Contacts of the helix formed by residues 7 - 24 (chain A) in PDB entry 3EUS
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 THR 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A THR 5.2 2.0 - - - +
6A ARG* 1.3 84.6 - - + +
8A PRO* 1.3 75.3 - - + +
9A GLU* 3.3 15.4 + - - +
10A HIS* 2.4 50.6 + - + +
11A VAL* 3.1 20.9 + - - +
55B ILE* 5.8 0.3 - - - +
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Residues in contact with PRO 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG 4.2 2.9 - - - +
7A THR* 1.3 89.3 - - - +
9A GLU* 1.3 64.4 + - - +
11A VAL* 3.5 8.5 + - + +
12A TYR* 3.0 29.1 + - - +
82A ALA* 3.8 22.3 - - + +
83A GLN 5.3 0.5 - - - +
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 3.1 19.9 + - - +
8A PRO* 1.3 83.5 - - - +
10A HIS* 1.3 59.0 + - - +
12A TYR* 3.4 2.9 + - - +
13A LEU* 2.9 30.0 + - - +
77A ILE* 3.9 26.5 - - + +
80A GLY* 4.3 14.0 - - - -
82A ALA* 3.7 21.5 - - + -
55B ILE* 3.7 27.2 - - + +
59B LYS* 4.6 14.7 + - - -
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Residues in contact with HIS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 3.7 19.7 + - - +
5A LEU* 3.3 45.7 - - + +
7A THR* 2.4 46.4 + - + +
9A GLU* 1.3 74.0 - - - +
11A VAL* 1.3 62.5 + - - +
13A LEU* 3.3 8.1 + - + +
14A CYS* 2.9 38.1 + - - -
48A ARG* 4.5 2.5 - - + -
51A ARG* 6.2 0.4 - - + -
53B ASP* 4.2 16.0 + - - -
55B ILE* 4.5 22.3 - - + +
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU 4.7 0.9 - - - +
6A ARG 4.5 8.5 - - - +
7A THR 3.1 15.6 + - - +
8A PRO* 3.8 7.4 - - + +
10A HIS* 1.3 81.0 - - - +
12A TYR* 1.3 64.3 + - - +
14A CYS* 3.3 2.4 + - - +
15A GLN* 3.0 23.3 + - + +
18A ARG* 5.5 0.2 + - - -
48A ARG* 3.9 32.8 - - - +
83A GLN 5.6 4.3 - - - +
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Residues in contact with TYR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PRO 3.0 19.1 + - - +
9A GLU 3.7 2.7 - - - +
10A HIS 3.2 0.2 - - - -
11A VAL* 1.3 76.5 - - - +
13A LEU* 1.3 67.7 + - - +
15A GLN* 3.1 11.5 + - + +
16A ARG* 3.0 69.8 + - + +
72A GLU* 5.2 0.2 - - - +
73A ILE* 3.8 24.0 - - + -
76A THR* 3.4 26.9 + - + +
77A ILE* 3.7 17.5 - - + -
82A ALA* 4.1 7.2 - - - -
83A GLN* 3.2 57.2 + - + -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU 2.9 20.8 + - - +
10A HIS* 3.7 9.0 - - + +
12A TYR* 1.3 78.1 - - - +
14A CYS* 1.3 61.6 + - - +
16A ARG* 3.1 6.1 + - + -
17A LEU* 2.8 50.6 + - + +
52A LEU* 5.3 7.6 - - + +
57A PHE* 3.9 28.3 - - + -
73A ILE* 4.2 14.1 - - + -
77A ILE* 4.2 7.0 - - + -
54B VAL* 3.7 22.7 - - + -
55B ILE* 3.5 24.0 - - + -
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Residues in contact with CYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A HIS* 2.9 22.8 + - - +
11A VAL 3.7 4.3 - - - +
12A TYR 3.1 0.2 - - - -
13A LEU* 1.3 82.5 - - - +
15A GLN* 1.3 62.7 + - - +
17A LEU* 3.3 12.9 + - - +
18A ARG* 3.0 29.8 + - - +
45A VAL* 3.2 26.2 - - - +
46A GLU* 3.6 17.5 - - - +
48A ARG* 3.5 23.8 - - + -
