Contacts of the helix formed by residues 13 - 28 (chain A) in PDB entry 2L1R
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 THR 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU* 1.3 80.3 - - - +
14A GLU* 1.3 57.5 + - - +
15A GLU* 3.2 27.9 + - + +
16A GLN* 3.0 39.2 + - + +
17A LYS* 2.7 39.5 + - - +
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Residues in contact with GLU 14 (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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13A THR* 1.3 74.4 + - - +
15A GLU* 1.3 71.9 + - - +
17A LYS* 3.9 8.9 - - + +
18A ASN* 2.8 67.9 + - - +
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Residues in contact with GLU 15 (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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13A THR* 3.1 20.4 + - + +
14A GLU* 1.3 89.0 - - - +
16A GLN* 1.3 60.2 + - + +
18A ASN* 4.6 1.3 - - - +
19A GLU* 3.2 28.1 + - - +
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Residues in contact with GLN 16 (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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12A LEU* 3.3 25.3 - - + +
13A THR* 3.0 22.5 + - + +
15A GLU* 1.3 81.0 - - + +
17A LYS* 1.3 66.6 + - - +
19A GLU* 3.3 7.6 - - - +
20A PHE* 3.0 35.0 + - + -
85A MET* 3.6 34.1 - - - +
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Residues in contact with LYS 17 (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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9A VAL 2.8 25.6 + - - +
10A GLU* 2.9 20.0 + - - +
11A GLN 3.0 15.5 + - - -
12A LEU* 3.8 17.8 - - + +
13A THR 2.7 25.1 + - - +
14A GLU* 3.9 9.4 - - - +
16A GLN* 1.3 73.7 - - - +
18A ASN* 1.3 62.8 + - - +
20A PHE* 3.2 19.8 + - - +
21A LYS* 3.2 11.4 + - - +
74A PHE* 4.1 16.3 - - + -
78A LEU* 4.8 10.9 - - + +
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Residues in contact with ASN 18 (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 GLU* 2.8 47.7 + - - +
15A GLU* 4.6 1.6 - - - +
17A LYS* 1.3 74.4 - - - +
19A GLU* 1.3 62.4 + - - +
21A LYS* 3.1 17.0 + - - +
22A ALA* 2.9 24.6 + - - +
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Residues in contact with GLU 19 (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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15A GLU 3.2 22.7 + - - +
16A GLN* 3.3 11.4 + - + +
18A ASN* 1.3 79.3 - - - +
20A PHE* 1.3 60.8 + - + +
22A ALA* 3.2 11.9 + - - +
23A ALA* 2.9 31.3 + - - +
154B MET* 3.4 37.8 - - - +
158B LEU* 5.8 1.7 - - - +
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Residues in contact with PHE 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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12A LEU* 4.1 10.1 - - + -
16A GLN* 3.0 29.5 + - + -
17A LYS* 3.5 8.7 - - - +
19A GLU* 1.3 79.7 - - + +
21A LYS* 1.3 57.8 + - - +
23A ALA* 3.5 6.5 - - + -
24A PHE* 2.8 31.7 + - - +
74A PHE* 4.0 7.2 - - + -
77A PHE* 3.5 10.3 - + + -
78A LEU* 3.6 43.7 - - + -
81A MET* 3.2 50.7 - - + -
82A VAL* 4.8 0.9 - - + -
85A MET* 3.8 22.9 - - + -
150B ALA* 5.7 0.7 - - + -
154B MET* 5.5 8.5 - - - -
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Residues in contact with LYS 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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17A LYS 3.2 6.4 + - - +
18A ASN* 3.1 21.5 + - - +
20A PHE* 1.3 80.0 - - - +
22A ALA* 1.3 62.7 + - + +
24A PHE* 3.2 12.0 + - + +
25A ASP* 2.8 46.3 + - - +
74A PHE* 3.5 27.7 - - + -
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Residues in contact with ALA 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 ASN* 2.9 14.8 + - - +
19A GLU* 3.6 15.9 - - - +
21A LYS* 1.3 81.5 - - + +
23A ALA* 1.3 58.2 + - - +
25A ASP* 2.8 17.5 - - - +
26A ILE* 3.0 22.3 - - + +
158B LEU* 5.2 4.9 - - + -
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Residues in contact with ALA 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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19A GLU 2.9 16.7 + - - +
20A PHE* 3.5 7.0 - - + +
22A ALA* 1.3 76.5 - - - +
24A PHE* 1.3 61.8 + - - +
26A ILE* 4.4 8.7 - - - +
27A PHE* 3.2 29.6 + - + +
77A PHE* 3.5 13.0 - - + -
154B MET* 4.3 29.8 - - + -
157B LEU* 4.6 5.7 - - + +
158B LEU* 4.8 6.3 - - + +
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Residues in contact with PHE 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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20A PHE 2.8 17.3 + - - +
21A LYS* 3.2 12.7 + - + +
23A ALA* 1.3 77.5 - - - +
25A ASP* 1.3 72.7 + - + +
26A ILE 3.2 1.3 - - - -
27A PHE* 3.0 13.0 + - - +
28A VAL* 3.0 28.4 + - + +
34A GLY* 3.1 30.5 - - - -
36A ILE* 3.4 22.9 - - + -
72A VAL 3.4 12.3 - - - -
73A ASP* 3.3 22.0 - - - -
74A PHE* 3.5 31.6 - + + -
77A PHE* 3.5 19.7 - + + -
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Residues in contact with ASP 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 LYS* 2.8 42.4 + - - +
22A ALA* 2.8 15.9 - - - +
24A PHE* 1.3 83.4 - - + +
26A ILE* 1.3 81.8 + - - +
28A VAL* 2.9 27.9 - - - +
29A LEU* 3.5 8.8 + - - +
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Residues in contact with ILE 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 ALA 3.0 23.1 + - - +
23A ALA 4.6 0.7 - - - +
24A PHE 3.2 0.6 - - - -
25A ASP* 1.3 88.1 + - - +
27A PHE* 1.3 62.1 + - - +
29A LEU* 3.1 32.4 - - + +
157B LEU* 3.2 32.3 - - + +
158B LEU* 3.8 36.1 - - + -
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Residues in contact with PHE 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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23A ALA* 3.2 20.0 + - + +
24A PHE 3.0 10.4 + - - +
26A ILE* 1.3 82.6 - - - +
28A VAL* 1.3 57.2 + - - +
29A LEU* 3.8 2.3 + - - +
36A ILE* 3.5 19.1 - - + -
40A GLU* 3.2 34.3 - - - +
41A LEU* 4.4 5.6 - - - -
43A LYS* 5.7 0.5 - - - +
44A VAL* 3.1 36.3 - - + -
77A PHE* 3.7 16.8 - + - -
81A MET* 5.2 1.1 - - + -
91A SXK 3.0 31.2 - + - -
153B MET* 3.6 32.8 - - + -
154B MET* 6.2 0.2 - - - -
157B LEU* 3.3 24.9 - - + -
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Residues in contact with VAL 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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24A PHE* 3.0 41.0 + - + +
25A ASP* 2.9 14.4 - - - +
27A PHE* 1.3 74.4 - - - +
29A LEU* 1.3 60.4 + - - +
31A ALA* 3.3 24.5 - - + +
34A GLY* 3.3 10.6 - - - +
35A CYS 3.1 27.6 - - - +
36A ILE* 3.5 25.4 - - + +
40A GLU* 3.2 5.6 - - - -
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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