Contacts of the helix formed by residues 5 - 18 (chain B) in PDB entry 1JT6
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 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ASN* 3.6 32.0 + - + -
3B LEU 2.7 6.9 + - - -
4B LYS* 1.3 90.8 + - - +
6B LYS* 1.3 75.1 + - - +
7B ILE 3.2 1.1 - - - -
8B LEU* 3.9 16.7 - - - +
9B GLY* 3.3 17.2 + - - -
600B SO4 5.5 0.9 + - - -
700B SO4 4.9 2.6 + - - -
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Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASN 3.6 35.2 - - - +
3B LEU* 3.0 6.0 + - + +
5B ASP* 1.3 92.6 + - - +
7B ILE* 1.3 62.9 + - - +
9B GLY* 3.5 3.9 - - - +
10B VAL* 2.9 38.5 + - + +
32B SER* 3.5 9.6 - - - +
700B SO4 3.9 16.8 + - - -
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Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 3.2 25.9 + - + +
4B LYS* 4.5 2.7 - - - -
6B LYS* 1.3 76.3 - - - +
8B LEU* 1.3 55.5 + - - +
9B GLY 2.8 1.1 + - - -
10B VAL* 2.9 4.3 + - - +
11B ALA* 2.8 33.7 + - - +
28B ILE* 4.2 9.3 - - + +
29B VAL* 5.9 0.2 - - - -
32B SER* 2.8 36.6 - - - +
34B SER* 4.1 19.7 - - - +
38B ASN* 6.3 0.2 - - + -
39B LEU* 3.4 31.2 - - + -
43B PHE* 3.3 33.9 - - + -
49B LEU* 4.3 8.7 - - + -
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 3.5 23.1 - - - +
5B ASP* 3.9 20.7 + - - +
7B ILE* 1.3 79.5 - - - +
9B GLY* 1.3 59.8 + - - +
11B ALA* 4.2 2.7 - - - -
12B LYS* 3.1 9.0 + - - +
43B PHE* 3.8 15.3 - - + -
49B LEU* 3.7 18.2 - - + -
52B GLU* 3.9 23.8 - - + -
53B ILE* 3.0 48.9 - - + +
56B ILE* 5.0 9.0 - - + -
600B SO4 4.0 17.7 + - - +
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Residues in contact with GLY 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASP 3.3 12.5 + - - -
6B LYS* 3.3 5.6 + - - -
7B ILE 2.8 2.6 + - - -
8B LEU* 1.3 76.5 - - - +
10B VAL* 1.3 64.9 + - - -
12B LYS* 3.1 6.5 + - - +
13B GLU* 3.1 22.0 + - - +
600B SO4 4.1 11.9 - - - -
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LYS* 2.9 23.1 + - + +
7B ILE 3.8 1.8 - - - +
9B GLY* 1.3 71.4 - - - -
11B ALA* 1.3 62.2 + - - +
13B GLU* 3.4 8.2 + - - +
14B LEU* 3.0 37.6 + - + +
28B ILE* 4.2 8.5 - - + +
31B LEU* 3.9 45.3 - - + +
32B SER* 3.6 20.0 - - - +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE 2.8 16.6 + - - +
8B LEU* 3.8 6.1 - - - +
10B VAL* 1.3 74.7 - - - +
12B LYS* 1.3 66.3 + - - +
14B LEU* 3.0 7.0 + - - +
15B PHE* 2.9 34.5 + - + +
28B ILE* 4.3 14.7 - - + +
49B LEU* 3.9 28.5 - - + -
53B ILE* 4.0 10.8 - - + -
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU 3.1 14.9 + - - +
9B GLY* 3.1 6.1 + - - +
11B ALA* 1.3 77.5 - - - +
13B GLU* 1.3 64.0 + - - +
15B PHE* 3.3 4.8 + - - +
16B ILE* 3.2 45.7 + - + +
53B ILE* 3.7 20.0 - - + +
57B GLU* 3.3 30.6 + - - +
90B GLU* 3.9 16.0 + - - +
91B TYR* 4.1 12.9 - - - -
95B LEU* 4.5 3.5 - - + +
600B SO4 2.9 29.9 + - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLY 3.1 11.7 + - - +
10B VAL* 3.6 11.4 - - - +
12B LYS* 1.3 79.7 - - - +
14B LEU* 1.3 82.7 - - - +
16B ILE* 4.0 5.2 - - - +
17B LYS* 3.1 57.0 + - - +
31B LEU* 4.3 12.5 - - - +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.0 26.2 + - + +
11B ALA* 3.0 5.6 + - - +
13B GLU* 1.3 109.5 - - - +
15B PHE* 1.3 60.5 + - + +
16B ILE 3.1 2.0 - - - -
17B LYS* 4.6 4.7 - - + +
18B ASN* 3.0 30.7 + - - +
23B THR* 2.8 33.4 - - + +
27B GLU* 4.2 14.6 - - + +
28B ILE* 3.8 42.4 - - + +
31B LEU* 4.8 5.8 - - + -
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Residues in contact with PHE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 2.9 32.7 + - + +
12B LYS* 3.9 3.4 - - - +
14B LEU* 1.3 75.9 - - - +
16B ILE* 1.3 61.3 + - - +
18B ASN 3.9 0.2 - - - +
19B GLY* 3.7 20.5 - - - -
20B TYR* 3.5 28.0 - + - -
23B THR* 2.9 26.7 - - - -
28B ILE* 5.2 8.5 - - + -
46B LYS* 4.0 16.6 - - + -
49B LEU* 4.9 3.1 - - + -
50B PHE* 3.3 53.2 - + + -
53B ILE* 4.8 8.1 - - + -
95B LEU* 3.8 17.0 - - + -
98B ALA* 3.6 18.7 - - + +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 4.1 12.3 + - - -
108A LYS* 5.4 0.2 + - - -
12B LYS* 3.2 42.7 + - + +
13B GLU* 4.0 4.9 - - - +
14B LEU 3.1 0.6 - - - -
15B PHE* 1.3 77.1 - - - +
17B LYS* 1.3 68.9 + - - +
18B ASN 3.2 9.9 - - - +
57B GLU* 5.5 0.4 - - - +
90B GLU 5.6 0.4 - - - +
94B PRO* 3.8 35.7 - - + +
95B LEU* 3.4 24.2 - - + -
98B ALA* 5.6 0.2 - - - -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LYS* 3.6 19.2 + - - +
13B GLU* 3.1 41.8 + - + +
14B LEU* 4.2 6.8 - - + +
16B ILE* 1.3 84.0 - - - +
18B ASN* 1.3 74.1 + - - +
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Residues in contact with ASN 18 (chain B).
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 4.7 4.3 - - - +
107A TYR* 4.5 5.5 + - - -
108A LYS* 3.8 18.8 + - - +
14B LEU* 3.0 16.4 + - - +
15B PHE 3.9 1.0 - - - +
16B ILE 3.2 12.8 - - - +
17B LYS* 1.3 95.3 - - - +
19B GLY* 1.3 60.3 + - - +
22B ALA* 3.3 22.1 + - + -
23B THR* 3.0 25.4 - - + +
27B GLU* 3.8 15.8 + - - -
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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