Contacts of the helix formed by residues 5 - 23 (chain A) in PDB entry 1DMU
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 HIS 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET 4.7 4.2 + - - -
2A TYR 5.1 0.2 + - - -
4A LEU* 1.3 113.1 + - + +
6A ARG* 1.3 65.3 + - - +
7A GLU 3.4 2.5 - - - -
8A LYS* 3.2 14.9 + - + +
9A ILE* 3.0 37.7 + - + +
202A SER* 3.6 38.3 + - - +
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Residues in contact with ARG 6 (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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2A TYR* 3.0 39.7 + - - +
3A ASN* 3.2 34.3 + - + +
5A HIS* 1.3 77.0 - - - +
7A GLU* 1.3 58.3 + - - +
9A ILE* 3.2 9.3 + - - +
10A PHE* 2.8 31.9 + - - +
168A TRP* 4.1 11.9 - - + -
171A LEU* 2.7 39.6 + - + +
172A GLU* 3.9 12.3 + - - +
173A GLY 2.8 24.9 + - - -
174A GLY* 4.7 2.4 - - - -
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Residues in contact with GLU 7 (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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3A ASN 4.6 2.0 + - - -
5A HIS 3.4 0.6 - - - -
6A ARG* 1.3 77.6 - - - +
8A LYS* 1.3 58.1 + - - +
10A PHE* 3.3 1.4 + - - +
11A MET* 2.9 39.9 + - + +
171A LEU* 3.4 22.8 - - + +
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Residues in contact with LYS 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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5A HIS* 3.2 17.7 + - + +
7A GLU* 1.3 79.3 - - - +
9A ILE* 1.3 63.4 + - + +
11A MET* 4.2 4.1 - - - +
12A SER* 3.2 27.4 + - - -
200A ILE* 5.0 0.4 - - + +
201A LEU 5.8 0.2 - - - +
202A SER 4.4 14.0 + - - +
203A ASP* 3.9 21.0 + - - +
204A GLY* 4.1 18.6 - - - +
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Residues in contact with ILE 9 (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 HIS* 3.0 36.5 + - + +
6A ARG* 3.7 6.3 - - - +
8A LYS* 1.3 76.1 - - + +
10A PHE* 1.3 57.3 + - - +
12A SER* 3.8 0.9 - - - -
13A TYR* 2.8 38.9 + - + +
168A TRP* 3.8 19.1 - - + -
200A ILE* 3.8 39.0 - - + +
201A LEU 4.1 10.5 - - - +
202A SER* 4.1 16.2 - - - +
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Residues in contact with PHE 10 (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 2.8 17.9 + - - +
7A GLU* 3.5 3.6 - - - +
9A ILE* 1.3 74.4 - - - +
11A MET* 1.3 83.3 + - - +
13A TYR* 3.8 0.5 - - - +
14A ASN* 3.1 45.1 + - - +
168A TRP* 3.3 52.5 - + + -
169A ALA 3.6 13.9 - - - -
170A GLN* 4.2 0.4 - - - -
171A LEU* 3.5 44.6 - - + -
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Residues in contact with MET 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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7A GLU* 2.9 27.6 + - + +
8A LYS* 4.2 4.5 - - - +
10A PHE* 1.3 92.5 - - + +
12A SER* 1.3 64.3 + - - +
14A ASN* 4.0 2.5 - - - +
15A GLN* 3.2 24.3 + - - +
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Residues in contact with SER 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 LYS* 3.2 20.0 + - - -
9A ILE 4.0 2.0 - - - -
11A MET* 1.3 76.3 - - - +
13A TYR* 1.3 60.8 + - - +
15A GLN* 4.8 3.1 - - - -
16A ASN* 2.7 55.1 + - - +
200A ILE* 3.5 21.7 - - - +
204A GLY* 4.7 6.4 + - - -
206A ILE* 4.7 0.3 - - - +
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Residues in contact with TYR 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 ILE* 2.8 24.8 + - + +
10A PHE 3.8 2.7 - - - +
12A SER* 1.3 71.1 + - - +
14A ASN* 1.3 60.5 + - - +
16A ASN* 4.7 0.4 - - - -
17A LYS* 2.7 60.3 + - + +
166A GLY* 2.7 34.1 + - - -
168A TRP* 3.5 39.0 - + + -
175A ILE* 3.8 15.7 - - + +
196A PRO* 4.1 0.8 - - + +
197A PRO* 3.5 13.2 - - - +
198A LEU* 3.4 48.2 - - + -
199A TYR* 5.2 0.2 - - - -
200A ILE* 3.6 18.6 - - + +
