Contacts of the helix formed by residues 14 - 26 (chain A) in PDB entry 1LTQ
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 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY 3.2 2.4 + - - -
13A SER* 1.3 80.4 - - - +
15A LYS* 1.3 64.7 + - - +
16A SER 3.4 2.2 - - - -
17A THR* 3.4 4.4 + - - -
18A TRP* 3.0 26.5 + - - +
112A PHE* 3.9 6.3 - - - -
900A ADP 3.2 34.3 + - - -
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Residues in contact with LYS 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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7A THR* 3.3 17.7 - - + +
9A GLY 2.8 39.9 - - - +
10A CYS 3.6 4.2 + - - -
11A PRO* 4.4 2.0 - - - +
13A SER* 3.5 9.8 - - - +
14A GLY* 1.3 78.2 - - - +
16A SER* 1.3 57.9 + - - +
18A TRP* 3.5 5.7 + - - +
19A ALA* 3.0 28.3 + - - +
84A SER* 4.2 14.4 + - - +
85A ASP 3.3 24.7 + - - +
86A THR* 4.0 11.0 - - - +
112A PHE* 3.7 24.0 - - + -
900A ADP 2.8 42.0 + - - +
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Residues in contact with SER 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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14A GLY 3.4 0.2 - - - -
15A LYS* 1.3 70.8 - - - +
17A THR* 1.3 65.1 + - - +
19A ALA* 3.1 7.2 + - - +
20A ARG* 2.9 24.8 + - - +
33A ASN* 4.5 14.6 + - - -
84A SER* 4.9 4.7 + - - -
129A LYS* 5.7 1.8 + - - -
900A ADP 2.8 40.0 + - - -
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Residues in contact with THR 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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14A GLY* 3.8 7.9 - - - -
15A LYS 3.4 0.4 - - - -
16A SER* 1.3 77.6 - - - +
18A TRP* 1.3 65.1 + - - +
20A ARG* 3.2 6.3 + - - +
21A GLU* 3.1 24.2 + - + +
900A ADP 2.9 36.2 + - + +
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Residues in contact with TRP 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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5A ILE* 4.0 18.2 - - + -
7A THR* 3.9 22.9 - - + -
14A GLY 3.0 17.7 + - - +
15A LYS 3.7 0.9 - - - +
17A THR* 1.3 77.5 - - - +
19A ALA* 1.3 66.5 + - - +
21A GLU* 3.2 10.7 + - + +
22A PHE* 2.8 75.9 + + + +
82A ILE* 3.9 21.5 - - + -
110A LYS* 3.7 38.2 - - + +
112A PHE* 3.5 30.1 - + + -
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Residues in contact with ALA 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 LYS 3.0 19.6 + - - +
16A SER* 3.1 8.5 + - - +
18A TRP* 1.3 90.8 - - + +
20A ARG* 1.3 62.9 + - - +
22A PHE* 3.8 2.2 - - - +
23A ILE* 3.0 33.1 + - + +
31A ASN* 3.9 26.0 - - - +
82A ILE* 4.4 7.2 - - + -
84A SER* 4.3 5.8 - - - -
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Residues in contact with ARG 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 SER 2.9 12.6 + - - +
17A THR* 3.2 9.3 + - - +
19A ALA* 1.3 77.4 - - - +
21A GLU* 1.3 59.4 + - - +
23A ILE* 3.3 6.6 + - - +
24A ALA* 2.9 33.4 + - + +
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Residues in contact with GLU 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 THR* 3.1 16.1 + - + +
18A TRP* 3.6 9.4 - - + +
20A ARG* 1.3 80.3 - - - +
22A PHE* 1.3 65.3 + - - +
24A ALA* 3.2 8.8 + - - +
25A LYS* 3.1 60.1 + - + +
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Residues in contact with PHE 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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3A LYS* 6.2 1.1 - - + -
5A ILE* 5.6 3.8 - - + -
18A TRP* 2.8 61.2 + + + +
19A ALA* 3.8 3.4 - - - +
21A GLU* 1.3 75.8 - - - +
23A ILE* 1.3 57.0 + - - +
25A LYS* 3.2 1.9 + - - -
26A ASN* 2.8 56.2 + - - +
29A PHE* 3.5 51.8 - + + -
82A ILE* 4.4 13.9 - - + -
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Residues in contact with ILE 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 ALA* 3.0 24.8 + - + +
20A ARG* 3.8 5.6 - - - +
22A PHE* 1.3 77.9 - - - +
24A ALA* 1.3 64.2 + - - +
25A LYS 3.2 0.7 + - - -
26A ASN 3.4 19.6 + - - +
27A PRO* 4.1 5.0 - - + +
29A PHE* 3.6 26.2 - - + +
30A TYR* 4.2 1.8 - - - -
31A ASN* 3.6 38.8 - - + +
82A ILE* 4.3 13.9 - - + -
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Residues in contact with ALA 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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20A ARG* 2.9 22.0 + - + +
21A GLU* 3.2 16.1 + - - +
23A ILE* 1.3 78.6 - - - +
25A LYS* 1.3 63.0 + - + +
27A PRO* 5.2 3.7 - - - +
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Residues in contact with LYS 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 GLU* 3.1 46.3 + - + +
22A PHE* 4.6 1.1 - - - -
23A ILE 3.1 0.2 - - - -
24A ALA* 1.3 85.2 - - + +
26A ASN* 1.3 74.7 + - - +
27A PRO* 3.5 9.1 - - - +
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Residues in contact with ASN 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 PHE* 2.8 52.0 + - + +
23A ILE 3.4 8.1 + - - +
25A LYS* 1.3 92.6 + - - +
27A PRO* 1.3 69.6 - - - +
28A GLY 3.5 1.2 + - - -
29A PHE* 3.5 36.8 + - + +
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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