Contacts of the helix formed by residues 22 - 45 (chain A) in PDB entry 2QNU
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 PRO 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLY 4.4 3.1 - - - +
21A LEU* 1.3 89.3 - - + +
23A ASN* 1.3 60.1 + - - +
24A THR* 3.4 22.9 - - + +
25A PHE* 3.0 20.4 + - + +
26A VAL* 3.0 13.1 + - - +
70A GLU* 5.4 1.1 - - - +
94A LEU* 3.7 31.9 - - + -
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Residues in contact with ASN 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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21A LEU 4.0 0.2 + - - -
22A PRO* 1.3 69.2 - - - +
24A THR* 1.3 63.2 + - + +
25A PHE 3.1 2.0 - - - -
26A VAL* 4.1 11.3 - - - +
27A GLU* 2.9 67.6 + - - +
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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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22A PRO* 3.4 21.9 - - + +
23A ASN* 1.3 78.2 - - + +
25A PHE* 1.3 56.7 + - - +
28A PRO* 3.3 17.2 - - - +
67A LEU 3.2 17.6 - - - +
68A GLY* 3.6 11.8 + - - -
69A GLY 5.9 0.2 - - - -
70A GLU* 4.3 11.2 + - - -
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Residues in contact with PHE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 5.2 0.9 - - + -
21A LEU* 3.7 34.3 - - + -
22A PRO* 3.0 14.4 + - + +
24A THR* 1.3 82.4 + - - +
26A VAL* 1.3 66.1 + - + +
27A GLU 3.4 0.7 - - - -
28A PRO* 3.3 4.4 - - - +
29A TRP* 3.0 71.6 + + - +
60A PHE* 5.2 0.4 - + - -
67A LEU* 3.6 39.1 - - + +
72A VAL* 3.6 25.6 - - + -
90A THR* 4.7 1.8 - - + -
92A ALA* 4.0 17.9 - - + -
94A LEU* 4.1 17.0 - - + -
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Residues in contact with VAL 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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7A TYR* 3.6 39.7 - - + +
18A SER* 4.1 11.9 - - - +
21A LEU* 3.8 31.4 - - + +
22A PRO 3.0 18.8 + - - +
23A ASN* 4.3 11.7 - - - +
25A PHE* 1.3 80.2 - - + +
27A GLU* 1.3 59.6 + - - +
29A TRP* 4.2 2.9 - - - -
30A ASP* 2.7 40.2 + - + +
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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 ASN* 2.9 40.8 + - - +
26A VAL* 1.3 77.6 - - - +
28A PRO* 1.3 72.0 - - + +
30A ASP* 3.9 4.6 - - - +
31A ALA* 3.1 24.7 + - + +
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Residues in contact with PRO 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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23A ASN 3.5 2.0 - - - +
24A THR* 3.3 26.0 - - - +
25A PHE 3.3 9.0 - - - +
27A GLU* 1.3 101.3 - - + +
29A TRP* 1.3 58.5 + - - -
31A ALA* 3.8 6.3 - - + +
32A TRP* 3.0 24.3 + - - +
66A LEU 5.0 3.1 - - - +
67A LEU* 3.9 25.2 - - + +
68A GLY 4.8 0.9 - - - +
201A LEU* 5.1 2.1 - - + +
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Residues in contact with TRP 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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7A TYR* 4.0 20.3 - + - -
25A PHE* 3.0 44.9 + + + +
26A VAL 3.1 2.9 + - - +
28A PRO* 1.3 74.4 - - - +
30A ASP* 1.3 57.2 + - - +
32A TRP* 3.1 35.8 + + - +
33A LEU* 2.8 47.8 + - + +
60A PHE* 3.9 22.9 - + - -
62A ILE* 3.8 22.9 - - + -
67A LEU* 3.6 23.7 - - + +
76A VAL* 4.4 8.3 - - + -
90A THR* 3.2 44.2 + - + +
183A TRP* 4.1 9.6 - + - -
201A LEU* 5.3 1.3 - - + -
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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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7A TYR* 2.5 37.9 + - + +
16A PHE* 4.1 8.2 - - - -
26A VAL* 2.7 23.6 + - + +
27A GLU* 3.9 4.5 - - - +
29A TRP* 1.3 73.3 - - - +
31A ALA* 1.3 59.5 + - - +
32A TRP 3.2 0.3 + - - -
33A LEU* 3.3 2.2 + - - +
34A ALA* 2.8 36.7 + - - +
87A PHE* 3.4 20.2 - - - -
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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* 3.1 20.3 + - + +
28A PRO* 3.8 7.2 - - + +
29A TRP 3.3 0.2 - - - -
30A ASP* 1.3 78.9 + - - +
32A TRP* 1.3 62.1 + - - +
34A ALA* 3.8 5.4 - - - +
35A SER* 3.0 30.4 + - - +
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Residues in contact with TRP 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 PRO 3.0 19.2 + - - +
29A TRP* 3.1 24.9 + + + +
31A ALA* 1.3 75.8 - - - +
33A LEU* 1.3 96.6 + - + +
35A SER* 3.5 5.7 + - - -
36A GLY* 3.1 19.5 + - - -
76A VAL* 6.1 0.9 - - + -
183A TRP* 3.5 30.1 - + - -
201A LEU* 3.9 28.3 - - + -
202A PRO* 2.7 57.9 + - + +
203A PRO 5.0 1.4 - - - -
204A ALA* 5.5 3.9 - - - +
207A PHE* 4.1 15.6 - + - +
210A PHE* 3.9 17.5 - + - -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 5.4 0.9 - - + -
29A TRP* 2.8 46.5 + - + +
30A ASP* 3.7 2.9 - - - +
