Contacts of the helix formed by residues 31 - 44 (chain A) in PDB entry 2LE4
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 ASN 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG* 5.2 2.0 - - - +
30A HIS* 1.3 88.7 + - + +
32A SER* 1.3 85.9 + - - +
33A GLU* 2.6 24.0 + - - +
34A ILE* 3.0 15.8 + - - +
35A SER* 3.3 12.2 + - - -
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Residues in contact with SER 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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31A ASN* 1.3 92.7 + - - +
33A GLU* 1.3 56.5 + - - +
35A SER* 2.9 15.0 + - - -
36A LYS* 2.8 28.6 + - - +
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Residues in contact with GLU 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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28A LYS 4.4 6.1 - - - +
29A MET* 3.9 24.2 - - + -
30A HIS* 2.7 16.7 + - - -
31A ASN* 2.6 42.2 + - - +
32A SER* 1.3 77.0 + - - +
34A ILE* 1.3 65.0 + - - +
36A LYS* 3.1 8.8 + - - +
37A ARG* 2.8 35.2 + - + +
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Residues in contact with ILE 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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19A ARG* 4.2 28.0 - - + -
22A MET* 3.7 33.2 - - + -
29A MET* 3.5 30.3 - - + +
30A HIS* 3.5 16.8 - - - +
31A ASN 3.0 11.5 + - - +
33A GLU* 1.3 93.9 + - - +
35A SER* 1.3 59.3 + - - +
37A ARG* 3.2 5.8 + - + -
38A LEU* 2.9 56.7 + - + +
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Residues in contact with SER 35 (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 ASN 3.3 11.1 + - - -
32A SER* 2.9 18.3 + - - -
34A ILE* 1.3 80.4 - - - +
36A LYS* 1.3 59.4 + - - +
38A LEU* 4.2 4.9 - - - +
39A GLY* 3.3 18.9 + - - -
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Residues in contact with LYS 36 (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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32A SER 2.8 11.5 + - - +
33A GLU* 3.1 11.0 + - - +
35A SER* 1.3 77.1 - - - +
37A ARG* 1.3 83.0 + - - +
39A GLY* 3.6 1.2 + - - -
40A ALA* 3.2 27.5 + - + +
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Residues in contact with ARG 37 (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 MET* 5.9 0.7 - - + -
29A MET* 4.8 21.6 - - - -
33A GLU* 2.8 22.6 + - + +
34A ILE* 3.5 12.3 - - + +
36A LYS* 1.3 91.3 - - - +
38A LEU* 1.3 59.2 + - + +
40A ALA* 3.1 6.7 + - - +
41A GLU* 2.7 50.4 + - + +
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Residues in contact with LEU 38 (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 TRP* 3.4 52.1 - - + +
15A SER* 3.6 26.0 - - - +
18A GLN* 3.9 5.8 - - + -
22A MET* 3.6 28.0 - - + -
34A ILE* 2.9 41.4 + - + +
35A SER* 4.3 5.2 - - - +
37A ARG* 1.3 78.4 - - + +
39A GLY* 1.3 58.8 + - - +
41A GLU* 4.3 1.3 - - + -
42A TRP* 2.8 36.9 + - + +
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Residues in contact with GLY 39 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 5.8 6.5 - - - -
35A SER 3.3 15.0 + - - -
36A LYS 4.0 1.3 - - - -
37A ARG 3.3 0.6 - - - -
38A LEU* 1.3 77.4 - - - +
40A ALA* 1.3 61.7 + - - +
42A TRP* 3.4 7.7 + - - +
43A LYS* 3.3 19.8 + - - +
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Residues in contact with ALA 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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36A LYS* 3.2 21.9 + - + +
37A ARG* 3.1 10.6 + - - +
39A GLY* 1.3 75.2 - - - +
41A GLU* 1.3 70.4 + - - +
43A LYS* 3.2 13.6 + - - +
44A LEU* 3.2 24.5 - - + +
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Residues in contact with GLU 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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14A TRP* 3.5 28.8 - - + -
37A ARG* 2.7 38.4 + - + +
38A LEU* 3.8 1.8 - - + +
40A ALA* 1.3 79.7 - - - +
42A TRP* 1.3 62.6 + - - +
44A LEU* 3.2 9.8 + - - +
45A LEU* 3.1 22.7 + - - +
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Residues in contact with TRP 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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10A ALA* 3.9 8.3 - - + -
11A PHE* 3.1 69.3 + + + +
14A TRP* 3.4 32.5 - + - +
15A SER* 5.5 1.8 - - - -
38A LEU* 2.8 18.4 + - + +
39A GLY* 3.5 9.0 - - - +
40A ALA 3.2 0.2 - - - -
41A GLU* 1.3 77.6 - - - +
43A LYS* 1.3 62.4 + - - +
45A LEU* 3.1 26.9 - - + +
53A PHE* 3.3 36.8 - + - -
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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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39A GLY 3.3 7.8 + - - +
40A ALA* 3.2 12.6 + - - +
42A TRP* 1.3 79.8 - - - +
44A LEU* 1.3 74.9 + - + +
45A LEU 3.2 2.5 + - - +
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Residues in contact with LEU 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 ALA* 3.2 20.2 + - + +
41A GLU* 3.2 12.6 + - - +
42A TRP 3.2 0.4 - - - -
43A LYS* 1.3 98.2 - - + +
45A LEU* 1.3 64.2 + - - +
46A SER* 3.2 9.4 + - - -
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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