Contacts of the helix formed by residues 9 - 19 (chain A) in PDB entry 1AXC
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 GLY 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.4 2.9 - - - -
7A VAL 3.3 1.4 + - - -
8A GLN* 1.3 70.8 - - - +
10A SER* 1.3 63.8 + - - +
12A LEU* 3.1 12.8 + - - +
13A LYS* 3.3 18.7 + - - +
83A GLY 4.9 2.0 - - - -
84A ASN 4.8 3.2 + - - -
85A GLU 5.1 0.4 - - - -
86A ASP 2.9 30.0 + - - -
88A ILE* 3.6 24.7 - - - +
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Residues in contact with SER 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 GLN* 3.7 19.1 + - - -
9A GLY* 1.3 75.4 - - - +
11A ILE* 1.3 71.3 + - - +
13A LYS* 2.8 16.4 + - - +
14A LYS* 2.8 51.2 + - - +
84A ASN* 3.8 34.2 + - - -
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Residues in contact with ILE 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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6A LEU* 4.2 16.8 - - + -
8A GLN* 3.5 34.0 + - + +
9A GLY 3.2 0.6 + - - -
10A SER* 1.3 84.2 + - - +
12A LEU* 1.3 59.0 + - - +
14A LYS* 3.6 10.9 + - + +
15A VAL* 2.9 38.8 + - + +
52A LEU* 4.8 2.0 - - + -
221A LEU* 4.0 3.2 - - + +
241A ILE* 3.7 28.5 - - + -
242A ALA* 4.6 9.6 - - + +
244A MET* 3.9 27.6 - - + -
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Residues in contact with LEU 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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6A LEU* 4.2 18.1 - - + +
9A GLY 3.1 9.6 + - - +
11A ILE* 1.3 78.0 - - - +
13A LYS* 1.3 66.8 + - - +
15A VAL* 3.7 10.0 - - + +
16A LEU* 3.2 23.8 + - + +
28A TRP* 4.7 18.2 - - + -
52A LEU* 4.2 24.7 - - + -
57A PHE* 5.8 2.0 - - + -
75A MET* 5.3 3.8 - - + -
79A LEU* 3.7 18.0 - - + +
88A ILE* 3.9 32.1 - - + -
90A LEU* 4.1 27.1 - - + -
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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 GLY 3.5 8.3 - - - +
10A SER* 2.8 24.2 + - - +
12A LEU* 1.3 76.2 - - - +
14A LYS* 1.3 63.4 + - + +
16A LEU* 3.1 5.9 + - - +
17A GLU* 3.0 30.1 + - + +
79A LEU* 3.4 31.4 + - + +
80A LYS* 4.5 7.5 + - - +
82A ALA* 3.1 31.3 + - + -
83A GLY 3.9 12.6 - - - +
84A ASN* 3.6 33.9 - - - +
88A ILE* 4.4 4.0 - - + -
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Residues in contact with LYS 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 SER* 2.8 46.0 + - - +
11A ILE* 4.6 4.6 - - - +
13A LYS* 1.3 72.0 - - + +
15A VAL* 1.3 65.4 + - - +
17A GLU* 3.4 7.0 + - - +
18A ALA* 3.0 24.9 + - - +
84A ASN* 5.2 4.5 - - - +
217A LYS 5.0 1.6 - - - +
220A PRO* 3.6 46.3 + - + +
221A LEU* 3.6 23.2 - - + +
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Residues in contact with VAL 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 ILE* 2.9 34.8 + - + +
12A LEU* 3.7 13.0 - - + +
13A LYS 3.3 0.2 - - - -
14A LYS* 1.3 76.1 - - - +
16A LEU* 1.3 63.3 + - + +
18A ALA* 3.4 2.8 + - - +
19A LEU* 3.3 30.9 + - + +
28A TRP* 4.9 8.3 - - + -
50A LEU* 3.6 35.2 - - + -
52A LEU* 4.6 4.7 - - + -
221A LEU* 3.9 13.5 - - + -
241A ILE* 3.7 28.5 - - + -
247A LEU* 4.6 2.1 - - + +
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Residues in contact with LEU 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 LEU* 3.2 12.4 + - + +
13A LYS 3.1 5.2 + - - +
15A VAL* 1.3 80.2 - - + +
17A GLU* 1.3 60.3 + - + +
19A LEU* 4.8 2.9 - - + -
20A LYS* 2.9 37.2 + - - +
28A TRP* 4.5 10.1 - - + -
72A LEU* 3.7 40.4 - - + +
75A MET* 3.3 38.6 - - + +
76A SER* 3.7 14.4 - - - -
79A LEU* 3.2 29.8 - - + -
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Residues in contact with GLU 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* 3.0 22.6 + - + +
14A LYS* 3.4 7.1 + - - +
16A LEU* 1.3 76.3 - - - +
18A ALA* 1.3 59.9 + - - +
19A LEU 3.3 0.4 - - - -
20A LYS* 2.7 40.6 + - - +
21A ASP* 4.7 1.9 + - - +
76A SER* 2.8 27.2 + - - +
80A LYS* 3.7 26.4 - - + +
217A LYS* 4.4 17.2 - - - +
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Residues in contact with ALA 18 (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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14A LYS 3.0 17.3 + - - +
15A VAL 3.5 6.1 - - - +
16A LEU 3.2 0.2 - - - -
17A GLU* 1.3 79.5 - - - +
19A LEU* 1.3 57.0 + - - +
21A ASP* 5.3 0.6 - - - +
22A LEU* 5.0 4.2 + - - +
214A PHE 4.3 8.3 - - - +
217A LYS* 3.8 15.0 + - - +
218A ALA* 3.7 23.3 - - + -
221A LEU* 4.4 1.1 - - + -
247A LEU* 4.0 7.9 - - + -
249A TYR* 2.9 35.4 + - - +
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Residues in contact with LEU 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 VAL* 3.4 29.6 - - + +
16A LEU* 3.3 5.0 + - + +
18A ALA* 1.3 83.7 - - - +
20A LYS* 1.3 56.3 + - - +
21A ASP 3.1 2.9 - - - -
22A LEU* 2.8 28.0 + - + -
23A ILE* 2.9 32.8 + - + +
28A TRP* 5.1 4.5 - - + -
37A LEU* 4.4 21.1 - - + -
48A VAL* 3.3 37.0 - - + -
50A LEU* 4.5 7.6 - - + -
72A LEU* 4.2 8.3 - - + -
247A LEU* 3.6 14.4 - - + -
249A TYR* 4.2 5.2 - - + +
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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