Contacts of the helix formed by residues 39 - 50 (chain A) in PDB entry 1L42
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 LEU 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.0 27.4 - - + -
25A TYR* 3.7 36.5 - - + +
37A PRO 3.6 5.1 + - - -
38A SER* 1.3 71.4 + - - +
40A ASN* 1.3 60.5 + - - +
42A ALA* 3.8 2.0 - - + -
43A LYS* 2.9 50.6 + - + +
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Residues in contact with ASN 40 (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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38A SER* 2.9 9.5 + - - +
39A LEU* 1.3 81.6 - - - +
41A ALA* 1.3 69.2 + - - +
43A LYS* 3.1 24.9 + - - +
44A SER* 3.1 14.1 + - - -
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Residues in contact with ALA 41 (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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34A THR* 4.4 7.9 - - + +
36A SER* 3.4 26.2 - - - +
38A SER* 2.8 19.7 + - - +
40A ASN* 1.3 72.7 - - - +
42A ALA* 1.3 64.3 + - - +
44A SER* 3.0 9.8 + - - -
45A GLU* 3.0 25.6 + - + +
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Residues in contact with ALA 42 (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 ILE* 4.1 13.5 - - + -
25A TYR* 3.7 35.9 - - + -
33A LEU* 4.1 8.1 - - + +
34A THR* 3.7 11.6 - - + +
38A SER 2.9 11.7 + - - +
39A LEU* 3.6 9.6 - - - +
41A ALA* 1.3 78.2 - - - +
43A LYS* 1.3 58.5 + - - +
45A GLU* 3.4 4.5 + - - +
46A LEU* 2.9 28.4 + - - +
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Residues in contact with LYS 43 (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 ILE* 3.9 18.8 - - + -
39A LEU* 2.9 49.1 + - + +
40A ASN* 3.1 17.4 + - - +
42A ALA* 1.3 78.9 - - - +
44A SER* 1.3 58.6 + - - +
46A LEU* 3.4 5.4 + - - +
47A ASP* 3.1 34.5 + - - +
55A ASN* 4.4 21.4 + - - +
56A GLY* 4.1 20.1 + - - +
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Residues in contact with SER 44 (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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40A ASN 3.1 10.2 + - - -
41A ALA* 3.3 12.8 - - - -
43A LYS* 1.3 75.0 - - - +
45A GLU* 1.3 67.9 + - - +
46A LEU 3.1 1.1 - - - -
47A ASP* 3.3 7.3 + - - +
48A LYS* 3.1 25.2 + - - +
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Residues in contact with GLU 45 (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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33A LEU* 3.8 33.0 - - + +
34A THR* 4.4 10.3 - - - -
41A ALA* 3.0 15.8 + - + +
42A ALA 3.6 8.5 - - - +
44A SER* 1.3 79.2 + - - +
46A LEU* 1.3 59.1 + - - +
48A LYS* 2.6 44.4 + - - +
49A ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 46 (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 ILE* 4.3 3.6 - - + -
27A ILE* 3.7 47.3 - - + -
33A LEU* 3.9 16.3 - - + +
42A ALA 2.9 18.5 + - - +
43A LYS* 3.6 6.1 - - - +
44A SER 3.1 0.4 - - - -
45A GLU* 1.3 80.1 - - - +
47A ASP* 1.3 57.2 + - - +
49A ALA* 3.2 3.3 + - + -
50A ILE* 3.0 34.1 + - + +
54A CYS* 3.9 20.4 - - + -
56A GLY* 3.8 25.1 - - - +
58A ILE* 3.9 14.8 - - + -
66A LEU* 5.0 2.2 - - + -
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Residues in contact with ASP 47 (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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43A LYS* 3.1 18.9 + - - +
44A SER* 3.3 6.7 + - - +
46A LEU* 1.3 76.5 - - - +
48A LYS* 1.3 55.1 + - - +
50A ILE 4.4 0.2 - - - +
51A GLY* 2.7 29.6 + - - -
52A ARG 2.9 23.2 + - - +
53A ASN* 3.7 18.7 + - - +
54A CYS* 2.4 39.4 + - - +
55A ASN 3.7 4.1 + - - -
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Residues in contact with LYS 48 (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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44A SER* 3.1 15.5 + - - +
45A GLU* 2.6 44.6 + - - +
47A ASP* 1.3 78.3 - - - +
49A ALA* 1.3 63.3 + - - +
50A ILE 3.4 0.2 + - - -
51A GLY* 3.8 6.1 + - - -
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Residues in contact with ALA 49 (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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31A HIS* 4.7 12.6 - - + +
33A LEU* 5.1 4.0 - - + -
45A GLU 2.9 17.4 + - - +
46A LEU* 3.2 6.7 + - + +
48A LYS* 1.3 81.8 - - - +
50A ILE* 1.3 65.3 + - + +
66A LEU* 4.5 22.3 - - + +
69A GLN* 5.3 2.4 + - - -
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Residues in contact with ILE 50 (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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46A LEU* 3.0 23.9 + - + +
49A ALA* 1.3 81.6 - - - +
51A GLY* 1.3 60.7 + - - +
52A ARG* 3.7 9.1 - - + +
54A CYS* 3.7 20.4 - - - -
58A ILE* 3.9 19.7 - - + -
62A GLU* 3.6 44.9 - - + +
65A LYS* 6.3 1.3 - - + -
66A LEU* 3.9 33.7 - - + -
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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