with ALA 4 (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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3D GLU* 1.3 78.9 - - + +
5D GLU* 1.3 75.1 + - - +
7D GLU* 3.8 16.2 - - - +
8D SER* 3.0 27.0 + - - -
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Residues in contact with GLU 5 (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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3D GLU* 3.2 22.7 - - - +
4D ALA* 1.3 86.7 + - - +
6D GLY* 1.3 57.5 + - - +
8D SER* 3.6 4.0 - - - -
9D LEU* 3.1 33.8 + - - +
35D GLN* 4.7 0.9 - - - +
39D GLU* 3.4 32.6 - - + +
40D LEU 6.2 0.2 - - - +
41D GLU* 6.3 1.1 - - + +
45D ILE* 4.2 6.5 - - + -
205D SER* 3.7 27.8 + - - +
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Residues in contact with GLY 6 (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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58C GLN* 3.7 8.5 - - - +
1D MSE 3.6 16.2 - - - -
3D GLU 3.4 0.2 + - - -
4D ALA 3.3 0.2 - - - -
5D GLU* 1.3 76.8 - - - +
7D GLU* 1.3 59.9 + - - +
9D LEU* 3.8 0.7 - - - +
10D GLU* 2.9 32.2 + - - +
45D ILE* 4.1 22.2 - - - +
49D LEU* 4.2 1.9 - - - +
205D SER 3.2 10.1 + - - -
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Residues in contact with GLU 7 (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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19C PRO* 3.4 40.0 - - + +
20C SER* 5.2 1.3 - - - -
58C GLN* 3.6 15.0 - - - +
60C TRP* 3.7 21.4 - - - +
2D ALA 4.1 9.2 - - - +
3D GLU* 2.8 26.6 - - - +
4D ALA* 3.4 14.6 + - - +
6D GLY* 1.3 76.1 - - - +
8D SER* 1.3 53.5 + - - +
11D SER* 2.7 35.7 + - - -
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Residues in contact with SER 8 (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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20C SER* 6.1 1.1 - - - -
4D ALA 3.0 18.1 + - - -
5D GLU* 3.6 5.4 - - - -
7D GLU* 1.3 75.2 - - - +
9D LEU* 1.3 66.2 + - - +
11D SER* 3.0 8.2 + - - -
12D TRP* 2.9 36.2 + - - -
35D GLN* 3.1 20.8 + - - -
39D GLU* 5.7 0.4 - - - -
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Residues in contact with LEU 9 (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 3.1 19.6 + - - +
6D GLY 3.8 2.2 - - - +
8D SER* 1.3 79.4 - - - +
10D GLU* 1.3 57.2 + - - +
12D TRP* 3.1 6.6 + - - +
13D LEU 2.9 24.1 + - - -
32D PHE* 3.6 19.2 - - + -
35D GLN* 3.3 31.4 - - + +
36D ILE* 3.9 26.9 - - + +
39D GLU* 4.3 7.9 - - + -
42D GLY* 4.1 18.4 - - - +
45D ILE* 3.7 29.6 - - + -
46D ALA* 4.7 1.8 - - + +
49D LEU* 3.6 15.0 - - + -
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Residues in contact with GLU 10 (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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19C PRO* 3.5 24.9 - - + -
56C SER* 5.2 0.2 - - - -
58C GLN* 4.2 3.6 - - + -
61C GLU* 2.8 32.8 - - - +
6D GLY 2.9 20.9 + - - +
7D GLU 3.9 2.7 - - - +
9D LEU* 1.3 73.7 - - - +
11D SER* 1.3 57.7 + - - +
13D LEU* 3.8 8.3 - - - +
14D ASN* 2.8 43.3 + - - +
49D LEU* 3.2 38.4 - - + +
53D LYS* 3.2 14.2 - - - -
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Residues in contact with SER 11 (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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18C ASN* 3.2 30.5 + - - +
