Contacts of the helix formed by residues 26 - 48 (chain A) in PDB entry 4U7Y
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 26 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 3.2 40.7 + - - +
24A ALA* 3.3 20.1 - - - +
25A GLY* 1.3 75.1 - - - +
27A TYR* 1.3 59.6 + - - +
28A GLU 3.3 2.0 - - - -
29A GLU* 3.5 8.0 + - + +
30A ALA* 2.9 27.7 + - - +
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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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22A ASP* 3.3 39.6 + - - -
25A GLY* 3.1 21.8 + - - +
26A ASN* 1.3 72.0 - - - +
28A GLU* 1.3 61.1 + - - +
30A ALA* 4.1 2.0 - - - -
31A LEU* 2.9 31.4 + - - +
68A ARG* 3.9 13.2 + - - -
72A LEU* 3.5 25.7 - - + +
75A TYR* 3.4 46.0 - + + -
76A LEU* 4.0 17.6 - - + +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN 3.3 0.6 - - - -
27A TYR* 1.3 80.3 - - - +
29A GLU* 1.3 61.4 + - - +
31A LEU* 3.5 4.4 + - - +
32A GLN* 3.4 18.7 + - - +
76A LEU* 3.8 25.5 - - + +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.3 26.2 - - - +
26A ASN* 3.5 10.7 + - + +
27A TYR 3.4 0.2 - - - -
28A GLU* 1.3 75.6 - - - +
30A ALA* 1.3 65.9 - - - +
32A GLN* 3.2 8.0 + - + +
33A LEU* 3.1 39.3 + - + +
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Residues in contact with ALA 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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18A ALA 3.8 5.4 - - - +
21A GLU* 4.1 8.2 - - - +
22A ASP* 3.6 31.4 - - + +
26A ASN 2.9 18.8 + - - +
27A TYR* 3.6 5.8 - - - +
28A GLU 3.3 0.2 - - - -
29A GLU* 1.3 75.6 - - - +
31A LEU* 1.3 57.6 + - - +
33A LEU* 3.1 6.7 + - - +
34A TYR* 2.8 36.0 + - + -
72A LEU* 3.7 11.4 - - + -
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Residues in contact with LEU 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 19.1 + - - +
28A GLU 3.7 5.2 - - - +
30A ALA* 1.3 75.3 - - - +
32A GLN* 1.3 64.1 + - - +
34A TYR* 3.4 4.5 + - - +
35A GLN* 3.0 25.3 + - + +
69A ALA* 3.2 39.5 - - + +
72A LEU* 3.9 11.9 - - + +
73A LYS* 4.4 15.9 - - + +
76A LEU* 3.7 21.8 - - + -
331B LEU* 4.5 13.5 - - + -
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Residues in contact with GLN 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 GLU 3.4 9.1 + - - +
29A GLU* 3.2 10.6 + - + +
31A LEU* 1.3 80.0 - - - +
33A LEU* 1.3 64.0 + - + +
35A GLN* 3.3 9.4 + - - +
36A HIS* 3.0 42.8 + - + +
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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
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14A LEU* 3.8 33.5 - - + +
17A LYS* 3.7 23.1 - - + +
18A ALA* 3.5 15.3 - - + -
21A GLU* 3.7 31.2 - - + -
29A GLU* 3.1 23.3 + - + +
30A ALA 3.5 5.4 - - - +
32A GLN* 1.3 74.5 - - + +
34A TYR* 1.3 64.5 + - - +
36A HIS* 3.5 5.5 + - - +
37A ALA* 3.0 23.9 + - - +
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Residues in contact with TYR 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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15A ALA* 4.7 2.5 - - - -
18A ALA* 3.5 22.2 - - + -
19A ALA* 3.6 13.4 - - + +
22A ASP* 2.6 44.7 + - + +
30A ALA* 2.8 35.2 + - + +
31A LEU* 3.7 7.9 - - - +
33A LEU* 1.3 71.4 - - - +
35A GLN* 1.3 57.6 + - - +
37A ALA* 3.2 6.4 + - - +
38A VAL* 2.9 33.6 + - - +
65A TYR* 3.8 45.2 - + + +
68A ARG* 3.8 19.6 - - + +
69A ALA* 3.9 18.2 - - + -
72A LEU* 4.3 6.1 - - + -
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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 LEU* 3.0 22.3 + - - +
32A GLN* 3.6 9.3 - - - +
34A TYR* 1.3 77.6 - - - +
36A HIS* 1.3 77.4 + - + +
38A VAL* 3.3 5.2 + - - +
39A GLN 3.0 21.3 + - - -
69A ALA* 5.3 0.4 - - - -
328B PHE* 3.2 19.2 - - + -
331B LEU* 3.1 51.0 - - + +
332B LYS* 3.7 23.5 - - - +
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Residues in contact with HIS 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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14A LEU* 3.7 21.3 - - + +
32A GLN* 3.0 30.6 + - + +
33A LEU* 4.1 4.2 - - - +
35A GLN* 1.3 96.4 + - + +
37A ALA* 1.3 66.4 + - - +
39A GLN* 3.3 23.0 + - - +
40A TYR* 3.1 31.7 + + + -
328B PHE* 6.1 0.2 - + - -
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Residues in contact with ALA 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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11A ALA* 3.6 21.7 - - - +
14A LEU* 3.8 9.5 - - + +
15A ALA* 3.7 22.0 - - + +
33A LEU 3.0 15.0 + - - +
34A TYR* 3.3 10.5 - - - +
36A HIS* 1.3 77.1 - - - +
38A VAL* 1.3 63.1 + - - +
40A TYR* 3.0 4.9 + - - +