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Residues in contact with GLN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.0 15.2 + - + +
12A TYR* 3.1 15.9 + - + +
14A CYS* 1.3 76.6 - - - +
16A ARG* 1.3 65.1 + - - +
18A ARG* 2.8 38.6 + - - +
19A GLN* 2.8 57.2 + - - +
83A GLN 6.4 0.9 - - - -
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.0 61.7 + - + +
13A LEU* 3.6 7.4 - - + +
15A GLN* 1.3 79.4 - - - +
17A LEU* 1.3 59.5 + - + +
19A GLN* 4.4 7.8 - - - +
20A ALA* 2.9 31.5 + - - +
61A MET* 4.9 0.5 - - - +
69A VAL* 3.8 27.5 - - - +
72A GLU* 3.0 31.7 + - - +
73A ILE* 3.6 35.3 - - + +
83A GLN* 5.5 2.4 - - - +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 2.8 38.5 + - + +
14A CYS* 3.3 12.8 + - - +
16A ARG* 1.3 73.7 - - + +
18A ARG* 1.3 64.3 + - - +
20A ALA* 3.4 2.6 + - - +
21A ARG* 3.2 14.9 + - - +
45A VAL* 3.6 29.4 - - + -
46A GLU* 5.0 2.0 - - + -
52A LEU* 3.7 13.9 - - + -
57A PHE* 4.0 18.4 - - + -
60A TRP* 3.1 55.8 + - + +
61A MET* 4.0 13.2 - - - -
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL 5.5 0.2 + - - -
14A CYS* 3.0 12.8 + - - +
15A GLN* 2.8 43.2 - - - +
17A LEU* 1.3 80.0 - - - +
19A GLN* 1.3 59.8 + - - +
21A ARG* 3.1 23.5 + - - +
22A LEU* 2.9 44.2 + - + +
46A GLU* 3.4 48.8 + - - +
47A THR* 5.3 4.0 - - - +
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 2.8 38.8 + - + +
16A ARG* 4.1 10.3 - - - +
18A ARG* 1.3 74.8 + - - +
20A ALA* 1.3 56.3 + - - +
22A LEU* 3.9 26.5 - - - +
23A ASP* 2.7 67.5 + - - +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG 2.9 18.9 + - - +
17A LEU 3.7 4.7 - - - +
19A GLN* 1.3 76.9 - - - +
21A ARG* 1.3 61.6 + - - +
23A ASP* 3.7 7.1 - - - +
24A ALA* 3.1 23.7 + - - +
61A MET* 3.7 32.3 - - + -
64A CYS* 3.7 18.7 - - + +
66A GLY* 5.5 2.7 - - - -
69A VAL* 5.6 2.7 - - + -
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 3.2 11.5 + - - +
18A ARG* 3.1 22.9 + - - +
20A ALA* 1.3 76.7 - - - +
22A LEU* 1.3 84.5 + - - +
24A ALA* 3.2 12.4 + - - +
25A GLY 3.3 0.2 + - - -
26A LEU* 2.9 58.0 + - + +
27A THR* 3.7 17.9 - - - +
28A GLN* 3.5 29.0 - - - +
31A LEU* 3.7 27.4 - - + -
42A VAL* 4.0 0.9 - - - -
46A GLU* 2.7 39.8 + - - +
64A CYS* 3.6 9.8 - - - -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 2.9 39.1 + - + +
19A GLN* 3.9 27.8 - - - +
21A ARG* 1.3 101.8 - - - +
23A ASP* 1.3 59.5 + - - +
25A GLY* 3.1 18.4 + - - +
26A LEU 4.5 4.7 - - - +
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 2.7 52.6 + - - +
20A ALA* 3.7 7.8 + - - +
21A ARG 3.2 0.2 - - - -
22A LEU* 1.3 73.0 - - - +
24A ALA* 1.3 57.3 + - - +
25A GLY* 3.3 1.0 + - - -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA 3.1 12.0 + - - +
21A ARG 3.2 6.0 + - - +
23A ASP* 1.3 76.0 - - - +
25A GLY* 1.3 61.8 + - - +
26A LEU* 4.0 24.5 - - + +
34A ARG* 5.2 3.3 + - - +
63A ALA 5.1 0.4 - - - +
64A CYS* 3.5 27.4 - - - +
65A GLU* 5.0 9.4 - - - +
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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