Contacts of the helix formed by residues 9 - 27 (chain A) in PDB entry 4QPQ
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 SER 9 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 1.3 82.0 - - - +
10A ASN* 1.3 64.5 + - - +
11A ASP* 3.7 10.3 + - - +
12A ALA* 3.1 24.0 + - - +
13A TYR* 3.0 19.7 + - - +
2D ALA* 4.9 0.2 - - - -
44D GLU* 3.5 16.3 + - - -
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Residues in contact with ASN 10 (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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8A ILE 3.9 0.2 + - - -
9A SER* 1.3 71.1 - - - +
11A ASP* 1.3 66.9 + - - +
13A TYR* 3.5 7.9 + - + +
14A GLU* 3.0 38.8 + - + +
2D ALA* 4.1 20.8 + - - +
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 3.2 10.1 + - - +
10A ASN* 1.3 76.8 - - - +
12A ALA* 1.3 59.1 + - - +
14A GLU* 3.3 12.8 + - - +
15A LYS* 3.0 48.2 + - - +
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.2 16.8 - - + -
9A SER* 3.1 21.1 + - - +
11A ASP* 1.3 78.6 - - - +
13A TYR* 1.3 62.5 + - - +
15A LYS* 3.3 4.3 + - - +
16A ILE* 3.0 31.3 + - + +
43D LEU* 5.7 1.8 - - + -
44D GLU* 4.3 16.4 - - + +
47D LEU* 4.1 22.8 - - + +
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Residues in contact with TYR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.8 9.8 - - + +
9A SER 3.0 16.6 + - - +
10A ASN* 3.6 6.7 - - + +
11A ASP 3.2 0.2 - - - -
12A ALA* 1.3 78.1 - - - +
14A GLU* 1.3 70.5 + - + +
16A ILE* 3.4 5.2 + - - +
17A ASN* 3.2 45.0 + - - -
35A PHE* 3.6 31.3 - + - -
2D ALA* 4.2 18.2 - - + -
3D LYS 5.5 2.0 - - - -
4D VAL* 4.1 16.4 - - + -
23Q C 5.6 1.9 + - - -
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Residues in contact with GLU 14 (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 ASN* 3.0 29.5 + - + +
11A ASP* 3.9 12.3 - - - +
13A TYR* 1.3 83.6 - - + +
15A LYS* 1.3 60.5 + - + +
17A ASN* 3.4 7.8 + - - +
18A ALA* 2.8 28.6 + - - +
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Residues in contact with LYS 15 (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 ASP* 3.0 34.1 + - - +
12A ALA* 3.7 7.6 - - - +
14A GLU* 1.3 76.0 - - + +
16A ILE* 1.3 64.2 + - - +
18A ALA* 3.3 9.2 + - - +
19A ILE* 3.1 28.2 + - - +
47D LEU* 4.3 21.3 - - + +
48D ARG* 6.3 1.2 - - - +
51D GLU* 3.8 23.9 + - - +
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.3 7.9 - - + -
12A ALA 3.0 18.2 + - - +
13A TYR 3.7 4.3 - - - +
14A GLU 3.3 0.2 - - - -
15A LYS* 1.3 74.3 - - - +
17A ASN* 1.3 63.1 + - - +
19A ILE* 3.1 19.2 + - + +
20A ILE* 3.1 14.3 + - + +
35A PHE* 3.6 37.5 - - + -
38A THR* 3.7 22.2 - - - +
39A ALA* 4.0 14.6 - - + +
42A LEU* 4.1 16.4 - - + -
43D LEU* 3.8 31.0 - - + -
47D LEU* 4.6 4.0 - - + -
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Residues in contact with ASN 17 (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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13A TYR* 3.2 47.1 + - - +
14A GLU* 3.7 9.7 - - - +
16A ILE* 1.3 78.4 - - - +
18A ALA* 1.3 63.1 + - - +
20A ILE* 3.3 11.3 + - - +
21A GLU* 3.0 39.8 + - + +
35A PHE* 3.4 22.6 - - - -
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Residues in contact with ALA 18 (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 GLU 2.8 18.1 + - - +
15A LYS* 3.3 11.9 - - - +
16A ILE 3.2 0.4 - - - -
17A ASN* 1.3 77.3 - - - +
19A ILE* 1.3 62.8 + - + +
21A GLU* 3.6 10.8 + - - +
