Contacts of the helix formed by residues 23 - 34 (chain A) in PDB entry 2LI7
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 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ASN* 1.3 72.9 - - - +
24A TYR* 1.3 64.8 + - - +
25A CYS 3.4 0.9 - - - -
26A LEU* 3.2 14.5 + - - +
27A ARG* 2.8 64.2 + - - +
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Residues in contact with TYR 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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14A TYR* 5.9 1.7 - - - +
15A GLU 3.0 18.5 + - - -
16A CYS* 3.7 9.1 - - - -
17A LEU* 3.5 61.0 + - + -
22A ASN* 3.4 10.3 + - + +
23A ASP* 1.3 77.7 - - - +
25A CYS* 1.3 63.9 + - - +
27A ARG* 3.4 38.1 - - - +
28A GLU* 3.5 20.5 - - + +
46A CYS* 4.0 15.9 - - - -
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Residues in contact with CYS 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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16A CYS* 4.1 6.3 - - - -
22A ASN* 2.9 20.4 + - - +
24A TYR* 1.3 73.8 - - - +
26A LEU* 1.3 60.4 + - - +
28A GLU* 3.2 2.5 + - - +
29A CYS* 3.0 33.9 + - - -
39A GLY 4.7 2.0 - - - -
40A TYR* 4.1 19.1 - - - +
41A CYS* 3.8 24.0 - - - -
46A CYS* 2.0 56.8 - - + -
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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 ASN 4.0 14.8 + - - +
23A ASP* 3.2 18.8 + - - +
25A CYS* 1.3 77.9 - - - +
27A ARG* 1.3 56.5 + - - +
29A CYS* 3.4 3.1 + - - +
30A LYS* 3.0 56.1 + - - +
37A SER 3.6 24.0 - - - +
38A GLY* 3.7 17.3 - - - -
39A GLY 3.8 13.8 + - - +
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Residues in contact with ARG 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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17A LEU* 6.2 1.2 - - - +
23A ASP* 2.8 49.6 + - - +
24A TYR* 3.4 37.7 - - - +
26A LEU* 1.3 76.1 - - - +
28A GLU* 1.3 68.9 + - - +
30A LYS* 3.5 9.1 + - - +
31A GLN* 3.3 30.8 + - - +
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Residues in contact with GLU 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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5A LEU* 3.4 30.6 - - + +
13A LYS* 3.7 25.7 + - + -
24A TYR* 3.5 24.5 + - + +
25A CYS* 3.2 13.8 + - - +
27A ARG* 1.3 84.7 - - - +
29A CYS* 1.3 58.0 + - - +
31A GLN* 3.4 36.4 + - - +
32A GLN* 4.1 4.0 + - - +
46A CYS* 4.4 10.3 - - + -
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Residues in contact with CYS 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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5A LEU* 4.5 1.8 - - - -
25A CYS 3.0 20.0 + - - +
26A LEU 3.7 4.5 - - - +
28A GLU* 1.3 73.7 - - - +
30A LYS* 1.3 59.0 + - + +
31A GLN 3.2 1.8 - - - -
32A GLN* 2.9 7.3 + - - +
33A TYR* 2.9 30.5 + - + +
37A SER* 3.8 7.4 - - - +
38A GLY 3.6 17.5 - - - +
39A GLY* 3.8 4.0 - - - -
46A CYS* 5.0 4.0 - - - -
47A TRP 3.6 8.7 - - - -
48A CYS* 2.0 56.1 - - + -
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Residues in contact with LYS 30 (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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26A LEU* 3.0 46.3 + - + +
27A ARG* 3.5 7.8 + - - +
29A CYS* 1.3 74.5 - - - +
31A GLN* 1.3 56.5 + - - +
34A GLY* 3.5 32.1 + - - +
35A LYS* 3.2 32.0 + - + +
36A SER 5.2 0.4 - - - -
37A SER* 3.6 23.1 - - - +
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Residues in contact with GLN 31 (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 LYS* 4.3 29.8 + - - +
13A LYS* 6.1 1.3 - - - +
27A ARG* 3.3 19.9 + - - +
28A GLU* 3.4 39.7 + - - +
30A LYS* 1.3 75.3 - - - +
32A GLN* 1.3 59.7 + - + +
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Residues in contact with GLN 32 (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 LEU* 3.6 31.0 - - + -
6A VAL* 3.9 28.5 + - - +
7A SER 5.1 3.3 + - - -
8A LYS* 5.0 17.3 + - - +
13A LYS* 5.6 2.6 + - - -
28A GLU 4.3 3.1 - - - +
29A CYS 2.9 7.6 + - - +
31A GLN* 1.3 82.8 - - + +
33A TYR* 1.3 78.1 + - + +
34A GLY 3.7 2.1 + - - -
56A VAL 5.4 0.2 + - - -
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Residues in contact with TYR 33 (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 LEU* 3.5 33.7 - - + +
6A VAL* 3.9 3.3 + - - +
29A CYS* 2.9 16.4 + - + +
32A GLN* 1.3 93.9 - - + +
34A GLY* 1.3 62.1 + - - +
37A SER* 3.7 11.8 + - - +
48A CYS* 3.6 36.3 - - + -
50A HIS 5.7 0.2 - - - +
51A LEU* 3.5 22.8 - - + +
52A TYR* 4.2 24.3 + - - +
55A ALA* 4.0 24.9 - - + -
56A VAL 2.7 30.6 + - - -
57A VAL* 3.6 14.5 - - + +
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Residues in contact with GLY 34 (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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30A LYS* 3.5 17.2 + - - -
32A GLN 3.7 1.8 - - - -
33A TYR* 1.3 76.8 - - - +
35A LYS* 1.3 60.6 + - - -
36A SER 3.3 2.9 - - - -
37A SER* 2.7 29.5 + - - -
52A TYR* 5.3 8.7 - - - -
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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