Contacts of the helix formed by residues 20 - 37 (chain A) in PDB entry 2LSR
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLU 3.8 1.4 + - - +
19A ASN* 1.3 75.9 - - - +
21A ALA* 1.3 54.6 + - - +
22A GLU 3.4 0.7 - - - -
23A LYS* 3.1 14.0 + - - +
24A ASP* 2.8 35.4 + - - +
27A TYR* 4.9 1.6 - - - -
112B LYS* 3.3 28.2 + - - -
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Residues in contact with ALA 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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19A ASN* 3.6 13.8 - - - +
20A ASP* 1.3 74.2 - - - +
22A GLU* 1.3 59.8 + - + +
23A LYS 2.9 1.6 - - - -
24A ASP* 2.6 29.3 + - - +
25A TYR* 2.8 14.1 + - - +
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Residues in contact with GLU 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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17A ILE* 2.8 51.3 - - + +
18A GLU 4.8 0.3 + - - -
19A ASN* 4.0 22.1 + - - +
20A ASP 4.6 0.4 - - - +
21A ALA* 1.3 78.7 - - + +
23A LYS* 1.3 57.8 + - - +
25A TYR* 3.6 3.0 + - - +
26A LEU* 3.1 28.2 + - - +
49A VAL* 3.7 22.2 - - + +
55A ARG* 3.1 25.8 + - - +
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Residues in contact with LYS 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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10A ARG* 3.5 3.8 - - - +
13A VAL* 5.5 0.4 - - + -
14A ASP* 3.1 37.6 + - - +
17A ILE* 3.0 30.1 - - + -
18A GLU 4.7 2.7 - - - +
19A ASN 3.1 20.0 - - - +
20A ASP* 3.2 23.6 - - - +
21A ALA 2.9 0.4 - - - -
22A GLU* 1.3 75.6 - - - +
24A ASP* 1.3 52.5 + - - +
26A LEU* 3.3 8.2 + - - +
27A TYR* 2.7 63.4 + - + +
108B TYR* 3.4 31.8 + - + +
112B LYS* 4.6 3.6 - - - +
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Residues in contact with ASP 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 ASP* 2.8 14.3 + - - +
21A ALA* 2.6 22.0 + - - +
23A LYS* 1.3 72.2 - - - +
25A TYR* 1.3 60.2 + - - +
27A TYR* 3.3 16.1 + - + +
28A ASP* 3.1 34.3 + - - +
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Residues in contact with TYR 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 ALA 2.8 10.3 + - - +
22A GLU* 3.8 8.7 - - - +
24A ASP* 1.3 76.0 + - - +
26A LEU* 1.3 55.2 + - - +
28A ASP* 3.3 10.3 + - + +
29A VAL* 2.7 39.8 + - + +
45A ASP* 3.1 45.7 + - + -
48A LEU* 3.5 32.9 - - + +
49A VAL* 4.2 18.8 - - + -
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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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9A PHE* 6.0 1.3 - - + -
13A VAL* 3.6 34.1 - - + -
17A ILE* 5.7 0.7 - - + -
22A GLU 3.1 18.4 + - - +
23A LYS* 3.6 7.9 - - - +
25A TYR* 1.3 78.4 - - - +
27A TYR* 1.3 64.8 + - + +
29A VAL* 3.1 11.9 + - + +
30A LEU* 2.9 40.7 + - + +
46A LEU* 5.2 6.1 - - + -
49A VAL* 4.5 14.1 - - + +
50A ILE* 5.7 0.9 - - + -
58A LEU* 4.1 23.1 - - + -
62A ILE* 3.7 20.4 - - + -
108B TYR* 5.2 4.9 - - + +
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Residues in contact with TYR 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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20A ASP* 4.9 1.8 - - - -
23A LYS* 2.7 49.4 + - + +
24A ASP* 3.4 15.9 - - + +
26A LEU* 1.3 79.9 - - + +
28A ASP* 1.3 57.4 + - - +
30A LEU* 3.3 11.8 + - + +
31A ARG* 2.9 34.0 + - - +
108B TYR* 2.7 66.6 - + + -
112B LYS* 3.3 30.1 + - - -
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Residues in contact with ASP 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 ASP* 3.1 29.5 + - - +
25A TYR* 3.6 12.6 - - + +
26A LEU 3.2 0.2 - - - -
27A TYR* 1.3 78.3 - - - +
29A VAL* 1.3 58.8 + - + +
31A ARG* 3.8 13.1 + - - +
32A MET* 3.0 37.5 + - + +
