Contacts of the helix formed by residues 2 - 19 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LEU* 1.3 70.2 + - + +
4C LYS* 2.9 7.6 - - - +
5C ASP* 2.6 46.1 + - - +
6C LYS* 2.8 18.9 + - - +
42C HIS* 5.7 2.0 + - - -
11F T 5.1 7.3 + - - -
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Residues in contact with LEU 3 (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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2C ASN* 1.3 85.3 - - + +
4C LYS* 1.3 54.1 + - - +
6C LYS* 3.8 15.5 - - + +
7C ILE* 2.6 45.4 + - + +
32C SER 5.3 5.4 - - - +
33C GLU 5.0 2.5 - - - +
34C SER* 3.4 27.4 - - - +
38C ASN* 3.6 21.3 - - - +
11F T 3.6 30.2 + - - +
12F A 3.9 11.2 - - - +
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Residues in contact with LYS 4 (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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2C ASN* 2.9 6.1 - - - +
3C LEU* 1.3 81.8 - - - +
5C ASP* 1.3 59.8 + - - +
7C ILE* 4.3 4.9 - - - -
8C LEU* 3.0 33.8 + - + +
42C HIS* 3.8 41.8 + - + -
43C PHE* 3.5 27.1 - - + -
52C GLU* 3.3 32.1 + - - -
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Residues in contact with ASP 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ASN* 2.6 38.0 + - - +
4C LYS* 1.3 76.1 - - - +
6C LYS* 1.3 66.3 + - - +
8C LEU* 3.2 12.7 + - - +
9C GLY* 2.7 22.3 + - - -
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Residues in contact with LYS 6 (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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2C ASN* 2.8 18.0 + - - +
3C LEU* 3.3 21.7 - - + +
5C ASP* 1.3 74.4 - - - +
7C ILE* 1.3 55.7 + - + +
9C GLY* 2.8 22.1 + - - -
10C VAL* 2.9 22.3 + - + +
31C LEU 4.2 6.5 - - - -
32C SER* 3.2 42.6 + - - +
33C GLU* 3.7 18.3 + - - +
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Residues in contact with ILE 7 (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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3C LEU* 2.6 28.5 + - + +
4C LYS* 4.0 5.8 - - - +
6C LYS* 1.3 70.7 - - + +
8C LEU* 1.3 69.0 + - - +
9C GLY 2.9 0.2 + - - -
10C VAL* 3.2 1.8 + - - +
11C ALA* 2.9 24.6 + - - +
28C ILE* 4.2 8.7 - - + -
29C VAL* 6.3 0.4 - - - -
32C SER* 3.7 26.4 - - - +
34C SER* 4.0 25.4 - - - +
38C ASN* 4.2 8.3 - - - +
39C LEU* 3.6 47.1 - - + -
42C HIS* 4.9 0.7 - - - +
43C PHE* 3.6 14.8 - - + -
49C LEU* 4.9 4.5 - - + -
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Residues in contact with LEU 8 (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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4C LYS* 3.0 32.3 + - + +
5C ASP* 3.2 15.0 + - - +
7C ILE* 1.3 75.4 - - - +
9C GLY* 1.3 61.9 - - - +
11C ALA* 3.4 3.5 + - - -
12C LYS* 3.0 20.6 + - - +
43C PHE* 3.8 15.0 - - + -
49C LEU* 3.8 14.1 - - + +
52C GLU* 4.3 9.4 - - - +
53C ILE* 3.3 41.8 - - + +
56C ILE* 3.8 27.8 - - + -
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Residues in contact with GLY 9 (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 ASP 2.7 14.1 + - - -
6C LYS* 2.8 7.0 + - - -
8C LEU* 1.3 72.7 - - - +
10C VAL* 1.3 65.2 + - - -
12C LYS* 2.8 17.3 + - - +
13C GLU* 2.8 22.6 + - - +
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Residues in contact with VAL 10 (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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6C LYS* 2.9 21.3 + - + +
7C ILE 3.6 6.5 - - - +
9C GLY* 1.3 70.6 - - - -
11C ALA* 1.3 68.0 + - - +
13C GLU* 3.1 21.1 + - - +
14C LEU* 3.1 20.2 + - + +
28C ILE* 3.5 38.4 - - + +
31C LEU* 4.0 19.5 - - + +
32C SER* 3.7 27.6 - - - +
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Residues in contact with ALA 11 (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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7C ILE 2.9 13.9 + - - +
8C LEU 3.6 4.9 - - - +
10C VAL* 1.3 85.5 - - - +
12C LYS* 1.3 60.0 + - - +
14C LEU* 4.0 2.5 - - - +
15C PHE* 2.8 35.6 + - + -
