Contacts of the helix formed by residues 20 - 42 (chain A) in PDB entry 1ISA
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 ALA 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LYS* 3.6 26.9 + - + +
12A ASP* 4.1 19.9 - - + +
15A ALA* 4.9 3.6 - - + +
18A ILE 4.0 0.2 + - - -
19A SER* 1.3 72.8 - - - +
21A GLU* 1.3 58.2 + - - +
23A ILE* 3.2 4.3 + - - +
24A GLU* 2.9 30.0 + - - +
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Residues in contact with GLU 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 SER* 3.2 10.5 + - - +
20A ALA* 1.3 76.3 - - - +
22A THR* 1.3 64.4 + - - +
24A GLU* 3.2 14.4 + - - +
25A TYR* 3.2 40.3 + - + -
164A ILE* 3.8 17.4 - - + +
167B ARG* 2.9 36.4 + - - -
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.8 15.5 - - + -
19A SER* 3.0 13.1 + - - -
21A GLU* 1.3 78.5 - - - +
23A ILE* 1.3 58.3 + - - +
25A TYR* 3.4 0.9 + - - +
26A HIS* 2.9 39.1 + - + +
77A TRP* 5.9 0.4 - - + -
160A HIS 4.4 8.1 - - - +
161A ALA 3.6 25.0 + - - +
162A TYR* 5.5 0.6 - - - -
164A ILE* 3.6 20.9 + - + +
165A ASP* 2.8 30.8 + - - +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.3 34.5 - - + -
9A TYR* 5.9 2.0 - - + -
11A LYS* 3.4 41.7 - - + +
14A LEU* 4.7 11.7 - - + -
18A ILE* 3.9 19.3 - - + +
19A SER 3.1 16.0 + - - +
20A ALA 3.2 4.0 + - - +
22A THR* 1.3 76.8 - - - +
24A GLU* 1.3 59.8 + - - +
26A HIS* 4.4 3.4 - - - -
27A TYR* 2.8 47.7 + - + +
28A GLY 3.4 0.2 + - - -
77A TRP* 4.5 16.4 - - + -
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.4 5.8 - - + -
20A ALA 2.9 16.9 + - - +
21A GLU* 3.2 16.2 + - - +
23A ILE* 1.3 77.7 - - - +
25A TYR* 1.3 75.5 + - + +
28A GLY* 3.1 26.4 + - - +
29A LYS* 3.6 11.6 + - - +
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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 GLU* 3.2 48.1 + - + +
22A THR 4.1 1.6 - - - +
24A GLU* 1.3 89.1 + - + +
26A HIS* 1.3 60.1 + - - +
29A LYS* 2.9 31.7 + - + +
30A HIS* 2.9 29.7 + - + -
164A ILE* 4.0 15.0 - - + -
163B TYR* 3.8 14.1 - - - +
167B ARG* 3.6 37.1 + - + +
168B ASN* 3.5 26.5 - - - -
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Residues in contact with HIS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 6.2 0.2 - - - +
22A THR* 2.9 29.3 + - + +
25A TYR* 1.3 71.5 - - - +
27A TYR* 1.3 57.6 + - - +
30A HIS* 3.3 13.5 - - + +
31A HIS* 2.9 26.3 + - - +
73A HIS* 3.1 14.7 + + - -
76A TYR* 3.8 19.7 + + - -
77A TRP* 3.6 18.7 - + + -
156A ASP* 2.8 16.3 + - - -
160A HIS* 3.1 17.2 + + - +
161A ALA* 3.6 29.7 + - + -
193A FE2 2.2 27.8 - - - -
163B TYR* 5.1 0.2 + - - -
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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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4A LEU* 3.6 33.6 + - + +
5A PRO 2.7 29.2 + - - -
6A ALA* 3.5 10.2 - - - -
7A LEU* 3.7 34.9 + - + -
11A LYS* 5.7 5.4 - - + -
23A ILE* 2.8 30.4 + - + +
24A GLU* 6.3 0.2 - - - -
26A HIS* 1.3 72.6 - - - +
28A GLY* 1.3 68.4 + - - +
29A LYS 3.4 0.2 + - - -
31A HIS* 3.5 12.4 - + - +
32A GLN* 3.3 23.6 + - - +
77A TRP* 3.6 33.8 - + + -
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Residues in contact with GLY 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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4A LEU* 5.4 1.8 - - - -
23A ILE 3.4 1.0 + - - -
24A GLU* 3.1 19.4 + - - +
27A TYR* 1.3 88.0 - - - +
29A LYS* 1.3 63.0 + - - +
32A GLN* 3.5 17.0 - - - +
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Residues in contact with LYS 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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24A GLU* 3.6 9.0 + - - +
25A TYR* 2.9 52.0 + - + +
28A GLY* 1.3 83.1 - - - +
30A HIS* 1.3 59.1 + - - +
31A HIS 3.6 0.2 - - - -
32A GLN* 3.7 1.7 + - - +
33A THR* 2.9 35.7 + - - +
168B ASN* 3.8 30.9 - - + +
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Residues in contact with HIS 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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25A TYR 2.9 30.6 + - - -
26A HIS* 3.3 19.5 - - + +
29A LYS* 1.3 69.7 - - - +
31A HIS* 1.3 65.3 + - - +
33A THR* 3.1 15.4 + - - -
34A TYR* 3.2 33.6 + - + -
160A HIS* 3.6 33.2 + + + +
159B GLU* 3.6 12.5 + - - -
163B TYR* 2.7 31.8 + + - -
168B ASN* 3.5 26.1 - - + +
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Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 23.8 - - + +
5A PRO* 4.6 3.5 - - + +
26A HIS 2.9 16.6 + - - +
27A TYR* 3.5 18.9 + + - +
30A HIS* 1.3 72.0 - - - +
32A GLN* 1.3 61.9 + - - +
34A TYR* 3.3 17.2 + + - +
35A VAL* 3.3 13.1 + - + +
69A GLN 4.5 0.2 - - - -
70A VAL* 3.1 34.4 + - - +