22A LYS* 3.2 38.4 + - - +
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Residues in contact with ILE 19 (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 LYS 3.1 15.8 + - - +
16A ILE* 3.1 8.9 + - + +
18A ALA* 1.3 75.2 - - + +
20A ILE* 1.3 62.9 + - + +
22A LYS* 3.0 20.0 + - + +
23A ARG* 2.9 55.2 + - + +
38A THR* 5.2 10.3 - - - -
41A MET* 5.6 2.7 - - + -
42A LEU* 4.1 27.1 - - + -
47D LEU* 4.2 10.3 - - + -
50D HIS* 3.8 35.0 - - + +
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Residues in contact with ILE 20 (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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16A ILE 3.1 14.3 + - - +
17A ASN* 3.7 13.2 - - - +
19A ILE* 1.3 75.6 - - - +
21A GLU* 1.3 58.6 + - + +
23A ARG* 3.6 8.1 - - - +
24A ARG* 2.9 46.0 + - + +
33A VAL* 3.3 20.4 - - + +
34A SER 3.9 2.5 - - - +
35A PHE* 3.7 37.0 - - + +
38A THR* 3.6 31.4 - - + +
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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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17A ASN* 3.0 29.9 + - + +
18A ALA* 3.9 9.1 - - - +
19A ILE 3.2 0.2 - - - -
20A ILE* 1.3 78.1 - - + +
22A LYS* 1.3 59.8 + - + +
24A ARG* 4.1 6.3 - - - +
25A GLN* 3.2 31.2 + - - +
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Residues in contact with LYS 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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18A ALA* 3.2 27.7 + - - +
19A ILE* 3.0 18.5 + - + +
21A GLU* 1.3 76.9 - - + +
23A ARG* 1.3 59.8 + - + +
25A GLN* 3.1 8.6 + - - +
26A GLU* 2.8 45.2 + - - +
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Residues in contact with ARG 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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19A ILE* 2.9 35.7 + - + +
20A ILE* 3.2 8.9 + - - +
22A LYS* 1.3 77.9 - - - +
24A ARG* 1.3 53.6 + - - +
26A GLU* 4.1 17.2 + - - -
27A GLY 2.7 30.8 + - - -
28A ALA* 3.2 10.1 - - + +
33A VAL* 3.9 28.0 - - + +
38A THR* 5.3 5.3 - - + +
41A MET* 3.9 20.4 - - - +
50D HIS* 3.6 28.0 - - - -
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Residues in contact with ARG 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 ILE* 2.9 29.2 + - + +
21A GLU* 4.1 6.7 - - - +
23A ARG* 1.3 75.3 - - - +
25A GLN* 1.3 57.5 + - - +
27A GLY 3.1 12.9 - - - +
28A ALA* 3.7 12.9 + - + +
30A GLU* 4.1 11.9 - - - +
31A LYS* 3.1 35.0 - - - +
33A VAL* 3.7 28.1 + - + +
34A SER* 5.8 1.2 - - - +
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Residues in contact with GLN 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 22.6 + - - +
22A LYS* 3.1 8.5 + - - +
23A ARG 3.0 0.4 - - - -
24A ARG* 1.3 78.5 - - - +
26A GLU* 1.3 66.9 + - + +
27A GLY 3.6 2.8 - - - +
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Residues in contact with GLU 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 LYS* 2.8 28.3 + - + +
23A ARG* 3.9 22.8 + - - +
25A GLN* 1.3 76.8 - - + +
27A GLY* 1.3 66.2 + - - +
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Residues in contact with GLY 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 ARG 2.7 13.1 + - - -
24A ARG 3.1 13.7 - - - +
25A GLN 3.6 3.5 - - - +
26A GLU* 1.3 82.0 - - - +
28A ALA* 1.3 61.5 + - - -
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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