Contacts of the helix formed by residues 9 - 23 (chain A) in PDB entry 2HOT
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 SER 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ALA 3.7 3.0 + - - -
8A PHE* 1.3 75.1 - - - +
10A SER* 1.3 60.9 + - - +
11A GLU* 3.9 8.6 + - - +
12A GLN* 3.1 35.0 + - - +
13A LEU* 2.9 26.1 + - - +
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Residues in contact with SER 10 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A SER* 1.3 74.7 - - - +
11A GLU* 1.3 57.4 + - - +
13A LEU* 3.9 10.8 - - - +
14A ALA* 2.8 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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9A SER* 3.2 9.3 + - - +
10A SER* 1.3 79.6 + - - +
12A GLN* 1.3 63.2 + - + +
14A ALA* 3.8 6.2 + - - +
15A ARG* 3.3 23.0 + - - +
18A ARG* 5.2 3.3 + - - +
38A LEU* 4.6 3.3 - - + +
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Residues in contact with GLN 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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7A ALA 4.8 0.3 - - - +
8A PHE* 3.5 17.1 - - + +
9A SER* 3.1 35.8 + - - +
11A GLU* 1.3 75.6 - - + +
13A LEU* 1.3 61.1 + - - +
15A ARG* 3.2 3.1 + - - +
16A LEU* 2.8 40.6 + - + +
38A LEU* 2.7 49.2 + - + +
39A GLY 4.0 4.0 + - - -
40A LEU* 3.7 24.0 - - + +
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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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8A PHE* 3.5 40.2 - - + +
9A SER 2.9 14.3 + - - +
10A SER* 3.9 9.6 - - - +
12A GLN* 1.3 76.6 - - - +
14A ALA* 1.3 61.8 + - - +
16A LEU* 3.2 4.6 + - + +
17A LYS* 2.9 47.1 + - - +
48A TRP* 3.5 32.1 - - + +
12C A 4.8 6.1 - - - +
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Residues in contact with ALA 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 SER 2.8 24.3 + - - +
11A GLU* 3.9 6.3 - - - +
12A GLN 3.3 0.2 - - - -
13A LEU* 1.3 74.3 - - - +
15A ARG* 1.3 59.6 + - - +
17A LYS* 3.8 8.2 - - - +
18A ARG* 3.1 51.2 + - - +
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Residues in contact with ARG 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 3.3 15.5 + - - +
12A GLN 3.2 4.4 + - - +
14A ALA* 1.3 76.8 - - - +
16A LEU* 1.3 60.9 + - - +
18A ARG* 3.6 27.3 + - - +
19A GLU* 2.8 68.3 + - + +
34A LEU* 3.9 4.8 - - + +
37A GLU* 2.9 39.9 + - - +
38A LEU* 3.5 29.8 - - + +
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.5 17.9 - - + -
12A GLN 2.8 28.7 + - - +
13A LEU* 3.7 5.8 - - - +
15A ARG* 1.3 77.8 - - - +
17A LYS* 1.3 51.0 + - - +
19A GLU* 3.3 6.1 + - - +
20A PHE* 2.7 35.2 + - - +
34A LEU* 4.8 2.9 - - + -
38A LEU* 3.9 18.4 - - + -
40A LEU* 4.6 6.5 - - + -
45A VAL* 4.4 18.4 - - + -
48A TRP* 3.7 47.5 - - + +
49A PHE* 3.9 24.4 - - + -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 2.9 38.5 + - - +
14A ALA* 3.8 6.7 - - - +
16A LEU* 1.3 72.5 - - - +
18A ARG* 1.3 60.2 + - + +
20A PHE* 3.3 4.2 + - - +
21A ASN* 2.8 31.1 + - - +
48A TRP* 3.9 23.8 - - + -
52A MET* 5.3 8.1 - - + -
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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 GLU* 5.2 3.4 + - - +
14A ALA* 3.1 37.7 + - - +
15A ARG* 3.7 36.6 - - - +
17A LYS* 1.3 75.3 - - + +
19A GLU* 1.3 63.5 + - + +
21A ASN* 3.2 10.3 + - - +
22A GLU* 3.1 28.1 + - + +
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Residues in contact with GLU 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 ARG* 2.8 64.6 + - - +
16A LEU* 3.5 5.4 - - - +
18A ARG* 1.3 74.1 - - - +
20A PHE* 1.3 64.8 + - - +
22A GLU* 3.3 9.6 + - - +
23A ASN* 2.9 27.2 + - - +
30A ARG* 4.1 22.3 + - - +
34A LEU* 3.6 23.5 - - + +
49A PHE* 4.0 13.9 - - + -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU 2.7 21.5 + - - +
17A LYS* 3.5 6.7 - - - +
19A GLU* 1.3 71.9 - - - +
21A ASN* 1.3 66.6 + - - +
23A ASN 3.3 21.3 - - - -
24A ARG* 3.3 37.8 + - + +
48A TRP* 3.8 11.9 - + + -
49A PHE* 3.7 23.5 - + + -
52A MET* 3.7 33.0 - - + -
53A ARG* 3.7 25.6 - - + -
56A ILE* 3.4 29.8 - - + -
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Residues in contact with ASN 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 LYS 2.8 21.2 + - - +
18A ARG* 3.3 11.0 - - - +
19A GLU 3.2 0.2 - - - -
20A PHE* 1.3 78.2 - - - +
22A GLU* 1.3 65.6 + - - +
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Residues in contact with GLU 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* 3.1 18.6 + - + +
19A GLU* 3.3 12.5 + - - +
21A ASN* 1.3 83.2 - - - +
23A ASN* 1.3 63.8 + - + +
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Residues in contact with ASN 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 GLU 2.9 15.8 + - - +
20A PHE 3.3 3.3 + - - +
22A GLU* 1.3 81.3 - - + +
24A ARG* 1.3 68.7 + - - +
25A TYR* 3.1 30.7 + - - +
27A THR* 5.8 1.8 - - - +
30A ARG* 3.0 37.5 + - - +
49A PHE* 3.4 6.1 - - - -
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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