Contacts of the helix formed by residues 2 - 18 (chain D) in PDB entry 1JT0
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 ASN 2 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 1.3 77.1 + - + +
4D LYS* 3.9 7.0 + - - +
5D ASP* 3.3 25.1 + - - +
6D LYS* 3.3 18.0 + - - +
42D HIS* 3.7 15.1 - - - -
10E A 3.8 15.2 + - - +
11E T 2.5 45.4 + - - +
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Residues in contact with LEU 3 (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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2D ASN* 1.3 83.0 - - - +
4D LYS* 1.3 57.0 + - - +
5D ASP 3.0 1.8 - - - -
6D LYS* 2.9 28.6 + - + +
7D ILE* 2.6 40.3 + - + +
32D SER 5.5 0.2 - - - +
34D SER* 3.5 29.4 - - - +
38D ASN* 3.5 7.6 - - - +
11E T 3.2 50.9 - - - +
12E A 3.9 9.2 - - - +
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Residues in contact with LYS 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ASN* 3.8 11.1 - - - +
3D LEU* 1.3 77.8 - - - +
5D ASP* 1.3 61.7 + - - +
7D ILE* 3.8 6.7 - - - +
8D LEU* 3.0 34.6 + - + +
42D HIS* 3.0 60.8 + - + +
43D PHE* 3.8 13.6 - - + -
52D GLU* 3.0 33.9 + - - -
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Residues in contact with ASP 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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2D ASN* 3.3 21.9 + - - +
3D LEU 3.0 0.8 - - - -
4D LYS* 1.3 83.7 - - - +
6D LYS* 1.3 65.6 + - - +
8D LEU* 3.1 19.7 + - - +
9D GLY* 3.0 17.8 + - - -
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Residues in contact with LYS 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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2D ASN 3.3 10.1 + - - +
3D LEU* 2.9 27.6 + - + +
5D ASP* 1.3 77.3 - - - +
7D ILE* 1.3 58.4 + - - +
9D GLY* 2.8 19.4 + - - -
10D VAL* 3.1 20.2 + - + +
32D SER* 3.0 40.0 + - - +
33D GLU* 4.3 15.7 + - - +
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Residues in contact with ILE 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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3D LEU* 2.6 26.7 + - + +
4D LYS* 3.8 5.4 - - - +
6D LYS* 1.3 72.9 - - + +
8D LEU* 1.3 63.6 + - - +
10D VAL* 3.4 1.6 + - - +
11D ALA* 3.0 23.3 + - + +
28D ILE* 3.9 13.2 - - + -
29D VAL* 6.5 0.2 - - - -
32D SER* 4.0 22.9 - - - +
34D SER* 3.6 27.8 - - - +
38D ASN* 4.1 11.4 - - - +
39D LEU* 3.6 46.2 - - + -
42D HIS* 5.2 0.4 - - + -
43D PHE* 3.8 15.0 - - + -
49D LEU* 5.1 1.6 - - + -
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Residues in contact with LEU 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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4D LYS* 3.0 28.0 + - + +
5D ASP* 3.1 22.2 + - - +
7D ILE* 1.3 76.9 - - - +
9D GLY* 1.3 57.7 + - - +
11D ALA* 3.6 5.3 - - - +
12D LYS* 2.9 30.7 + - - +
43D PHE* 3.2 33.0 - - + -
49D LEU* 3.8 10.1 - - + -
52D GLU* 4.6 13.0 - - + +
53D ILE* 4.0 18.0 - - + +
56D ILE* 3.8 25.4 - - + -
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Residues in contact with GLY 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 ASP 3.0 8.6 + - - -
6D LYS* 2.8 10.9 + - - -
8D LEU* 1.3 75.0 - - - +
10D VAL* 1.3 64.1 + - - -
12D LYS* 3.1 7.9 + - - +
13D GLU* 3.0 31.0 + - - +
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Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LYS* 3.1 17.2 + - + +
7D ILE 3.7 2.9 - - - +
9D GLY* 1.3 72.9 - - - +
11D ALA* 1.3 68.3 + - - +
13D GLU* 3.1 8.1 + - - +
14D LEU* 2.9 28.2 + - + +
28D ILE* 3.5 43.7 - - + +
31D LEU* 4.1 20.2 - - + +
32D SER* 3.4 26.5 - - - +
