Contacts of the helix formed by residues 10 - 24 (chain A) in PDB entry 1SDS
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 PRO 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS* 3.7 13.9 - - + +
9A VAL* 1.3 85.5 - - - +
11A GLU* 1.3 66.8 + - - +
12A GLU* 4.3 7.6 - - + +
13A ILE* 2.9 28.4 + - + +
14A GLN* 2.9 10.2 + - - +
115A LEU* 3.7 31.2 - - + -
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Residues in contact with GLU 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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8A LYS* 4.6 2.8 - - - +
9A VAL 3.5 1.8 + - - -
10A PRO* 1.3 72.4 - - - +
12A GLU* 1.3 61.9 + - - +
14A GLN* 3.2 18.3 + - + +
15A LYS* 3.0 22.8 + - + +
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Residues in contact with GLU 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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10A PRO* 3.1 5.5 - - + +
11A GLU* 1.3 79.0 - - - +
13A ILE* 1.3 65.6 + - + +
15A LYS* 3.4 9.7 - - - +
16A GLU* 3.4 25.9 + - - +
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Residues in contact with ILE 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 VAL* 3.8 15.7 - - + -
10A PRO* 2.9 23.5 + - + +
12A GLU* 1.3 76.1 - - + +
14A GLN* 1.3 68.2 + - - +
15A LYS 3.1 1.3 - - - -
16A GLU* 2.9 16.9 + - - +
17A LEU* 2.9 25.1 + - + +
108A LEU* 4.1 21.1 - - + -
111A LYS* 4.5 20.2 - - + +
112A VAL* 4.8 6.3 - - + -
115A LEU* 3.6 33.0 - - + -
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Residues in contact with GLN 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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8A LYS* 4.1 8.1 - - - +
9A VAL* 2.9 26.8 + - + +
10A PRO 2.9 12.0 + - - +
11A GLU* 3.2 21.4 + - + +
13A ILE* 1.3 75.3 - - - +
15A LYS* 1.3 63.5 + - - +
17A LEU* 3.1 12.1 + - - +
18A LEU* 2.9 31.8 + - + +
50A GLU* 4.4 11.3 + - - -
74A TYR 3.5 17.7 - - - +
75A VAL* 3.5 7.9 - - + +
76A ALA* 2.8 38.9 + - - +
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Residues in contact with LYS 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 GLU 3.0 11.7 + - - +
12A GLU* 3.4 14.6 - - - +
14A GLN* 1.3 77.9 - - - +
16A GLU* 1.3 56.1 + - + +
18A LEU* 3.4 11.7 + - + +
19A ASP* 2.9 28.9 + - + +
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Residues in contact with GLU 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 GLU* 3.4 17.1 + - - +
13A ILE* 2.9 18.5 + - - +
15A LYS* 1.3 77.1 - - + +
17A LEU* 1.3 59.2 + - - +
19A ASP* 3.5 8.1 - - - +
20A ALA* 2.9 27.9 + - - +
23A LYS* 5.2 0.5 + - - -
107A VAL* 6.0 0.3 - - - +
108A LEU* 3.8 28.7 - - + +
111A LYS* 3.1 33.9 + - - +
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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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9A VAL* 4.1 11.9 - - + -
13A ILE* 2.9 21.9 + - + +
14A GLN* 3.1 7.4 + - - +
16A GLU* 1.3 73.5 - - - +
18A LEU* 1.3 65.6 + - - +
20A ALA* 3.2 4.5 + - - +
21A VAL* 3.1 25.1 + - - +
45A LEU* 4.1 16.6 - - + -
47A ILE* 3.5 16.7 - - + +
73A ALA* 3.6 30.5 - - + -
74A TYR 3.3 28.0 - - - +
75A VAL* 4.0 6.5 - - + -
108A LEU* 3.8 26.9 - - + -
112A VAL* 4.5 4.3 - - + -
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Residues in contact with LEU 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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14A GLN* 2.9 24.1 + - + +
15A LYS* 3.7 9.4 - - + +
17A LEU* 1.3 76.2 - - - +
19A ASP* 1.3 62.3 + - - +
21A VAL* 3.3 6.0 + - - +
22A ALA* 3.0 19.6 + - - +
75A VAL* 4.0 22.9 - - + -
80A ASP* 3.8 26.5 - - + +
81A LEU* 3.8 35.7 - - + +
84A ALA* 3.6 15.8 - - + +
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Residues in contact with ASP 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 LYS* 2.9 18.4 + - + +
16A GLU* 3.5 8.7 - - - +
17A LEU 3.2 0.2 - - - -
18A LEU* 1.3 78.2 - - - +
20A ALA* 1.3 62.3 + - - +
22A ALA* 3.2 7.4 + - - +
23A LYS* 3.0 56.9 + - - +
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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 GLU 2.9 14.9 + - - +
17A LEU* 3.2 9.8 + - - +
19A ASP* 1.3 77.0 - - - +
21A VAL* 1.3 61.4 + - - +
23A LYS* 3.4 12.2 + - - +
24A ALA* 3.0 24.6 + - - +
45A LEU* 5.3 1.6 - - + -
96A ILE* 3.8 18.8 - - + +
99A GLU* 5.7 0.9 - - - -
105A LEU* 5.5 4.5 - - + -
108A LEU* 3.8 18.8 - - + -
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Residues in contact with VAL 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 3.1 6.8 + - - +
18A LEU* 3.5 8.3 - - - +
19A ASP 3.2 0.2 - - - -
20A ALA* 1.3 77.1 - - - +
22A ALA* 1.3 63.0 + - - +
24A ALA* 3.3 18.8 + - - +
27A ILE* 4.2 9.7 - - + +
47A ILE* 3.2 33.4 - - + -
81A LEU* 4.3 11.0 - - + +
84A ALA* 3.6 26.9 - - + +
85A ALA* 3.7 16.4 - - + +
94A VAL* 4.1 23.6 - - + -
96A ILE* 4.2 8.5 - - + -
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Residues in contact with ALA 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 LEU 3.0 13.4 + - - +
19A ASP* 3.6 10.3 - - - +
21A VAL* 1.3 77.8 - - - +
23A LYS* 1.3 62.1 + - + +
24A ALA 4.4 2.9 - - - +
84A ALA* 3.4 21.7 + - - +
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Residues in contact with LYS 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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16A GLU 5.2 0.6 + - - -
19A ASP* 3.0 49.6 + - - +
20A ALA* 3.7 10.0 - - - +
22A ALA* 1.3 78.8 - - + +
24A ALA* 1.3 67.3 + - - +
25A GLN* 3.2 15.6 + - - -
100A GLY* 3.4 16.0 - - - +
101A ASP* 5.8 3.8 - - - +
104A GLU* 3.1 30.3 + - - -
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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 3.0 18.0 + - - +
21A VAL 3.3 7.1 + - - +
22A ALA 4.4 2.8 - - - +
23A LYS* 1.3 80.2 - - - +
25A GLN* 1.3 64.1 + - - +
26A LYS* 4.7 0.2 - - - -
27A ILE* 3.3 32.6 - - + +
96A ILE* 4.1 12.8 - - + -
98A ASN 3.7 10.3 - - - +
99A GLU* 4.5 0.4 - - - -
100A GLY 3.8 7.9 - - - +
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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