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Residues in contact with ASN 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 PHE* 3.1 49.4 + - - +
11A MET* 4.1 2.9 - - - +
13A TYR* 1.3 90.2 - - - +
15A GLN* 1.3 63.5 + - - +
17A LYS* 4.2 16.0 - - - +
18A GLN* 3.2 23.0 + - - +
168A TRP* 3.1 20.2 + - - +
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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 MET 3.2 17.6 + - - +
12A SER* 4.1 4.0 - - - +
14A ASN* 1.3 76.3 - - - +
16A ASN* 1.3 64.4 + - - +
18A GLN* 3.5 5.8 + - - +
19A TYR* 3.3 20.4 + - - +
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Residues in contact with ASN 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 SER* 2.7 46.2 + - - +
13A TYR 3.9 1.3 - - - +
15A GLN* 1.3 76.3 - - - +
17A LYS* 1.3 58.6 + - - +
19A TYR* 3.3 7.6 + - - +
20A LEU* 2.9 33.7 + - - +
133A PHE* 3.4 23.8 - - + -
198A LEU* 4.2 14.6 - - + -
200A ILE* 4.1 0.6 - - + +
206A ILE* 3.4 26.7 - - + +
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Residues in contact with LYS 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 TYR* 2.7 52.5 + - + +
14A ASN* 4.2 14.8 - - - +
16A ASN* 1.3 73.1 - - - +
18A GLN* 1.3 57.9 + - - +
20A LEU* 3.6 2.4 - - - +
21A GLU* 2.9 34.1 + - - +
165A ASN 3.0 25.1 + - - +
166A GLY 3.7 9.4 + - - -
167A ASP* 3.1 22.6 + - - +
197A PRO* 4.2 4.3 - - + -
198A LEU* 3.6 19.0 - - + +
244A LEU* 3.9 17.2 - - + +
303A BME 3.7 11.5 - - - -
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Residues in contact with GLN 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 ASN 3.2 16.1 + - - +
15A GLN* 3.6 6.7 - - - +
16A ASN 3.2 0.6 - - - -
17A LYS* 1.3 76.4 - - - +
19A TYR* 1.3 61.7 + - - +
21A GLU* 3.4 19.3 + - - +
22A ASP* 2.9 69.7 + - - +
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Residues in contact with TYR 19 (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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15A GLN 3.3 9.9 + - - +
16A ASN* 3.3 12.0 + - - +
18A GLN* 1.3 81.0 - - - +
20A LEU* 1.3 62.9 + - - +
22A ASP* 3.2 2.7 + - + -
23A ASN* 2.9 56.3 + - - +
26A ILE* 3.5 30.5 - - + +
133A PHE* 3.7 34.1 - + + -
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Residues in contact with LEU 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 ASN 2.9 16.3 + - - +
17A LYS 3.6 4.3 - - - +
19A TYR* 1.3 78.3 - - + +
21A GLU* 1.3 63.9 + - - +
23A ASN* 3.0 24.4 + - - +
24A PRO* 3.5 4.2 - - - +
26A ILE* 4.5 16.8 - - + -
27A GLN* 4.1 23.5 - - + +
133A PHE* 3.4 36.6 - - + -
197A PRO 5.4 0.7 - - - +
198A LEU* 3.9 42.4 - - + -
208A PRO* 4.2 11.4 - - + -
244A LEU* 3.8 13.2 - - + +
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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 LYS* 2.9 23.9 + - - +
18A GLN* 3.6 21.4 + - - +
20A LEU* 1.3 78.0 - - - +
22A ASP* 1.3 65.4 + - - +
23A ASN 3.5 0.3 + - - -
24A PRO* 3.5 2.9 - - - +
244A LEU* 3.9 21.9 - - + +
248A CYS* 4.1 19.5 - - + +
249A ASN* 3.4 26.9 + - + +
303A BME 3.7 36.9 - - - +
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Residues in contact with ASP 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 GLN* 2.9 47.9 + - - +
19A TYR* 4.0 4.2 - - + +
21A GLU* 1.3 78.4 - - - +
23A ASN* 1.3 70.1 + - - +
24A PRO* 3.2 11.3 - - - +
249A ASN* 4.4 7.3 + - - +
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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 TYR* 2.9 58.2 + - - +
20A LEU* 3.0 9.3 + - - +
22A ASP* 1.3 91.1 - - - +
24A PRO* 1.3 64.4 - - - +
25A GLU* 3.0 6.5 + - + -
26A ILE* 3.2 33.1 + - + +
27A GLN 4.1 1.2 + - - -
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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