Contacts of the helix formed by residues 9 - 21 (chain A) in PDB entry 1Q8G
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 ASP 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 VAL* 3.2 14.8 - - - +
8A SER* 1.3 82.3 + - - +
10A GLY* 1.3 53.1 + - - +
11A VAL 2.9 2.0 - - - -
12A ILE* 2.6 47.2 + - + +
13A LYS* 3.2 3.1 + - - -
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Residues in contact with GLY 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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8A SER* 2.6 16.5 + - - -
9A ASP* 1.3 71.8 - - - +
11A VAL* 1.3 52.0 + - - +
13A LYS* 2.6 37.3 + - - +
14A VAL* 2.6 20.4 + - - +
49A LEU* 3.6 15.0 - - - +
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Residues in contact with VAL 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 VAL* 3.1 16.6 - - + -
8A SER* 4.1 2.5 - - - +
9A ASP 2.8 0.4 + - - -
10A GLY* 1.3 75.1 - - - +
12A ILE* 1.3 58.4 + - - +
14A VAL* 3.2 15.7 - - - +
15A PHE* 3.1 22.2 - - - +
38A PHE* 4.0 22.7 - - + -
47A ILE* 2.7 45.3 - - + +
48A ILE* 3.4 13.2 - - - -
49A LEU* 3.7 3.4 - - + +
124A ILE* 4.7 1.6 - - + -
127A LYS* 3.0 31.6 - - - +
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Residues in contact with ILE 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 VAL* 5.2 2.0 - - + -
9A ASP* 2.6 27.4 + - - +
11A VAL* 1.3 71.6 - - - +
13A LYS* 1.3 51.8 - - - +
15A PHE* 3.6 9.6 - - + +
16A ASN* 2.6 49.4 + - - +
127A LYS* 3.1 50.9 - - + +
128A LEU* 5.7 1.3 - - + -
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Residues in contact with LYS 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 ASP 3.2 5.1 + - - +
10A GLY* 2.6 29.3 + - - +
12A ILE* 1.3 75.0 - - - +
14A VAL* 1.3 60.1 + - - +
16A ASN* 3.3 18.4 + - - +
17A ASP* 3.8 7.8 + - - +
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Residues in contact with VAL 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 GLY 2.6 15.6 + - - +
11A VAL 3.2 18.6 - - - +
13A LYS* 1.3 75.7 - - + +
15A PHE* 1.3 58.1 + - - +
17A ASP* 3.9 8.5 + - - +
18A MET* 4.0 5.2 + - - +
33A LYS* 4.0 16.8 - - + +
36A VAL* 4.2 21.7 - - + +
38A PHE* 3.5 18.8 - - + -
49A LEU* 3.2 38.6 - - + -
54A GLU* 5.5 4.3 - - - +
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Residues in contact with PHE 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 VAL 3.1 21.1 + - - +
12A ILE* 3.2 10.9 + - + +
13A LYS 3.2 0.6 - - - -
14A VAL* 1.3 75.4 - - + +
16A ASN* 1.3 59.7 + - - +
17A ASP 3.0 2.5 - - - -
18A MET* 2.7 34.7 + - + -
19A LYS* 2.9 39.3 + - + +
36A VAL* 5.8 0.4 - - - -
38A PHE* 4.9 4.3 - - + -
84A LEU* 3.0 40.6 - - + -
99A LEU* 4.8 3.8 - - + -
127A LYS* 5.6 0.7 - - - +
128A LEU* 3.5 40.4 - - + -
131A ILE* 3.3 23.6 - - + -
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Residues in contact with ASN 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 ILE* 2.6 35.5 + - - +
13A LYS* 3.3 12.8 + - - +
15A PHE* 1.3 75.1 - - - +
17A ASP* 1.3 61.7 + - - +
19A LYS* 4.2 4.6 - - - +
20A VAL* 3.3 35.7 + - - +
22A LYS* 4.6 2.5 - - - +
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Residues in contact with ASP 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 LYS 3.8 7.7 + - - +
14A VAL* 4.1 6.7 - - - +
15A PHE 3.0 0.6 - - - -
16A ASN* 1.3 79.0 - - - +
18A MET* 1.3 55.9 + - - +
21A ARG* 2.6 43.9 + - - +
22A LYS* 3.3 48.2 + - - +
32A ARG* 5.8 0.2 - - - +
33A LYS* 3.7 26.4 + - - +
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Residues in contact with MET 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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15A PHE* 2.7 28.8 + - + +
17A ASP* 1.3 78.2 - - - +
19A LYS* 1.3 63.0 + - - +
21A ARG* 3.5 10.2 + - - +
32A ARG* 5.4 4.9 - - - -
33A LYS* 2.9 51.9 - - + +
34A LYS* 4.4 0.2 - - - -
36A VAL* 4.3 10.5 - - + -
84A LEU* 2.8 33.9 - - + +
85A TYR 4.3 1.6 - - - -
86A ASP* 2.7 36.2 - - - +
99A LEU* 3.0 33.6 - - + +
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Residues in contact with LYS 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 PHE* 2.9 37.4 + - + +
16A ASN* 4.2 6.3 - - - +
18A MET* 1.3 79.9 - - - +
20A VAL* 1.3 67.8 + - + +
21A ARG* 3.7 0.7 + - - +
99A LEU* 4.2 14.0 - - + +
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Residues in contact with VAL 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* 3.3 29.3 + - - +
19A LYS* 1.3 85.3 - - + +
21A ARG* 1.3 58.7 + - - +
22A LYS* 2.6 37.7 + - + +
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Residues in contact with ARG 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 ASP* 2.6 29.7 + - - +
18A MET* 3.5 6.7 + - - +
19A LYS 3.3 4.1 - - - +
20A VAL* 1.3 76.0 - - - +
22A LYS* 1.3 71.8 + - - +
23A SER* 3.0 22.8 + - - +
29A VAL* 5.1 6.8 - - - +
32A ARG* 3.0 42.9 - - - +
33A LYS* 5.4 2.4 + - - -
86A ASP* 5.7 0.9 - - - +
97A GLU* 3.4 27.2 + - - -
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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