19C PRO* 4.4 2.2 - - - -
20C SER* 3.3 19.9 + - - -
7D GLU 2.7 22.6 + - - -
8D SER* 3.0 9.6 + - - -
10D GLU* 1.3 74.6 - - - +
12D TRP* 1.3 62.9 + - - +
14D ASN* 3.4 14.6 + - - +
15D LYS* 3.5 17.6 + - - +
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Residues in contact with TRP 12 (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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8D SER* 2.9 40.7 + - - -
9D LEU 3.1 7.2 + - - +
11D SER* 1.3 76.1 - - - +
13D LEU* 1.3 65.6 + - - +
15D LYS* 3.2 10.7 + - + +
16D ALA* 3.0 21.5 + - - +
27D GLU 4.6 2.9 - - - -
28D TYR* 4.1 31.8 - + - +
31D GLY* 3.7 23.8 - - - -
32D PHE* 3.9 29.4 - - + -
35D GLN* 4.0 26.1 - - + +
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Residues in contact with LEU 13 (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 2.9 15.8 + - - +
10D GLU* 3.3 11.0 + - - +
12D TRP* 1.3 72.7 - - - +
14D ASN* 1.3 67.8 + - - +
16D ALA* 3.1 4.2 + - + -
17D THR* 2.8 42.2 + - + +
32D PHE* 3.9 25.3 - - + -
49D LEU* 3.6 35.4 - - + +
50D LEU* 3.9 10.5 - - + +
53D LYS* 3.5 31.4 - - + -
68D VAL* 4.0 18.4 - - + -
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Residues in contact with ASN 14 (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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14C ASN* 3.4 40.9 + - + +
17C THR 4.9 0.5 - - - +
18C ASN* 4.1 6.0 + - - +
19C PRO* 4.0 15.4 - - - +
53C LYS* 5.1 0.2 - - - -
61C GLU* 3.7 6.6 + - - +
10D GLU* 2.8 30.6 + - - -
11D SER* 3.5 11.9 - - - +
13D LEU* 1.3 76.2 - - - +
15D LYS* 1.3 54.0 + - + +
17D THR 3.4 0.9 - - - -
18D ASN* 2.7 38.1 + - - +
53D LYS* 2.7 34.5 - - - +
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Residues in contact with LYS 15 (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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18C ASN* 5.6 4.9 - - - -
11D SER* 3.5 14.8 + - - +
12D TRP* 3.2 11.8 + - + +
13D LEU 3.2 0.6 - - - -
14D ASN* 1.3 82.1 - - + +
16D ALA* 1.3 57.6 + - - +
17D THR 3.3 0.3 + - - -
18D ASN* 3.5 12.4 + - - +
21D ASN* 3.0 22.0 + - - +
28D TYR* 3.6 55.5 + - + -
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Residues in contact with ALA 16 (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 3.0 15.5 + - - +
13D LEU* 3.1 10.1 + - + +
15D LYS* 1.3 76.9 - - - +
17D THR* 1.3 61.5 + - + +
18D ASN 3.6 0.2 - - - -
21D ASN* 3.9 2.4 - - - +
25D ASP* 5.0 2.2 + - - +
28D TYR* 3.7 24.0 - - + +
29D ILE* 3.7 33.2 - - + +
32D PHE* 4.9 2.2 - - + -
64D GLN* 3.5 16.5 + - - +
68D VAL* 4.0 10.0 - - + +
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Residues in contact with THR 17 (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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14C ASN* 5.2 0.2 - - - -
13D LEU* 2.8 38.4 + - + +
14D ASN 3.4 2.5 + - - -
16D ALA* 1.3 82.7 - - - +
18D ASN* 1.3 65.9 + - - +
19D PRO* 3.1 8.7 - - - +
53D LYS* 3.5 24.7 + - + +
61D GLU* 3.6 25.0 - - - +
64D GLN* 3.5 15.6 - - - +
65D ALA* 3.5 34.1 - - + +
68D VAL* 4.2 2.5 - - + -
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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