Contacts of the helix formed by residues 21 - 38 (chain A) in PDB entry 2QYP
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.2 15.1 + - - +
18A LEU* 3.1 29.9 - - - +
19A ILE 3.2 4.4 - - - +
20A ASP* 1.3 81.9 - - - +
22A ASN* 1.3 63.0 + - - +
23A LYS* 3.4 35.0 + - + +
24A THR* 4.1 1.3 - - - +
25A GLU* 3.3 19.1 + - - +
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Residues in contact with ASN 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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20A ASP 4.2 6.5 + - - -
21A ASN* 1.3 74.6 - - - +
23A LYS* 1.3 59.7 + - - +
24A THR 3.3 0.2 - - - -
25A GLU* 3.8 15.2 - - - +
26A LYS* 3.1 31.9 + - - +
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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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18A LEU* 4.0 10.7 - - - +
21A ASN* 3.4 27.1 + - + +
22A ASN* 1.3 79.8 - - - +
24A THR* 1.3 73.7 + - - +
26A LYS* 4.0 4.5 - - - +
27A GLU* 3.2 42.2 + - - +
27B GLU* 3.7 28.6 + - - +
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Residues in contact with THR 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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18A LEU* 3.2 17.9 + - + +
19A ILE* 3.7 32.5 - - + -
21A ASN* 3.7 2.2 + - - +
22A ASN 3.3 0.2 - - - -
23A LYS* 1.3 95.0 + - - +
25A GLU* 1.3 63.9 + - - +
26A LYS 3.2 0.2 - - - -
27A GLU* 3.2 17.2 + - - +
28A ILE* 2.9 49.0 + - + +
24B THR* 4.6 12.8 - - + +
27B GLU* 4.2 6.8 + - - +
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Residues in contact with GLU 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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19A ILE 4.1 4.0 + - - +
20A ASP* 4.1 15.2 - - - +
21A ASN 3.3 17.6 + - - +
22A ASN* 3.9 15.2 + - - +
23A LYS 3.5 0.2 - - - -
24A THR* 1.3 76.1 - - - +
26A LYS* 1.3 56.5 + - - +
28A ILE* 3.6 1.1 + - - +
29A LEU* 3.0 38.7 + - + +
56A SER* 4.0 24.5 + - - +
59A LEU* 3.8 36.8 - - + +
60A SER* 4.2 20.6 + - - -
63A LEU* 5.3 0.2 - - - +
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Residues in contact with LYS 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 ASN 3.1 17.9 + - - +
23A LYS* 4.0 5.6 - - - +
25A GLU* 1.3 74.3 - - - +
27A GLU* 1.3 56.4 + - - +
29A LEU* 3.2 6.9 + - + +
30A ASP* 2.7 69.6 + - - +
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Residues in contact with GLU 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 LYS* 3.2 33.3 + - - +
24A THR* 3.2 19.1 + - - +
26A LYS* 1.3 76.4 - - - +
28A ILE* 1.3 59.4 + - + +
30A ASP* 3.4 6.9 + - - +
31A ALA* 2.8 33.0 + - - +
23B LYS* 4.2 21.0 - - + +
24B THR* 4.5 6.2 + - - -
27B GLU* 3.8 22.6 - - - +
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Residues in contact with ILE 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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19A ILE* 4.2 10.1 - - + -
24A THR* 2.9 43.6 + - + +
25A GLU 3.9 2.9 - - - +
27A GLU* 1.3 76.2 - - + +
29A LEU* 1.3 59.7 + - + +
31A ALA* 3.4 6.5 + - - +
32A PHE* 3.0 27.4 + - + +
59A LEU* 3.8 24.2 - - + -
15B VAL* 4.4 21.8 - - + -
18B LEU* 4.0 17.6 - - + +
19B ILE* 3.7 34.1 - - + -
21B ASN* 5.6 3.8 - - - +
24B THR* 5.7 2.0 - - - +
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Residues in contact with LEU 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 GLU* 3.0 28.8 + - + +
26A LYS* 3.7 7.6 - - + +
28A ILE* 1.3 77.0 - - + +
30A ASP* 1.3 54.9 + - - +
32A PHE* 2.8 32.9 - - - +
33A ASP* 3.3 11.8 - - - +
51A VAL* 3.5 38.4 - - + +
52A ASP* 5.0 7.6 - - - +
