Contacts of the helix formed by residues 6 - 22 (chain A) in PDB entry 1O9D
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 THR 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PRO* 1.3 75.9 - - - +
7A ALA* 1.3 69.0 + - - +
8A ARG* 3.3 15.4 + - + +
9A GLU* 3.1 37.4 + - + +
10A GLU* 2.9 28.5 + - - +
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Residues in contact with ALA 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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6A THR* 1.3 73.7 + - - +
8A ARG* 1.3 65.5 + - - +
10A GLU* 3.3 4.9 + - - +
11A ASN* 2.9 37.2 + - - +
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Residues in contact with ARG 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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6A THR* 3.3 10.0 + - + +
7A ALA* 1.3 77.9 - - - +
9A GLU* 1.3 65.2 + - - +
11A ASN* 3.3 3.7 + - - +
12A VAL* 3.1 24.3 + - + +
34A VAL* 4.0 18.6 - - + +
37A SER* 4.9 10.1 - - - +
38A LEU* 3.6 25.9 - - + +
41A GLU* 3.2 28.1 + - - -
42A GLU 3.8 13.1 + - - -
44A THR* 4.0 11.1 - - - +
47A GLU* 2.6 45.2 + - - +
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Residues in contact with GLU 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 PRO* 4.0 12.0 - - + +
6A THR* 3.1 38.5 + - + +
7A ALA 3.2 0.6 - - - -
8A ARG* 1.3 84.3 - - - +
10A GLU* 1.3 62.5 - - - +
12A VAL* 3.4 7.0 + - - +
13A TYR* 3.1 21.7 + - + +
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Residues in contact with GLU 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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5A PRO* 3.8 19.8 - - - +
6A THR 2.9 13.8 + - - +
7A ALA* 3.9 4.7 - - - +
9A GLU* 1.3 75.8 - - - +
11A ASN* 1.3 62.6 + - - +
13A TYR* 3.3 8.6 + - + +
14A MET* 3.0 48.8 + - + +
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Residues in contact with ASN 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 ALA* 2.9 28.6 + - - +
8A ARG* 3.7 1.2 - - - +
10A GLU* 1.3 73.9 - - - +
12A VAL* 1.3 60.9 + - - +
14A MET* 3.5 4.8 + - - +
15A ALA* 2.9 28.6 + - - +
30A PHE* 3.6 22.6 - - - +
33A LYS* 3.4 49.5 + - - +
34A VAL* 3.6 22.5 - - + +
37A SER* 6.3 0.6 - - - -
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Residues in contact with VAL 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 ARG* 3.1 17.3 + - + +
9A GLU* 3.8 9.9 - - - +
10A GLU 3.2 0.2 - - - -
11A ASN* 1.3 75.6 - - - +
13A TYR* 1.3 64.3 + - - +
15A ALA* 3.3 8.1 + - - +
16A LYS* 3.1 40.2 + - + +
31A MET* 4.3 5.2 - - + -
34A VAL* 3.8 14.6 - - + -
46A GLU* 4.3 12.8 - - - +
47A GLU* 3.6 32.8 - - + +
50A LEU* 4.3 11.9 - - + -
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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 GLU* 3.1 16.9 + - + +
10A GLU* 3.3 10.9 + - + +
12A VAL* 1.3 78.5 - - - +
14A MET* 1.3 68.2 + - + +
16A LYS* 3.1 21.9 + - + +
17A LEU* 3.1 56.4 + - + +
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Residues in contact with MET 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 GLU* 3.0 36.7 + - + +
11A ASN* 3.7 5.2 - - - +
13A TYR* 1.3 81.7 - - + +
15A ALA* 1.3 57.0 + - - +
17A LEU* 3.1 27.8 + - + +
18A ALA* 2.7 36.0 + - - +
30A PHE* 3.6 43.3 - - + -
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Residues in contact with ALA 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 ASN 2.9 18.5 + - - +
12A VAL 3.3 6.5 + - - +
14A MET* 1.3 76.0 - - - +
16A LYS* 1.3 58.7 + - - +
18A ALA* 3.4 5.4 + - - +
19A GLU* 2.9 24.6 + - - +
27A MET* 3.5 17.6 - - + +
30A PHE* 3.9 16.7 - - + -
31A MET* 3.5 32.1 - - + -
50A LEU* 4.9 5.6 - - + -
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Residues in contact with LYS 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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12A VAL* 3.1 30.3 + - + +
13A TYR* 3.1 22.2 + - + +
15A ALA* 1.3 77.6 - - - +
17A LEU* 1.3 61.7 - - - +
19A GLU* 3.6 12.4 + - - +
20A GLN* 3.2 28.1 + - - +
46A GLU* 2.8 30.3 + - - +
50A LEU* 4.0 23.1 - - + -
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Residues in contact with LEU 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 TYR* 3.1 41.8 + - + +
14A MET* 3.1 37.1 + - + +
16A LYS* 1.3 73.0 - - - +
18A ALA* 1.3 67.4 + - - +
20A GLN* 3.1 12.2 + - + +
21A ALA* 2.9 24.3 + - - +
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Residues in contact with ALA 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 MET 2.7 16.3 + - - +
15A ALA* 3.5 6.3 - - - +
17A LEU* 1.3 77.4 - - - +
19A GLU* 1.4 57.1 + - - +
21A ALA* 3.3 6.3 + - - -
22A GLU 2.8 24.3 + - - -
23A ARG* 3.0 33.4 + - + +
26A GLU* 4.4 7.9 - - + +
27A MET* 3.8 18.2 - - - +
30A PHE* 4.5 5.4 - - + -
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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 ALA 2.9 13.2 + - - +
16A LYS* 3.8 12.6 - - - +
17A LEU 3.2 0.4 - - - -
18A ALA* 1.4 74.6 - - - +
20A GLN* 1.3 71.9 + - - +
22A GLU* 3.2 17.8 + - - +
24A TYR* 4.2 16.4 + - + +
27A MET* 3.6 31.1 - - + -
50A LEU* 3.7 19.4 - - - +
53A VAL* 3.6 21.5 - - - +
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Residues in contact with GLN 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 LYS 3.2 14.8 + - - +
17A LEU* 3.1 15.4 + - + +
19A GLU* 1.3 89.7 + - - +
21A ALA* 1.3 60.7 + - - +
22A GLU* 3.2 11.0 + - - +
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Residues in contact with ALA 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 2.9 16.0 + - - +
18A ALA* 3.8 6.3 - - - +
20A GLN* 1.3 75.9 - - - +
22A GLU* 1.3 69.4 + - - +
23A ARG* 3.5 27.2 + - - +
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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 ALA 2.8 6.4 + - - -
19A GLU 3.2 11.9 + - - +
20A GLN 3.8 8.8 - - - +
21A ALA* 1.3 81.4 - - - +
23A ARG* 1.3 62.1 + - - +
24A TYR* 3.4 43.0 + - + +
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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