28C ILE* 3.9 30.7 - - + -
49C LEU* 4.0 17.5 - - + -
53C ILE* 4.0 8.5 - - + -
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Residues in contact with LYS 12 (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 LEU 3.0 11.3 + - - +
9C GLY* 2.8 13.1 + - - +
11C ALA* 1.3 75.3 - - - +
13C GLU* 1.3 72.6 + - - +
15C PHE* 3.4 4.0 + - - +
16C ILE* 3.0 46.8 + - + +
53C ILE* 4.2 21.1 - - + -
57C GLU* 2.3 48.0 + - - +
90C GLU* 2.7 26.8 + - - +
91C TYR* 4.1 3.4 - - - -
92C TYR 5.1 1.3 - - - +
94C PRO* 5.7 0.2 - - - -
95C LEU* 4.6 8.1 - - + -
699C SO4 5.3 3.5 + - - +
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Residues in contact with GLU 13 (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 GLY* 2.8 23.0 - - - +
10C VAL* 3.1 12.3 + - + +
12C LYS* 1.3 86.4 - - - +
14C LEU* 1.3 59.7 + - + +
16C ILE* 2.9 14.0 + - - +
17C LYS* 2.6 43.4 + - + +
31C LEU* 6.3 0.4 - - + -
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Residues in contact with LEU 14 (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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10C VAL* 3.2 15.5 - - + +
11C ALA 4.2 0.9 - - - +
13C GLU* 1.3 79.4 - - + +
15C PHE* 1.3 56.3 + - - +
17C LYS* 4.4 11.7 - - + +
18C ASN* 2.8 32.4 + - - +
19C GLY 3.3 0.3 + - - -
23C THR* 2.8 34.6 + - + +
27C GLU* 4.0 24.7 - - + +
28C ILE* 3.7 44.0 - - + +
31C LEU* 3.7 26.2 - - + -
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Residues in contact with PHE 15 (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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11C ALA* 2.8 43.0 + - + +
12C LYS* 4.0 0.9 - - - +
14C LEU* 1.3 77.2 - - - +
16C ILE* 1.3 60.0 - - - +
19C GLY* 3.0 36.8 + - - -
20C TYR* 3.3 45.5 - + - -
23C THR* 3.6 18.4 - - + -
28C ILE* 4.8 4.9 - - + -
46C LYS* 4.1 15.9 - - + -
49C LEU* 4.7 6.3 - - + -
50C PHE* 3.8 34.5 - + + -
53C ILE* 4.4 10.1 - - + -
95C LEU* 3.7 20.0 - - + +
97C ASN* 5.6 0.9 - - - +
98C ALA* 3.9 9.5 + - + +
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Residues in contact with ILE 16 (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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12C LYS* 3.0 50.0 + - + +
13C GLU* 2.9 10.0 + - - +
15C PHE* 1.3 80.7 - - - +
17C LYS* 1.3 66.2 + - + +
19C GLY* 4.6 1.0 + - - -
90C GLU 5.0 0.7 - - - +
94C PRO* 3.1 45.0 - - + +
95C LEU* 3.5 13.2 - - + +
97C ASN* 4.9 11.4 - - - +
164C HIS* 5.9 1.9 - - - -
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Residues in contact with LYS 17 (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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104A THR 4.6 8.8 - - - +
13C GLU* 2.6 24.6 + - + +
14C LEU* 4.4 8.8 - - + +
16C ILE* 1.3 80.2 - - + +
18C ASN* 1.3 92.9 + - - +
27C GLU* 4.9 6.1 + - - -
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Residues in contact with ASN 18 (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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104A THR* 4.8 8.1 + - - -
105A GLU* 4.2 16.1 + - + +
14C LEU* 2.8 19.8 + - - +
17C LYS* 1.3 113.7 + - - +
19C GLY* 1.3 59.8 + - - +
22C ALA* 3.1 36.6 + - + +
23C THR* 4.3 4.5 - - - +
27C GLU* 4.1 21.0 + - - -
101C GLU* 4.4 2.6 - - - +
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Residues in contact with GLY 19 (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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104A THR* 5.5 2.5 - - - -
14C LEU 3.3 0.4 + - - -
15C PHE* 3.0 24.3 + - - -
16C ILE 4.6 0.8 + - - -
17C LYS 3.7 0.4 - - - -
18C ASN* 1.3 80.8 - - - +
20C TYR* 1.3 62.0 + - - +
21C ASN 3.9 0.2 - - - -
23C THR* 2.4 32.6 + - - -
97C ASN* 5.5 3.8 - - - -
98C ALA* 4.1 8.7 - - - -
101C GLU* 3.5 10.3 - - - -
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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
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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