55A GLY* 4.1 18.8 - - - -
56A SER* 4.3 9.0 - - - +
59A LEU* 3.6 24.0 - - + -
15B VAL* 5.8 4.0 - - + -
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Residues in contact with ASP 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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26A LYS* 2.7 51.3 + - - +
27A GLU* 3.6 6.3 + - - +
29A LEU* 1.3 68.9 - - - +
31A ALA* 1.3 55.2 + - - +
32A PHE 2.3 22.5 - - - +
33A ASP* 4.1 6.7 - - - +
34A LYS* 3.3 27.9 - - - +
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Residues in contact with ALA 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 GLU 2.8 22.8 + - - +
28A ILE* 3.8 6.3 - - - +
30A ASP* 1.3 69.0 - - - +
32A PHE* 1.3 62.2 + - - +
34A LYS* 3.3 24.6 - - - +
35A MET* 3.6 12.8 + - - +
18B LEU* 4.1 16.1 - - + +
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Residues in contact with PHE 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 ILE 3.0 13.7 + - - +
29A LEU* 2.8 15.8 - - - +
30A ASP 2.3 30.0 - - - +
31A ALA* 1.3 71.0 - - - +
33A ASP* 1.3 74.2 + - - +
34A LYS 3.0 6.0 + - - -
35A MET* 3.8 21.1 - - + +
36A CYS* 3.8 17.5 - - - -
47A CYS* 4.0 5.6 - - - -
51A VAL* 3.6 22.4 - - + -
10B PHE* 5.1 5.2 - + - -
11B LEU* 3.6 30.7 - - + -
14B GLU* 3.7 35.2 - - + -
15B VAL* 4.2 19.5 - - + -
18B LEU* 3.6 16.8 - - + +
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Residues in contact with ASP 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 LEU* 3.3 16.0 - - - +
30A ASP* 4.1 6.6 - - - +
32A PHE* 1.3 86.3 - - - +
34A LYS* 1.3 61.5 + - + +
35A MET 3.3 0.2 - - - -
36A CYS* 3.1 16.3 + - - +
37A SER* 3.0 25.3 + - - -
48A GLN* 3.6 40.8 + - + +
51A VAL* 3.5 17.6 - - - +
52A ASP* 4.0 12.2 - - - +
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Residues in contact with LYS 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 ASP* 3.3 28.4 + - - +
31A ALA* 3.3 16.9 - - - +
32A PHE 3.0 4.6 + - - -
33A ASP* 1.3 76.6 - - + +
35A MET* 1.3 71.1 + - + +
37A SER* 3.0 27.6 + - - +
38A LYS* 3.5 4.9 + - - +
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Residues in contact with MET 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 ALA 3.6 13.2 + - - +
32A PHE* 3.8 26.5 - - + -
34A LYS* 1.3 81.1 - - + +
36A CYS* 1.3 57.9 + - - +
38A LYS* 3.2 37.3 - - + +
39A LEU* 4.5 5.9 + - - +
47A CYS* 5.2 0.4 - - - -
14B GLU* 5.1 12.3 - - - +
18B LEU* 4.1 27.6 - - + -
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Residues in contact with CYS 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 PHE* 3.8 10.3 - - - -
33A ASP* 3.1 31.6 + - - +
34A LYS 3.0 0.8 - - - -
35A MET* 1.3 73.0 - - - +
37A SER* 1.3 54.5 + - - +
38A LYS 3.0 4.9 - - - -
39A LEU* 3.0 28.4 + - - +
44A SER* 2.9 20.1 + - - +
47A CYS* 2.0 62.8 - - + -
48A GLN* 4.3 5.4 - - + +
51A VAL* 4.2 0.4 - - - -
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Residues in contact with SER 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 ASP 3.0 12.4 + - - -
34A LYS* 3.0 18.4 + - - +
36A CYS* 1.3 70.3 - - - +
38A LYS* 1.3 56.5 + - - +
39A LEU 3.0 18.8 + - - +
40A PRO 4.5 0.6 - - - +
44A SER* 3.7 8.5 + - - -
48A GLN* 5.9 3.1 - - - -
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Residues in contact with LYS 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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34A LYS 3.5 3.3 + - - +
35A MET* 3.2 32.2 + - + +
36A CYS 3.0 0.6 - - - -
37A SER* 1.3 78.0 + - - +
39A LEU* 1.3 67.8 + - + +
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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