Contacts of the helix formed by residues 2 - 19 (chain E) in PDB entry 1JTY
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LYS* 6.3 0.6 - - - +
3E LEU* 1.3 53.9 + - - +
4E LYS* 2.9 9.6 - - - +
5E ASP* 2.8 28.4 + - + +
6E LYS* 2.7 55.1 + - - +
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Residues in contact with LEU 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ASN* 1.3 78.8 + - - +
4E LYS* 1.3 61.1 + - - +
6E LYS* 3.7 14.8 - - + +
7E ILE* 3.1 32.7 + - + +
32E SER 3.7 13.7 - - - +
33E GLU 5.1 0.7 - - - +
34E SER* 3.4 35.2 - - - +
38E ASN* 3.1 27.1 - - - +
42E HIS* 5.1 6.1 - - - +
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Residues in contact with LYS 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ASN* 4.6 2.9 - - - -
3E LEU* 1.3 78.3 - - - +
5E ASP* 1.3 68.2 + - - +
7E ILE* 3.0 12.7 + - - +
8E LEU* 2.8 34.3 + - + +
42E HIS* 3.2 42.9 + - + +
43E PHE* 3.5 31.1 - - + -
52E GLU* 3.5 16.9 + - - -
901E SO4 2.6 40.3 + - - +
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Residues in contact with ASP 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY* 5.2 3.6 - - - -
2E ASN* 2.8 28.2 + - + +
4E LYS* 1.3 85.7 - - - +
6E LYS* 1.3 57.8 + - - +
8E LEU* 4.1 13.2 - - - +
9E GLY* 2.8 26.5 + - - -
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Residues in contact with LYS 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.2 57.1 + - + +
2E ASN* 2.7 40.0 + - - +
3E LEU* 3.6 21.7 - - + +
5E ASP* 1.3 73.4 - - - +
7E ILE* 1.3 58.2 + - - +
9E GLY* 3.9 0.4 - - - -
10E VAL* 3.0 36.0 + - - +
32E SER* 3.8 17.6 + - - +
33E GLU* 4.7 9.3 + - - +
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Residues in contact with ILE 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU 3.1 16.9 + - - +
4E LYS 3.0 7.5 + - - +
6E LYS* 1.3 72.5 - - - +
8E LEU* 1.3 60.5 + - - +
9E GLY 3.1 1.1 - - - -
11E ALA* 2.8 35.9 + - - +
28E ILE* 3.7 20.8 - - + +
32E SER* 3.4 24.2 - - - +
34E SER* 3.5 21.8 - - - +
38E ASN* 4.0 9.2 - - - +
39E LEU* 4.2 24.7 - - + -
42E HIS* 4.6 8.5 - - + -
43E PHE* 3.8 20.0 - - + -
49E LEU* 4.2 10.5 - - + -
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Residues in contact with LEU 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LYS* 2.8 28.4 + - + +
5E ASP* 4.1 12.3 - - - +
7E ILE* 1.3 72.2 - - - +
9E GLY* 1.3 65.1 + - - +
11E ALA* 4.4 3.4 - - - -
12E LYS* 3.1 23.4 + - - +
43E PHE* 3.7 24.2 - - + -
49E LEU* 3.4 20.6 - - + +
52E GLU* 4.6 8.1 - - + +
53E ILE* 3.2 35.7 - - + +
56E ILE* 3.8 23.3 - - + -
399E SO4 4.2 13.8 + - - +
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Residues in contact with GLY 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY* 4.1 23.8 - - - -
40A TYR* 6.1 0.7 - - - -
5E ASP 2.8 19.9 + - - -
6E LYS 3.9 0.4 - - - -
8E LEU* 1.3 73.3 - - - +
10E VAL* 1.3 68.2 + - - +
12E LYS* 3.0 13.9 + - - +
13E GLU* 3.0 18.1 + - - +
399E SO4 4.6 7.6 - - - -
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Residues in contact with VAL 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 4.8 1.2 + - - -
40A TYR* 3.9 20.4 - - + +
41A TYR* 4.0 21.7 - - - +
44A LYS* 6.3 0.2 - - + -
6E LYS 3.0 22.8 + - - +
7E ILE 4.1 1.3 - - - +
9E GLY* 1.3 68.7 - - - -
11E ALA* 1.3 52.4 + - - +
13E GLU* 3.1 5.7 + - - +
14E LEU* 2.8 44.0 + - + +
28E ILE* 3.7 15.3 - - + +
31E LEU* 3.4 46.0 - - + -
32E SER* 3.9 7.9 - - - +
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Residues in contact with ALA 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E ILE 2.8 24.7 + - - +
10E VAL* 1.3 73.6 - - - +
12E LYS* 1.3 57.8 + - - +
14E LEU* 2.9 5.0 + - - +
15E PHE* 2.8 35.7 + - + -
28E ILE* 3.6 35.7 - - + -
49E LEU* 3.7 15.3 - - + -