41A PHE* 2.9 31.2 + - + -
65A TYR* 4.9 4.0 - - + -
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Residues in contact with VAL 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 TYR 2.9 18.3 + - - +
35A GLN* 3.6 8.3 - - - +
36A HIS 3.3 0.2 - - - -
37A ALA* 1.3 74.6 - - - +
39A GLN* 1.3 56.3 + - - +
41A PHE* 3.2 7.2 + - - +
42A LEU* 2.9 38.7 + - + +
62A CYS* 4.1 12.6 - - - +
65A TYR* 3.6 27.6 - - + -
66A LEU* 3.7 38.6 - - + +
69A ALA* 6.0 0.2 - - + -
328B PHE* 3.7 24.0 - - + -
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Residues in contact with GLN 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 GLN 3.0 9.1 + - - +
36A HIS* 3.4 26.5 - - - +
37A ALA 3.2 0.2 - - - -
38A VAL* 1.3 77.7 - - - +
40A TYR* 1.3 79.6 + - + +
42A LEU* 4.0 3.9 - - - +
43A HIS* 3.3 21.8 + - - +
328B PHE* 3.4 35.2 - - + -
332B LYS* 5.7 4.0 - - - +
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Residues in contact with TYR 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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7A ASN* 3.5 42.8 - - + +
10A LYS* 4.1 22.7 - - + +
11A ALA* 3.6 23.6 - - + -
14A LEU* 3.9 13.0 - - + -
36A HIS* 3.1 23.8 + + + +
37A ALA 3.0 4.6 + - - +
39A GLN* 1.3 96.6 - - - +
41A PHE* 1.3 59.0 + - - +
43A HIS* 3.3 8.0 + + + +
44A VAL* 3.0 34.3 + - - +
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.6 21.8 - - + -
11A ALA* 3.6 38.1 - - + -
12A ILE* 4.1 12.6 - - + -
15A ALA* 4.3 2.0 - - + -
37A ALA* 2.9 26.4 + - + +
38A VAL* 3.7 3.1 - - - +
40A TYR* 1.3 75.8 - - - +
42A LEU* 1.3 58.9 + - - +
44A VAL* 3.5 3.2 + - - +
45A VAL* 3.0 30.0 + - - +
58A ILE* 3.5 28.8 - - + +
61A LYS* 4.6 16.4 - - + -
62A CYS* 3.5 22.9 - - - -
65A TYR* 3.6 35.9 - + - -
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Residues in contact with LEU 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 VAL* 2.9 19.8 + - + +
39A GLN* 4.0 3.8 - - - +
41A PHE* 1.3 75.3 - - - +
43A HIS* 1.3 65.4 + - - +
45A VAL* 3.3 2.8 + - + +
46A LYS* 3.0 41.5 + - - +
62A CYS* 3.9 18.8 - - - -
321B PHE* 4.3 19.7 - - + -
324B LEU* 4.0 20.9 - - + +
325B SER* 4.0 23.8 - - - +
328B PHE* 3.8 39.9 - - + -
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Residues in contact with HIS 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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7A ASN* 4.0 28.0 + - + -
39A GLN 3.3 17.1 + - - +
40A TYR* 3.6 9.6 - + + +
41A PHE 3.3 0.2 - - - -
42A LEU* 1.3 80.4 - - - +
44A VAL* 1.3 60.5 + - - +
46A LYS* 4.9 2.9 - - - +
47A TYR* 2.9 62.9 + + + +
48A GLU* 3.9 6.0 + - + +
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Residues in contact with VAL 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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7A ASN* 3.8 15.0 - - + -
8A LEU* 3.5 48.7 - - + +
40A TYR 3.0 21.9 + - - +
41A PHE* 3.7 5.4 - - - +
43A HIS* 1.3 76.8 - - - +
45A VAL* 1.3 60.7 + - - +
48A GLU* 2.9 51.9 + - + +
50A GLN* 3.8 12.1 - - - +
58A ILE* 3.9 17.5 - - + -
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Residues in contact with VAL 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 PHE 3.0 16.7 + - - +
42A LEU* 3.4 15.7 - - + +
44A VAL* 1.3 77.8 - - - +
46A LYS* 1.3 70.3 + - + +
48A GLU 4.0 0.2 - - - +
50A GLN* 3.2 23.5 + - - +
55A LYS* 3.9 33.9 - - + -
58A ILE* 3.9 16.2 - - + -
321B PHE* 3.6 52.0 - - + -
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Residues in contact with LYS 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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42A LEU* 3.0 29.6 + - + +
43A HIS* 4.9 1.3 - - - +
45A VAL* 1.3 90.0 - - + +
47A TYR* 1.3 100.5 + - + +
48A GLU 3.7 1.4 - - - +
321B PHE* 4.9 13.7 - - + -
325B SER* 3.2 27.1 + - - +
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Residues in contact with TYR 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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43A HIS* 2.9 46.4 + + + +
46A LYS* 1.3 114.7 + - + +
48A GLU* 1.3 64.4 + - + +
49A ALA 4.3 0.2 + - - -
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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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5A SER* 2.7 34.3 + - - -
6A PRO* 5.7 0.5 - - - +
7A ASN* 3.0 31.4 + - - +
43A HIS* 4.6 7.0 + - + +
44A VAL* 2.9 36.9 + - + +
45A VAL 4.0 1.9 - - - +
46A LYS 4.6 1.2 - - - +
47A TYR* 1.3 83.8 + - + +
49A ALA* 1.3 62.0 + - - +
50A GLN* 3.0 26.4 + - - +
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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