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Residues in contact with VAL 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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25A TYR* 2.7 45.5 + - + +
26A LEU* 3.1 13.0 + - + +
28A ASP* 1.3 74.8 - - + +
30A LEU* 1.3 64.4 + - - +
32A MET* 3.3 8.2 + - + +
33A TYR* 3.1 21.5 + - - +
41A VAL 4.9 0.4 - - - +
42A LEU* 3.0 44.6 - - + +
45A ASP* 3.7 32.5 - - + +
46A LEU* 4.3 7.4 - - + +
49A VAL* 4.8 3.6 - - + -
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Residues in contact with LEU 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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9A PHE* 5.6 0.4 - - + -
26A LEU* 2.9 35.7 + - + +
27A TYR* 3.7 15.7 - - + +
29A VAL* 1.3 73.7 - - - +
31A ARG* 1.3 65.4 + - - +
33A TYR* 3.3 3.3 + - - +
34A HIS* 3.1 19.1 + - - +
42A LEU* 5.1 2.5 - - + -
62A ILE* 3.0 33.0 - - + -
65A LEU* 4.5 3.1 - - + -
101B LEU* 3.1 41.2 - - + +
104B VAL* 4.9 10.5 - - + -
105B LEU* 3.4 29.4 - - + -
108B TYR* 5.1 7.4 - - + -
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Residues in contact with ARG 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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27A TYR* 2.9 19.6 + - - +
28A ASP* 3.8 14.8 + - - +
30A LEU* 1.3 76.8 - - - +
32A MET* 1.3 58.3 + - - +
34A HIS* 3.4 6.7 + - + +
35A GLN* 2.9 43.6 + - + +
105B LEU* 4.9 8.5 - - + +
109B LEU* 6.1 4.4 - - - +
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Residues in contact with MET 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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28A ASP* 3.0 26.9 + - + +
29A VAL* 3.4 9.0 - - + +
30A LEU 3.2 0.2 - - - -
31A ARG* 1.3 74.5 - - - +
33A TYR* 1.3 55.6 + - - +
35A GLN* 3.4 24.7 - - - +
36A THR* 2.5 62.6 + - + +
41A VAL* 3.7 31.4 - - + -
42A LEU* 6.5 0.4 - - - -
45A ASP* 5.9 3.1 - - - +
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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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29A VAL 3.1 4.5 + - - +
30A LEU* 3.3 7.8 + - - +
32A MET* 1.3 78.1 - - - +
34A HIS* 1.3 56.2 + - - +
36A THR* 3.8 4.3 - - - -
37A MET* 2.6 42.2 + - - +
38A ASP 3.6 19.1 - - - -
39A VAL* 3.5 22.2 - - + -
41A VAL* 6.3 0.2 - - - -
42A LEU* 3.0 34.2 - - + +
66A ILE* 3.3 30.9 - - + +
67A PRO* 3.2 18.1 - - + +
70A HIS* 2.6 29.9 + + - +
101B LEU* 3.3 33.9 - - + -
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Residues in contact with HIS 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 LEU 3.1 15.7 + - - +
31A ARG* 3.7 6.3 - - + +
32A MET 3.2 0.2 - - - -
33A TYR* 1.3 80.7 - - - +
35A GLN* 1.3 61.1 + - - +
37A MET* 3.8 29.0 - - + +
99B SER* 3.9 10.2 + - - -
101B LEU* 3.6 21.0 - - + +
102B LYS* 3.5 41.1 - - + +
105B LEU* 4.3 11.2 - - + +
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Residues in contact with GLN 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 ARG* 2.9 42.9 + - + +
32A MET* 3.1 30.2 - - - +
34A HIS* 1.3 79.9 - - - +
36A THR* 1.3 79.0 + - + +
37A MET* 4.6 2.8 - - - +
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Residues in contact with THR 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 MET* 2.5 56.9 + - + +
33A TYR* 3.8 1.6 - - - -
35A GLN* 1.3 84.7 - - + +
37A MET* 1.3 69.6 + - - +
38A ASP* 3.2 37.0 + - - +
41A VAL* 4.4 7.7 - - + +
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Residues in contact with MET 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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33A TYR* 2.6 35.2 + - + +
34A HIS* 3.8 32.3 - - + +
35A GLN 4.6 2.2 - - - +
36A THR* 1.3 76.4 + - - +
38A ASP* 1.3 62.5 + - - +
70A HIS* 3.8 35.4 + - + -
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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