53E ILE* 4.0 9.4 - - + -
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Residues in contact with LYS 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 5.0 8.0 + - - -
8E LEU 3.1 17.9 + - - +
9E GLY 3.0 4.7 + - - +
11E ALA* 1.3 77.2 - - - +
13E GLU* 1.3 73.5 + - + +
15E PHE* 3.2 7.4 + - - +
16E ILE* 3.0 50.9 + - + +
53E ILE* 3.9 13.3 - - + +
57E GLU* 2.7 45.1 + - + +
90E GLU* 3.2 18.5 + - - +
91E TYR* 3.8 11.7 - - - -
95E LEU* 4.2 10.3 - - + -
399E SO4 3.2 23.1 + - - +
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Residues in contact with GLU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 4.6 1.2 + - - -
38A ASN* 2.7 49.0 + - - +
41A TYR* 3.5 46.2 - - + -
801A SO4 4.3 7.1 + - - -
9E GLY 3.0 12.2 + - - +
10E VAL 3.4 7.2 - - - +
12E LYS* 1.3 86.6 - - + +
14E LEU* 1.3 62.8 + - - +
16E ILE* 3.3 24.0 + - - +
17E LYS* 3.0 24.3 + - - +
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Residues in contact with LEU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 4.1 22.7 - - + +
10E VAL* 2.8 35.4 + - + +
11E ALA 2.9 7.6 + - - +
13E GLU* 1.3 75.2 - - - +
15E PHE* 1.3 63.5 + - - +
17E LYS* 4.5 4.7 - - + +
18E ASN* 3.0 41.6 + - - +
23E THR* 3.0 23.1 + - + +
27E GLU* 4.0 18.6 - - + +
28E ILE* 3.9 25.1 - - + +
31E LEU* 3.9 10.3 - - + -
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Residues in contact with PHE 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ALA* 2.8 26.2 + - + +
12E LYS* 3.2 2.2 + - - +
14E LEU* 1.3 73.4 - - - +
16E ILE* 1.3 59.5 + - - +
19E GLY* 2.9 34.4 + - - -
20E TYR* 3.6 29.4 - + - -
23E THR* 3.2 36.8 - - + -
28E ILE* 4.6 7.4 - - + -
46E LYS* 4.1 12.1 - - + -
49E LEU* 4.8 3.1 - - + -
50E PHE* 3.3 43.3 - + + -
53E ILE* 4.0 21.8 - - + -
95E LEU* 3.6 19.7 - - + -
97E ASN* 6.1 0.2 - - - +
98E ALA* 3.9 10.1 + - + +
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Residues in contact with ILE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D THR* 5.7 5.0 + - - +
12E LYS* 3.0 44.1 + - + +
13E GLU* 3.3 24.0 + - - +
15E PHE* 1.3 77.8 - - - +
17E LYS* 1.3 60.8 + - - +
18E ASN 5.2 0.2 - - - -
19E GLY 4.8 0.7 + - - -
90E GLU 5.4 0.2 - - - +
94E PRO* 3.5 40.4 - - + +
95E LEU* 3.2 20.9 - - + +
97E ASN* 5.9 3.3 - - - +
98E ALA* 5.6 0.2 - - - -
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Residues in contact with LYS 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TYR* 3.7 20.2 + - - +
299A SO4 4.3 14.6 + - - -
21D ASN* 4.2 0.7 - - - +
101D GLU* 5.7 1.0 - - - +
104D THR* 4.0 14.9 + - - -
105D GLU* 3.3 27.3 - - + +
13E GLU 3.0 15.8 + - - +
14E LEU* 4.1 7.4 - - + +
16E ILE* 1.3 80.3 - - - +
18E ASN* 1.3 75.1 + - - +
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Residues in contact with ASN 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASN* 3.1 21.6 - - + +
101D GLU* 3.2 17.5 - - - +
105D GLU* 3.6 9.0 + - - -
14E LEU* 3.0 24.3 + - - +
17E LYS* 1.3 109.4 + - - +
19E GLY* 1.3 59.7 + - - +
22E ALA* 3.8 24.7 + - + +
23E THR* 3.9 7.2 + - - +
27E GLU* 3.7 20.4 - - - +
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Residues in contact with GLY 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D GLU* 4.4 1.8 - - - -
15E PHE* 2.9 24.9 + - - +
16E ILE 4.7 0.6 + - - -
17E LYS 3.9 0.4 - - - -
18E ASN* 1.3 75.5 - - - +
20E TYR* 1.3 59.6 + - - -
21E ASN 3.5 1.8 - - - -
22E ALA 4.5 0.9 - - - -
23E THR* 2.6 26.5 + - - -
97E ASN* 4.6 4.7 - - - -
98E ALA* 4.2 8.5 - - - -
101E GLU* 3.9 15.3 - - - -
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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
------------------------------------------------------------
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