Contacts of the helix formed by residues 19 - 27 (chain A) in PDB entry 3LIO
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE 4.6 0.9 - - - -
15A GLU* 3.5 16.8 - - - -
16A PRO 5.2 0.6 + - - -
18A ILE* 1.3 77.9 - - - +
20A LYS* 1.3 66.8 + - - +
21A GLU* 3.4 9.9 + - - +
22A THR* 3.0 19.2 + - - -
23A LEU* 3.0 22.3 + - - +
165A ILE* 4.3 0.9 - - - +
166A ASP* 2.7 34.9 + - - -
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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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11A ILE* 3.4 49.0 + - + +
12A ASP* 4.5 9.6 - - + -
15A GLU* 3.0 17.1 + - - +
19A SER* 1.3 74.7 - - - +
21A GLU* 1.4 63.8 + - - +
23A LEU* 3.1 3.5 + - - +
24A GLU* 2.9 46.4 + - - +
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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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19A SER* 3.3 9.2 + - - +
20A LYS* 1.4 76.9 - - - +
22A THR* 1.3 63.2 + - - +
24A GLU* 3.2 16.3 + - - +
25A PHE* 3.0 47.6 + - + -
165A ILE* 3.7 17.5 - - + +
168B ARG* 2.8 38.4 + - - -
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Residues in contact with THR 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 ILE* 3.6 16.6 - - + -
19A SER* 3.0 14.3 + - - -
21A GLU* 1.3 78.1 - - - +
23A LEU* 1.3 52.4 + - + +
25A PHE* 3.9 0.5 - - - +
26A HIS* 2.7 53.6 + - + +
161A HIS 4.3 4.7 - - - +
162A ALA 3.5 26.9 + - - +
163A TYR* 5.4 0.3 - - - -
165A ILE* 3.5 22.6 + - + +
166A ASP* 2.8 31.3 + - - +
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Residues in contact with LEU 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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7A LEU* 4.2 18.4 - - + -
9A TYR* 4.2 5.2 - - + -
10A ALA 4.4 0.9 - - - +
11A ILE* 3.3 42.0 - - + +
14A LEU* 4.0 31.4 - - + -
18A ILE* 4.0 18.4 - - + +
19A SER 3.0 16.1 + - - +
20A LYS 3.1 3.8 + - - +
22A THR* 1.3 76.4 - - + +
24A GLU* 1.4 57.8 + - - +
26A HIS 4.4 0.2 - - - +
27A HIS* 2.8 34.9 + - - +
28A GLY 3.4 0.3 + - - -
77A TRP* 3.3 36.8 - - + -
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Residues in contact with GLU 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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11A ILE* 4.0 16.3 - - + +
20A LYS* 2.9 50.4 + - - +
21A GLU* 3.5 19.2 - - - +
23A LEU* 1.4 76.7 - - - +
25A PHE* 1.4 65.5 + - + +
28A GLY* 3.0 27.7 + - - +
29A LYS* 3.5 5.8 + - - +
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Residues in contact with PHE 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* 3.0 56.1 + - + +
22A THR 4.1 1.6 - - - +
24A GLU* 1.4 83.5 - - + +
26A HIS* 1.3 62.7 + - - +
29A LYS* 2.9 42.4 + - + +
30A HIS* 2.9 27.8 + - + -
165A ILE* 4.0 10.5 - - + -
164B TYR* 3.7 18.4 - - - +
168B ARG* 3.6 35.7 - - + -
169B ASN* 3.7 17.5 - - - -
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Residues in contact with HIS 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 THR* 2.7 33.8 + - + +
25A PHE* 1.3 77.0 - - - +
27A HIS* 1.3 56.4 + - - +
30A HIS* 3.4 8.8 - - + +
31A HIS* 3.0 26.2 + - - +
73A HIS* 3.1 12.5 + + - -
76A TYR* 3.6 18.6 + + - -
77A TRP* 3.4 18.1 - + + -
157A ASP* 2.8 18.1 + - - -
161A HIS* 2.9 18.9 + + - +
162A ALA* 3.5 28.5 + - + -
5000A FE 2.1 26.7 - - - -
164B TYR* 6.0 0.2 - - - +
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Residues in contact with HIS 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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4A LEU* 3.6 28.1 - - + +
5A PRO 2.8 29.3 + - - -
6A SER* 4.1 2.3 - - - -
7A LEU* 3.6 47.9 + - + +
11A ILE* 5.8 2.5 - - + -
23A LEU* 2.8 18.6 + - - +
26A HIS* 1.3 75.0 - - - +
28A GLY* 1.3 69.1 + - - +
29A LYS 3.4 0.7 + - - -
31A HIS* 3.4 22.4 + - - +
32A ASN 3.4 6.1 + - - -
77A TRP* 3.6 28.9 + + + -
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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