Contacts of the helix formed by residues 12 - 27 (chain A) in PDB entry 3DOW
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 12 (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 5.1 0.4 - - - +
10A GLU 4.4 3.1 - - - +
11A HIS* 1.3 86.3 - - + +
13A PHE* 1.3 60.5 + - - +
14A GLU* 3.5 6.7 - - + +
15A LYS* 3.4 16.8 + - + +
16A ARG* 3.0 30.7 + - - +
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Residues in contact with PHE 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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12A PRO* 1.3 71.3 - - - +
14A GLU* 1.3 69.3 + - - +
15A LYS 3.1 1.3 - - - -
16A ARG* 3.7 27.7 - - - +
17A ARG* 3.1 40.8 + - + +
102A GLU* 5.9 2.0 - - + -
103A GLU* 3.6 33.9 - - + -
104A ASP* 4.0 16.6 - - + -
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Residues in contact with GLU 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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12A PRO* 3.5 4.4 - - + +
13A PHE* 1.3 79.6 - - - +
15A LYS* 1.3 67.5 + - + +
17A ARG* 4.1 4.0 - - - +
18A SER* 2.9 37.1 + - - +
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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 HIS* 4.9 5.4 - - + -
12A PRO* 3.4 28.3 + - + +
13A PHE 3.1 0.4 - - - -
14A GLU* 1.3 86.3 - - + +
16A ARG* 1.3 63.4 + - + +
18A SER* 3.5 5.5 + - - -
19A GLU* 3.1 23.3 + - - +
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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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7A TYR* 3.8 25.1 - - + +
8A LYS* 3.2 33.3 + - - +
11A HIS* 2.8 42.6 + - + +
12A PRO* 3.0 24.1 + - - +
13A PHE* 3.7 25.9 - - - +
14A GLU 3.4 0.2 - - - -
15A LYS* 1.3 74.4 - - - +
17A ARG* 1.3 59.7 + - - +
19A GLU* 3.0 5.5 + - - -
20A GLY 2.8 25.8 + - - -
102A GLU* 4.0 8.7 + - - +
104A ASP* 2.9 35.3 + - + +
106A PHE* 3.5 15.0 - - + -
108A TYR* 3.3 11.9 + - - -
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Residues in contact with ARG 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 PHE* 3.1 34.1 + - + +
14A GLU* 4.1 3.6 - - - +
16A ARG* 1.3 77.0 - - - +
18A SER* 1.3 60.5 + - - +
21A GLU* 3.1 30.2 + - + +
103A GLU* 3.1 36.6 + - - +
104A ASP* 3.6 21.2 - - + +
105A PHE* 3.6 35.9 - - + -
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Residues in contact with SER 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 GLU* 2.9 29.6 + - - +
15A LYS* 3.8 5.4 - - - -
16A ARG 3.1 0.6 - - - -
17A ARG* 1.3 79.2 - - - +
19A GLU* 1.3 63.2 + - - +
21A GLU* 4.0 10.2 - - - +
22A LYS* 3.3 23.0 + - - +
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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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7A TYR* 3.1 20.3 + - - -
15A LYS 3.1 13.4 + - - +
16A ARG* 3.0 7.7 + - - +
18A SER* 1.3 75.6 - - - +
20A GLY* 1.3 58.7 + - - +
22A LYS* 3.5 4.9 + - - +
23A ILE* 3.0 30.1 + - + +
50A LYS* 3.1 18.8 + - - -
106A PHE* 3.8 12.6 - - + -
5B ASP* 4.2 2.9 - - - +
6B TRP* 3.0 29.5 + - - +
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Residues in contact with GLY 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 2.8 10.1 + - - -
19A GLU* 1.3 75.8 - - - +
21A GLU* 1.3 64.2 + - - +
23A ILE* 3.6 1.4 - - - +
24A ARG* 3.0 30.3 + - - +
104A ASP 3.5 12.8 - - - -
105A PHE* 3.8 8.5 - - - -
106A PHE* 3.3 24.6 - - - -
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Residues in contact with GLU 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 ARG* 3.1 23.0 + - - +
18A SER* 4.0 8.1 - - - +
19A GLU 3.4 0.2 - - - -
20A GLY* 1.3 75.7 - - - +
22A LYS* 1.3 57.9 + - - +
24A ARG* 3.8 4.0 - - - +
25A LYS* 3.0 64.9 + - + +
105A PHE* 3.8 23.3 - - + -
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Residues in contact with LYS 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 SER 3.3 16.3 + - - +
19A GLU* 3.8 6.1 - - - +
20A GLY 3.2 0.4 - - - -
21A GLU* 1.3 78.0 + - - +
23A ILE* 1.3 61.1 + - + +
25A LYS* 3.0 10.0 + - - +
26A LYS* 2.9 31.5 + - - +
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Residues in contact with ILE 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* 3.0 20.1 + - + +
20A GLY* 3.6 11.0 - - - +
22A LYS* 1.3 78.2 - - + +
24A ARG* 1.3 61.8 + - - +
26A LYS* 3.8 5.8 - - + -
27A TYR* 3.1 53.4 + - + +
30A ARG 5.3 0.2 - - - +
32A PRO* 3.7 34.5 - - + -
52A LEU* 4.2 12.0 - - + +
106A PHE* 4.3 3.1 - - + -
6B TRP* 3.5 37.2 - - + +
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Residues in contact with ARG 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 GLY 3.0 21.2 + - - +
21A GLU* 3.8 5.6 - - - +
23A ILE* 1.3 78.9 - - - +
25A LYS* 1.3 59.6 + - + +
26A LYS 3.1 2.3 + - - -
27A TYR 4.8 0.9 - - - -
28A PRO* 3.2 46.2 + - - +
30A ARG 3.0 24.2 + - - -
31A VAL* 4.2 7.7 - - - +
32A PRO* 3.5 26.0 - - + -
55A SER* 5.3 0.2 + - - -
97A TYR* 3.3 41.2 + - - +
105A PHE* 4.2 10.3 - - + +
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Residues in contact with LYS 25 (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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21A GLU* 3.0 54.0 + - + +
22A LYS* 3.0 8.9 + - - +
24A ARG* 1.3 78.2 - - + +
26A LYS* 1.3 57.6 + - - +
28A PRO* 4.5 4.0 - - - +
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Residues in contact with LYS 26 (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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22A LYS 2.9 16.6 + - - +
23A ILE* 4.2 4.9 - - + +
24A ARG 3.1 0.2 - - - -
25A LYS* 1.3 78.1 - - - +
27A TYR* 1.3 106.1 + - + +
28A PRO* 3.1 12.4 - - - +
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Residues in contact with TYR 27 (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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23A ILE* 3.1 42.4 + - + +
24A ARG* 4.4 0.7 + - - +
26A LYS* 1.3 124.6 + - + +
28A PRO* 1.3 63.0 - - - +
29A ASP* 3.3 8.1 - - - +
30A ARG* 3.0 37.6 + - + +
52A LEU* 4.8 7.3 - - + +
8B PHE* 3.8 35.5 - + - -
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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