73A HIS* 3.6 19.9 - + + -
74A THR* 3.2 32.5 + - - -
77A TRP* 3.1 25.9 + + - +
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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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4A LEU* 3.6 29.4 - - + +
27A TYR 3.3 7.0 + - - +
28A GLY 3.5 24.9 - - - +
29A LYS* 3.8 2.5 - - - +
31A HIS* 1.3 77.4 - - - +
33A THR* 1.3 63.3 + - - +
35A VAL* 3.1 16.5 + - - +
36A THR* 3.0 36.0 + - - +
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Residues in contact with THR 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 LYS* 2.9 21.5 + - - +
30A HIS* 3.1 6.9 + - - +
32A GLN* 1.3 76.1 - - - +
34A TYR* 1.3 61.9 + - + +
36A THR* 3.3 6.1 + - - -
37A ASN* 2.8 50.8 + - - +
168B ASN* 5.6 1.2 + - - -
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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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30A HIS* 3.2 36.2 + - + -
31A HIS* 3.3 11.2 + + - +
33A THR* 1.3 78.8 - - + +
35A VAL* 1.3 56.8 + - - +
37A ASN* 3.9 2.2 - - - +
38A LEU* 3.0 30.8 + - - +
66A ASN* 3.5 28.2 - - - +
69A GLN* 3.1 44.1 + - + -
70A VAL* 3.6 17.7 - - + +
73A HIS* 3.5 25.8 - + - -
158A TRP* 3.7 19.1 - - - -
160A HIS* 4.1 7.3 - + - -
118B PHE* 4.1 15.7 - + - -
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Residues in contact with VAL 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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2A PHE* 3.4 35.8 - - + +
3A GLU* 4.5 1.6 - - - +
4A LEU* 4.1 30.3 - - + +
31A HIS* 3.6 12.8 - - + +
32A GLN* 3.1 17.8 + - - +
34A TYR* 1.3 74.0 - - - +
36A THR* 1.3 65.5 + - - +
38A LEU* 3.3 4.2 + - - +
39A ASN* 2.9 28.7 + - - +
70A VAL* 3.6 29.2 - - + -
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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 GLN* 3.0 30.5 + - - +
33A THR* 3.7 7.2 - - - +
35A VAL* 1.3 75.3 - - - +
37A ASN* 1.3 67.6 + - - +
39A ASN* 3.4 7.5 + - - +
40A ASN* 3.1 41.8 + - - +
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Residues in contact with ASN 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 THR* 2.8 38.7 + - - +
34A TYR* 5.3 0.3 - - - -
36A THR* 1.3 79.6 - - - +
38A LEU* 1.3 56.4 + - - +
40A ASN* 3.4 10.3 + - - +
41A LEU* 2.9 36.9 + - + +
66A ASN* 3.2 29.9 + - - +
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Residues in contact with LEU 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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2A PHE* 3.8 32.8 - - + -
34A TYR 3.0 18.9 + - - +
35A VAL* 3.7 3.6 - - - +
37A ASN* 1.3 73.9 - - - +
39A ASN* 1.3 65.5 + - - +
41A LEU* 3.1 4.4 + - + +
42A ILE* 3.1 45.7 + - + +
52A LEU* 3.8 22.7 - - + -
55A ILE* 4.8 3.8 - - + -
63A VAL* 3.9 12.3 - - + +
66A ASN* 4.1 10.0 - - + +
67A ALA* 3.9 31.2 - - + +
70A VAL* 4.4 9.6 - - + -
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Residues in contact with ASN 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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1A SER* 3.1 20.4 + - - +
2A PHE* 2.8 56.0 + - - +
35A VAL* 2.9 24.7 + - - +
36A THR* 3.8 7.1 - - - +
38A LEU* 1.3 75.7 - - - +
40A ASN* 1.3 63.4 + - - +
42A ILE* 3.8 6.4 - - - +
43A LYS* 3.4 26.9 + - - +
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Residues in contact with ASN 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 THR* 3.1 33.9 + - - +
37A ASN* 3.7 10.2 - - - +
39A ASN* 1.3 79.6 - - - +
41A LEU* 1.3 64.6 + - + +
42A ILE 3.5 0.3 + - - -
43A LYS* 4.0 14.9 + - - +
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Residues in contact with LEU 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 ASN* 2.9 22.5 + - + +
38A LEU* 3.1 4.9 + - - +
40A ASN* 1.3 80.9 - - + +
42A ILE* 1.3 59.2 + - + +
43A LYS 3.8 1.0 + - - +
45A THR* 3.7 13.0 - - - +
62A GLY* 3.7 24.0 - - - +
63A VAL* 4.1 20.7 - - + +
66A ASN* 3.6 25.6 - - + +
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Residues in contact with ILE 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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1A SER 4.6 10.8 - - - +
2A PHE* 3.7 35.7 - - + -
38A LEU* 3.1 34.3 + - + +
39A ASN* 3.8 7.6 - - - +
41A LEU* 1.3 76.3 - - - +
43A LYS* 1.3 70.3 + - - +
44A GLY 3.1 0.5 + - - -
45A THR* 2.6 31.6 + - - +
47A PHE* 3.8 21.3 - - + -
48A GLU* 3.5 24.8 - - + +
55A ILE* 4.4 7.2 - - + -
63A VAL* 4.3 13.7 - - + -
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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
------------------------------------------------------------
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