Contacts of the helix formed by residues 17 - 29 (chain A) in PDB entry 1LUK
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 SER 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 1.3 86.1 - - - +
18A ARG* 1.3 71.2 + - - +
19A ASP* 3.4 4.7 + - - -
20A LYS* 2.6 33.7 - - - +
21A ALA* 3.6 11.6 + - - +
37A ARG* 2.9 20.3 + - - +
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Residues in contact with ARG 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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17A SER* 1.3 79.6 + - - +
19A ASP* 1.3 86.7 + - + +
22A GLU* 3.6 0.9 + - - +
37A ARG* 3.2 26.1 - - - +
63A HIS* 2.3 53.3 + - + -
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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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17A SER* 4.2 2.6 - - - -
18A ARG* 1.3 106.7 + - + +
20A LYS* 1.3 69.2 + - + +
22A GLU* 3.2 12.3 + - - +
23A LYS* 3.1 19.7 + - - +
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Residues in contact with LYS 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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15A SER 3.5 8.2 + - - -
16A ILE* 3.1 23.1 - - + +
17A SER* 2.6 55.4 - - - +
19A ASP* 1.3 77.2 - - + +
21A ALA* 1.3 54.0 + - - +
23A LYS* 2.7 31.7 + - - +
24A LEU* 2.5 39.1 + - + +
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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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16A ILE* 3.5 8.1 - - + +
17A SER 3.6 7.9 + - - +
19A ASP 3.3 0.4 - - - -
20A LYS* 1.3 77.4 - - - +
22A GLU* 1.3 52.5 + - - +
24A LEU* 2.3 37.3 - - - +
25A LEU* 2.5 21.1 + - - +
35A MET* 3.4 19.7 - - - -
37A ARG* 5.6 2.0 - - + -
48A SER* 2.8 26.0 - - - +
63A HIS* 3.6 8.7 - - + +
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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 ARG 3.6 2.5 - - - +
19A ASP* 3.2 11.3 + - - +
20A LYS 3.1 0.4 - - - -
21A ALA* 1.3 76.0 - - - +
23A LYS* 1.3 53.8 + - - +
26A LEU* 2.5 43.2 + - + +
61A ILE* 2.4 49.8 - - + +
63A HIS* 2.9 38.0 + - + +
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Residues in contact with LYS 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 ASP 3.1 11.7 + - - +
20A LYS* 2.7 45.1 + - - +
22A GLU* 1.3 72.6 - - - +
24A LEU* 1.3 59.7 + - - +
26A LEU* 3.7 5.6 - - - +
27A ASP* 3.0 30.3 + - - +
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Residues in contact with LEU 24 (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 ASN* 3.8 1.1 - - - +
16A ILE* 2.8 39.3 - - + -
20A LYS* 2.5 22.3 + - + +
21A ALA* 2.3 35.4 - - - +
23A LYS* 1.3 79.9 - - + +
25A LEU* 1.3 71.9 + - + +
27A ASP* 3.5 5.8 + - - +
28A THR* 3.1 27.7 + - - -
35A MET* 2.5 31.4 - - + -
109A VAL* 3.4 2.8 - - + +
111A GLY* 3.2 27.9 - - - -
112A NH2 4.7 1.8 - - - +
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Residues in contact with LEU 25 (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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21A ALA 2.5 32.3 + - - +
24A LEU* 1.3 81.5 - - + +
26A LEU* 1.3 56.0 - - - +
28A THR* 3.0 8.1 - - - +
33A ALA* 3.3 17.3 - - + +
35A MET* 4.3 0.2 - - + -
48A SER* 2.6 55.6 - - - +
50A PHE* 2.4 38.8 - - + -
61A ILE* 2.8 27.6 - - + -
109A VAL* 3.3 35.4 - - + -
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Residues in contact with LEU 26 (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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22A GLU* 2.5 22.3 + - + +
23A LYS* 3.7 6.7 - - - +
25A LEU* 1.3 74.2 - - - +
27A ASP* 1.3 61.9 + - - +
29A GLY* 3.6 8.8 + - - -
50A PHE* 3.7 3.6 - - - -
52A LYS* 4.5 2.1 + - - -
58A ASN 4.6 2.7 - - - +
59A PRO* 3.0 55.2 - - + +
61A ILE* 3.0 29.2 - - + +
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Residues in contact with ASP 27 (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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23A LYS 3.0 18.8 + - - +
24A LEU* 3.7 6.7 - - - +
26A LEU* 1.3 77.1 - - - +
28A THR* 1.3 69.6 + - - +
29A GLY* 3.3 1.2 + - - -
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Residues in contact with THR 28 (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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24A LEU 3.1 15.8 + - - -
25A LEU 3.0 13.7 + - - +
27A ASP* 1.3 80.0 - - - +
29A GLY* 1.3 77.4 + - - +
30A LYS* 2.8 48.2 + - + +
50A PHE* 3.2 11.0 - - + -
109A VAL* 3.4 21.0 - - + +
110A CYS 5.6 0.9 + - - -
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Residues in contact with GLY 29 (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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25A LEU 3.2 4.9 + - - -
26A LEU 4.1 2.0 - - - -
27A ASP 3.3 2.5 - - - -
28A THR* 1.3 85.1 - - - +
30A LYS* 1.3 69.8 + - - +
50A PHE* 3.4 5.6 - - - -
52A LYS* 3.3 33.6 - - - +
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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