Contacts of the helix formed by residues 43 - 55 (chain A) in PDB entry 1L2L
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 LYS 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A TYR 3.7 10.5 - - - +
42A LEU* 1.3 80.2 - - - +
44A ARG* 1.3 66.9 + - - +
45A GLU* 4.8 2.0 - - + +
46A ASP* 3.4 23.2 + - + +
47A LEU* 3.0 22.7 + - - +
188A PHE* 3.7 6.1 - - - -
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Residues in contact with ARG 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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43A LYS* 1.3 71.6 - - - +
45A GLU* 1.3 72.4 + - - +
47A LEU* 3.2 3.3 + - - -
48A GLU* 2.8 68.9 + - + +
188A PHE* 3.5 15.4 - - + -
189A LYS* 3.0 60.3 + - - +
190A VAL* 3.6 1.6 - - - +
191A LEU 3.8 18.2 + - - -
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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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43A LYS* 3.4 3.0 - - + +
44A ARG* 1.3 97.0 + - - +
46A ASP* 1.3 63.6 + - - +
48A GLU* 4.0 11.2 - - - +
49A LYS* 3.0 27.7 + - - +
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Residues in contact with ASP 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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40A LYS* 5.0 3.2 + - - +
42A LEU* 5.7 0.9 - - - +
43A LYS* 3.4 29.3 + - + +
45A GLU* 1.3 78.9 - - - +
47A LEU* 1.3 63.3 + - - +
49A LYS* 3.4 18.4 + - - +
50A ARG* 3.1 47.0 + - - +
106A TRP* 2.9 32.5 + - - -
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Residues in contact with LEU 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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42A LEU* 4.5 15.0 - - + -
43A LYS 3.0 18.3 + - - +
44A ARG* 3.7 2.9 - - - +
46A ASP* 1.3 80.0 + - - +
48A GLU* 1.3 64.2 + - - +
50A ARG* 3.3 4.5 + - + +
51A ILE* 3.0 37.4 + - + +
77A LEU* 4.4 13.2 - - + +
80A ILE* 4.5 10.1 - - + -
81A LEU* 4.5 5.2 - - + -
84A ILE* 3.9 24.7 - - + -
106A TRP* 4.1 25.8 - - + -
188A PHE* 4.2 8.1 - - + -
190A VAL* 3.7 27.1 - - + -
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Residues in contact with GLU 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 ARG* 2.8 54.7 + - + +
45A GLU* 4.0 13.3 - - - +
47A LEU* 1.3 71.0 - - - +
49A LYS* 1.3 63.3 + - - +
51A ILE* 3.2 10.7 + - - +
52A GLU* 2.9 32.8 + - + +
190A VAL* 3.9 13.0 - - + -
191A LEU* 2.7 41.8 + - + +
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Residues in contact with LYS 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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45A GLU 3.0 16.2 + - - +
46A ASP* 3.6 19.9 + - - +
48A GLU* 1.3 78.2 - - - +
50A ARG* 1.3 86.8 + - - +
52A GLU* 3.4 7.0 + - - +
53A LYS* 3.1 49.7 + - - +
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Residues in contact with ARG 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 ASP* 3.1 39.8 + - - +
47A LEU* 3.8 4.5 - - - +
49A LYS* 1.3 88.5 - - - +
51A ILE* 1.3 62.0 + - - +
53A LYS* 3.4 10.7 + - + +
54A VAL* 3.3 20.1 + - - +
77A LEU* 3.6 15.1 - - + +
102A TYR* 3.1 48.5 + - - +
105A LYS* 2.5 37.5 - - - +
106A TRP* 3.2 51.0 + - - +
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Residues in contact with ILE 51 (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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47A LEU* 3.0 36.9 + - + +
48A GLU* 3.2 10.5 + - - +
50A ARG* 1.3 75.4 - - - +
52A GLU* 1.3 60.8 + - - +
54A VAL* 3.2 4.5 - - - +
55A GLY 2.8 27.5 + - - -
56A LYS* 3.9 27.1 - - + -
59A VAL* 3.9 13.9 - - + -
77A LEU* 3.7 25.4 - - + -
81A LEU* 3.8 29.6 - - + -
190A VAL* 4.3 8.5 - - + -
191A LEU* 4.6 10.8 - - + -
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Residues in contact with GLU 52 (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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48A GLU* 2.9 24.2 + - + +
49A LYS* 3.4 7.2 + - - +
51A ILE* 1.3 77.5 - - - +
53A LYS* 1.3 64.8 + - + +
54A VAL 3.4 0.3 + - - -
55A GLY* 3.4 9.4 + - - +
56A LYS* 3.6 38.5 + - - +
191A LEU* 4.4 9.5 - - - +
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Residues in contact with LYS 53 (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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49A LYS* 3.1 39.6 + - + +
50A ARG* 3.5 12.6 - - - +
51A ILE 3.2 0.2 - - - -
52A GLU* 1.3 79.4 - - + +
54A VAL* 1.3 63.5 + - + +
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Residues in contact with VAL 54 (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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50A ARG 3.3 13.4 + - - +
51A ILE 3.2 13.5 - - - +
53A LYS* 1.3 80.9 - - + +
55A GLY* 1.3 58.6 + - - +
58A GLU* 4.8 4.2 - - - +
59A VAL* 3.5 25.4 - - + -
73A ILE* 3.4 35.4 - - + -
74A PRO* 3.9 25.6 - - + +
77A LEU* 3.9 7.4 - - + -
102A TYR* 5.1 3.8 - - + +
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Residues in contact with GLY 55 (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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51A ILE 2.8 9.9 + - - -
52A GLU 3.4 8.5 + - - -
54A VAL* 1.3 78.6 - - - +
56A LYS* 1.3 66.3 + - - -
57A GLU* 3.3 13.2 - - - -
58A GLU* 3.1 10.2 + - - +
59A VAL* 3.1 23.4 + - - +
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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