Contacts of the helix formed by residues 9 - 20 (chain A) in PDB entry 1R18
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 ASN 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 GLY 3.2 1.5 - - - -
8A ALA* 1.3 85.4 + - - +
10A ASN* 1.3 66.8 + - - +
11A GLU* 3.5 16.1 + - - +
12A ASP* 2.9 39.1 + - - +
13A LEU* 3.0 22.3 + - - +
46A TYR* 3.7 20.3 - - + +
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Residues in contact with ASN 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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9A ASN* 1.3 74.1 - - - +
11A GLU* 1.3 72.8 + - - +
13A LEU* 3.1 18.9 + - - +
14A ILE* 3.1 22.6 + - - +
32A MET 3.0 23.9 + - - +
33A LYS* 3.2 14.7 - - - +
35A THR 3.3 5.8 + - - +
36A ASP* 3.6 23.8 + - - +
37A ARG* 3.2 29.7 - - - +
46A TYR* 3.4 26.1 - - + -
91A TYR* 5.0 0.8 + - - -
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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 ASN* 3.4 11.9 - - - +
10A ASN* 1.3 88.4 + - - +
12A ASP* 1.3 57.1 + - - +
14A ILE* 3.3 3.3 + - - +
15A ARG* 3.0 29.2 + - - +
33A LYS* 4.3 39.9 + - + +
36A ASP* 4.9 2.9 - - - +
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Residues in contact with ASP 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 GLY* 4.6 2.2 - - - -
8A ALA* 3.7 28.7 - - - +
9A ASN* 2.9 25.6 + - - +
11A GLU* 1.3 76.2 - - - +
13A LEU* 1.3 62.7 + - - +
15A ARG* 3.9 24.5 + - - +
16A GLN* 3.1 28.7 + - - +
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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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5A SER* 5.9 0.7 - - - -
6A VAL* 4.9 2.5 - - - -
7A GLY* 4.2 14.1 - - - +
9A ASN 3.0 13.7 + - - +
10A ASN* 3.1 13.7 + - - +
12A ASP* 1.3 78.9 - - - +
14A ILE* 1.3 69.6 + - + +
16A GLN* 3.5 9.0 - - + +
17A LEU* 3.2 28.3 + - + +
37A ARG* 4.0 11.9 - - - -
46A TYR* 3.8 40.2 - - + +
48A ASP* 4.6 19.3 - - + +
62A PRO* 4.0 26.0 - - + -
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Residues in contact with ILE 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 ASN* 3.1 19.0 + - - +
11A GLU 3.3 5.1 + - - +
13A LEU* 1.3 89.1 - - + +
15A ARG* 1.3 65.2 + - - +
17A LEU* 3.1 11.3 + - + +
18A LYS* 2.9 20.8 + - - +
23A ILE* 3.6 17.9 - - + -
29A ALA* 3.6 25.8 - - + +
32A MET* 3.7 50.0 - - + +
33A LYS* 3.8 18.8 - - + +
91A TYR* 5.0 2.2 - - - +
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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 3.0 15.9 + - - +
12A ASP* 3.9 22.7 + - - +
14A ILE* 1.3 75.7 - - - +
16A GLN* 1.3 54.6 + - - +
18A LYS* 3.0 6.7 + - - +
19A ASP* 2.8 57.9 + - - +
33A LYS* 4.0 12.9 - - - +
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Residues in contact with GLN 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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5A SER* 3.8 24.4 - - - +
6A VAL 3.4 28.6 + - - +
7A GLY* 4.7 2.4 - - - -
12A ASP* 3.1 18.3 + - - +
13A LEU* 3.5 10.6 - - + +
15A ARG* 1.3 81.8 - - - +
17A LEU* 1.3 63.2 + - + +
19A ASP* 3.4 5.2 + - - -
20A HIS* 2.9 47.2 + - + +
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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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5A SER* 6.5 0.2 - - - -
13A LEU* 3.2 19.3 + - + +
14A ILE* 3.1 17.8 + - + +
16A GLN* 1.3 80.2 - - + +
18A LYS* 1.3 59.5 + - - +
20A HIS* 3.5 3.1 + - + +
21A GLY 3.4 3.1 + - - -
22A VAL* 2.9 52.8 + - + +
23A ILE* 3.4 23.7 + - + -
32A MET* 4.8 2.2 - - + -
48A ASP* 4.1 24.2 - - + +
62A PRO* 4.0 34.5 - - + +
63A HIS* 4.3 4.3 - - + +
66A ALA* 5.0 0.4 - - + -
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Residues in contact with LYS 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 ILE 2.9 12.4 + - - +
15A ARG* 3.5 9.6 - - + +
17A LEU* 1.3 74.7 - - - +
19A ASP* 1.3 69.9 + - - +
21A GLY* 3.2 12.6 + - - -
23A ILE* 3.8 30.4 - - + +
24A ALA 5.2 2.7 - - - -
25A SER 4.8 2.5 - - - -
26A ASP* 2.6 43.1 + - - +
29A ALA* 4.0 22.2 - - + +
30A GLN* 6.0 0.6 + - - +
33A LYS* 5.0 8.4 - - - +
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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 ARG* 2.8 52.6 + - - +
16A GLN* 3.7 7.6 - - - +
18A LYS* 1.3 77.0 - - - +
20A HIS* 1.3 67.1 + - + +
21A GLY 3.3 3.0 + - - -
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Residues in contact with HIS 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 GLN* 2.9 39.9 + - + +
17A LEU* 3.5 4.0 + - + +
18A LYS 3.2 0.6 - - - -
19A ASP* 1.3 83.3 - - + +
21A GLY* 1.3 60.1 + - - +
22A VAL* 3.4 11.9 + - + +
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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