32A TRP* 1.3 104.1 - - + +
34A ALA* 1.3 52.4 + - - +
37A MSE 2.6 42.6 + - + +
76A VAL* 4.7 6.5 - - + -
87A PHE* 3.8 29.4 - - + -
88A PRO* 4.2 24.0 - - + +
90A THR* 4.4 4.3 - - - +
207A PHE* 3.8 21.7 - - + -
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Residues in contact with ALA 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* 2.8 28.2 + - - +
31A ALA* 3.8 6.3 - - - +
33A LEU* 1.3 74.4 - - - +
35A SER* 1.3 60.2 + - - +
37A MSE 3.5 4.1 + - - +
38A ARG* 3.1 49.9 + - - +
87A PHE* 4.1 16.1 - - + -
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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 ALA 3.0 18.7 + - - -
32A TRP* 3.7 7.2 - - - -
34A ALA* 1.3 76.1 - - - +
36A GLY* 1.3 57.9 + - - +
38A ARG* 3.8 18.4 + - - +
39A ALA* 3.0 28.9 + - - +
204A ALA* 3.5 16.8 - - - +
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Residues in contact with GLY 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 TRP* 3.1 9.6 + - - -
33A LEU 3.8 0.4 - - - -
35A SER* 1.3 76.4 - - - +
37A MSE 1.3 67.3 + - - +
40A SER* 3.0 24.8 + - - -
204A ALA* 4.0 10.7 - - - +
207A PHE* 3.3 38.9 - - - +
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Residues in contact with MSE 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 LEU 2.6 32.1 + - - +
34A ALA* 3.7 6.7 - - - +
36A GLY* 1.3 69.1 - - - +
38A ARG* 1.3 64.6 + - + +
40A SER* 3.0 17.8 + - - -
41A GLN* 3.1 25.0 + - - +
48A TRP* 3.7 28.0 - - + -
52A TYR* 3.7 22.7 - - + -
86A TYR* 3.3 34.8 - - + +
87A PHE* 3.8 14.8 - - + -
88A PRO* 4.0 15.9 - - + -
207A PHE* 3.9 19.8 - - + -
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Residues in contact with ARG 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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31A ALA 5.2 0.2 + - - -
34A ALA* 3.1 39.6 + - - +
35A SER* 3.8 28.2 + - - +
37A MSE 1.3 74.1 - - + +
39A ALA* 1.3 64.5 + - - +
41A GLN* 3.4 14.0 + - - +
42A ASP* 3.0 31.8 + - - +
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Residues in contact with ALA 39 (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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35A SER 3.0 21.1 + - - +
36A GLY 4.1 0.2 - - - +
38A ARG* 1.3 74.4 - - - +
40A SER* 1.3 63.0 + - - +
42A ASP* 3.2 9.4 + - - +
43A GLU* 3.0 23.8 + - - +
204A ALA* 3.5 31.4 - - + +
205A PRO* 4.1 9.4 - - + -
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Residues in contact with SER 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 GLY 3.0 15.2 + - - -
37A MSE 3.0 13.5 + - - -
39A ALA* 1.3 78.1 - - - +
41A GLN* 1.3 49.7 + - - +
43A GLU* 3.4 9.6 + - - -
44A LEU* 2.8 40.9 + - - +
48A TRP* 2.9 28.3 + - - -
204A ALA 4.9 0.6 + - - -
207A PHE* 3.7 19.0 - - - -
208A GLY* 4.0 20.4 - - - +
211A LEU* 3.9 4.0 - - - +
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Residues in contact with GLN 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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37A MSE 3.1 31.4 + - - +
38A ARG* 3.6 17.6 - - - +
40A SER* 1.3 72.7 + - - +
42A ASP* 1.3 63.1 + - - +
45A GLY* 2.8 31.5 + - - -
48A TRP* 3.4 55.6 - - + -
86A TYR* 5.4 2.0 + - - +
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Residues in contact with ASP 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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38A ARG* 3.0 18.1 + - - +
39A ALA* 3.5 10.1 - - - +
41A GLN* 1.3 79.8 - - - +
43A GLU* 1.3 63.2 + - - +
45A GLY* 4.1 4.3 + - - -
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Residues in contact with GLU 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 ALA 3.0 15.1 + - - +
40A SER* 3.6 6.7 - - - +
42A ASP* 1.3 79.1 - - - +
44A LEU* 1.3 75.4 + - + +
205A PRO* 4.2 16.8 - - - +
208A GLY* 4.2 20.6 + - - -
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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 SER 2.8 20.9 + - - +
43A GLU* 1.3 93.6 - - + +
45A GLY* 1.3 65.0 + - - +
46A ALA 3.1 1.2 + - - -
47A ALA* 3.1 26.1 + - + +
48A TRP* 3.7 27.8 - - + +
51A ALA* 4.3 10.3 - - + -
208A GLY* 4.8 9.0 - - - -
211A LEU* 4.5 11.4 - - + -
212A THR* 3.9 35.9 - - + +
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Residues in contact with GLY 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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41A GLN 2.8 19.6 + - - +
42A ASP 4.1 3.6 + - - -
43A GLU 3.4 1.8 - - - -
44A LEU* 1.3 75.2 - - - +
46A ALA* 1.3 58.9 + - - -
48A TRP* 3.0 24.3 + - - +
49A LEU 4.7 0.3 + - - -
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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