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Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 3.0 15.5 + - + +
8D LEU* 3.6 6.3 - - - +
10D VAL* 1.3 85.6 - - - +
12D LYS* 1.3 63.2 + - - +
14D LEU* 3.9 2.0 - - - +
15D PHE* 3.0 34.9 + - + -
28D ILE* 4.2 15.7 - - + -
49D LEU* 4.1 22.0 - - + -
53D ILE* 3.8 14.8 - - + -
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Residues in contact with LYS 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 LEU 2.9 18.4 + - - +
9D GLY* 3.1 5.8 + - - +
11D ALA* 1.3 76.7 - - - +
13D GLU* 1.3 79.3 + - - +
15D PHE* 3.4 4.8 + - - +
16D ILE* 3.1 47.6 + - + +
53D ILE* 3.9 24.4 - - + +
57D GLU* 2.7 44.7 + - - +
90D GLU* 3.1 29.3 + - - -
91D TYR* 4.3 0.4 - - - +
92D TYR 4.4 1.6 - - - +
94D PRO* 5.7 0.2 - - - +
95D LEU* 4.0 5.2 - - + +
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Residues in contact with GLU 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 GLY* 3.0 18.8 + - - +
10D VAL* 3.5 11.2 - - - +
12D LYS* 1.3 93.9 - - - +
14D LEU* 1.3 60.4 + - + +
16D ILE* 3.2 17.5 + - - +
17D LYS* 2.9 30.5 + - - +
31D LEU* 6.5 0.2 - - + -
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Residues in contact with LEU 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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10D VAL* 2.9 18.8 + - + +
11D ALA 3.9 1.6 - - - +
13D GLU* 1.3 76.7 - - + +
15D PHE* 1.3 59.5 + - - +
16D ILE 3.0 0.3 + - - -
17D LYS* 3.1 14.0 + - + -
18D ASN* 2.7 42.6 + - - +
23D THR* 3.3 23.4 + - + +
27D GLU* 3.6 28.7 - - + +
28D ILE* 4.0 36.8 - - + +
31D LEU* 3.8 29.8 - - + -
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Residues in contact with PHE 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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11D ALA* 3.0 34.7 + - + +
12D LYS* 3.7 4.9 - - - +
14D LEU* 1.3 74.8 - - - +
16D ILE* 1.3 56.9 + - - +
18D ASN 2.4 18.2 - - - +
19D GLY 3.7 7.4 - - - +
20D TYR* 3.7 31.6 - + - -
23D THR* 3.4 32.7 + - + -
28D ILE* 4.9 2.0 - - + -
46D LYS* 4.1 13.7 - - + -
49D LEU* 4.4 10.5 - - + -
50D PHE* 3.6 39.0 - + + -
53D ILE* 4.0 20.4 - - + -
95D LEU* 3.8 15.3 - - + -
97D ASN* 5.6 0.9 - - - +
98D ALA* 3.7 17.0 + - + +
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Residues in contact with ILE 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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104B THR* 4.7 3.5 - - - +
12D LYS* 3.1 44.2 + - + +
13D GLU* 3.5 14.6 - - - +
14D LEU 3.0 0.6 - - - -
15D PHE* 1.3 76.1 - - - +
17D LYS* 1.3 66.4 + - - +
18D ASN 3.6 3.3 - - - +
90D GLU 5.2 0.2 - - - +
94D PRO* 3.3 41.7 - - + +
95D LEU* 3.3 24.7 - - + +
97D ASN* 4.2 13.8 - - - +
164D HIS* 5.8 6.5 + - - +
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Residues in contact with LYS 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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104B THR* 4.0 14.4 - - - +
108B LYS* 4.5 28.0 + - - +
13D GLU 2.9 16.2 + - - +
14D LEU* 3.8 14.6 - - + +
16D ILE* 1.3 81.0 - - - +
18D ASN* 1.3 75.2 + - - +
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Residues in contact with ASN 18 (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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104B THR* 5.1 10.3 - - - +
105B GLU* 5.5 3.6 - - - +
108B LYS* 5.4 2.3 + - - -
14D LEU* 2.7 22.0 + - - +
15D PHE 2.4 31.2 - - - +
16D ILE 3.6 2.7 - - - +
17D LYS* 1.3 99.5 - - - +
19D GLY* 1.3 58.2 + - - +
22D ALA* 3.5 26.2 + - + -
23D THR* 4.0 8.9 + - - +
27D GLU* 4.1 17.6 + - - -
97D ASN* 5.7 1.4 - - - +
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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