Contacts of the helix formed by residues 16 - 30 (chain A) in PDB entry 1QRJ
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 GLN 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU 5.3 6.4 + - - +
14A HIS 3.9 0.4 - - - +
15A MET* 1.3 78.4 + - - +
17A MET* 1.3 65.5 + - - +
18A LYS* 3.3 43.1 + - + +
19A ASP* 2.4 44.3 + - - +
20A LEU* 3.4 12.0 + - - +
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Residues in contact with MET 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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16A GLN* 1.3 75.7 - - - +
18A LYS* 1.3 54.7 + - - +
19A ASP 2.8 4.3 - - - -
20A LEU* 2.6 35.8 + - + +
21A GLN* 2.8 26.1 + - + +
57A ASP* 3.5 27.1 - - - +
61A TYR* 4.6 14.4 - - + -
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Residues in contact with LYS 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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16A GLN* 3.3 32.0 + - + +
17A MET* 1.3 79.2 - - - +
19A ASP* 1.3 74.9 + - - +
21A GLN* 3.2 13.8 + - - +
22A ALA* 2.9 30.1 + - - +
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Residues in contact with ASP 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 MET* 3.3 20.2 + - + -
16A GLN* 2.4 51.8 + - - +
17A MET 2.8 0.2 - - - -
18A LYS* 1.3 102.6 + - - +
20A LEU* 1.3 62.7 + - - +
22A ALA* 3.4 7.1 + - - +
23A ILE* 3.2 28.8 + - - +
48A PHE* 3.9 21.9 - - + +
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Residues in contact with LEU 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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15A MET* 2.9 48.0 - - + +
16A GLN 3.6 12.6 - - - +
17A MET* 2.6 22.8 + - + +
19A ASP* 1.3 73.8 - - - +
21A GLN* 1.3 57.6 + - - +
23A ILE* 3.3 6.4 + - + +
24A LYS 2.9 23.0 + - - -
54A ASP* 5.3 1.1 - - + +
57A ASP* 3.4 26.9 - - + +
58A LEU* 3.5 33.0 - - + -
61A TYR* 2.8 35.2 + - + -
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Residues in contact with GLN 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 MET* 2.8 29.8 + - + +
18A LYS* 3.4 16.4 - - - +
20A LEU* 1.3 75.9 - - - +
22A ALA* 1.3 64.3 + - - +
24A LYS* 3.3 20.6 + - - +
25A GLN* 3.2 22.6 + - - +
61A TYR* 2.9 31.6 + - - -
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Residues in contact with ALA 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 LYS 2.9 15.5 + - - +
19A ASP* 3.6 7.9 - - - +
20A LEU 3.3 0.2 - - - -
21A GLN* 1.3 74.8 - - - +
23A ILE* 1.3 66.3 + - + +
25A GLN* 2.9 22.7 + - - +
26A GLU* 3.0 20.7 + - - +
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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
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15A MET* 3.8 16.8 - - + -
19A ASP 3.2 18.1 + - - +
20A LEU* 3.6 9.0 - - + +
21A GLN 3.3 0.2 - - - -
22A ALA* 1.3 77.6 - - + +
24A LYS* 1.3 53.1 + - - +
25A GLN 2.9 0.2 + - - -
26A GLU* 3.0 22.9 - - - +
27A VAL* 2.7 48.2 + - + +
40A THR* 4.3 3.1 - - + -
41A ILE* 4.5 7.2 - - + -
44A ALA* 3.5 27.8 - - + -
48A PHE* 3.8 17.3 - - + -
58A LEU* 4.9 4.5 - - + -
62A LEU* 3.4 25.8 - - + -
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Residues in contact with LYS 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 LEU 2.9 14.1 + - - +
21A GLN* 3.4 27.1 + - - +
23A ILE* 1.3 75.9 - - - +
25A GLN* 1.3 52.1 + - - +
27A VAL* 3.6 1.9 - - - +
28A SER* 2.7 39.3 + - - +
61A TYR* 3.7 24.5 - - + +
62A LEU* 3.5 29.2 - - + -
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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 GLN 3.2 12.4 + - - +
22A ALA* 2.9 17.2 + - - +
24A LYS* 1.3 71.8 - - - +
26A GLU* 1.3 56.1 - - - +
27A VAL 2.6 6.0 + - - -
28A SER* 2.5 32.3 + - - -
29A GLN* 3.1 8.9 + - - +
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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 ALA* 3.0 10.8 + - - +
23A ILE* 3.0 39.9 - - - +
25A GLN* 1.3 76.0 - - - +
27A VAL* 1.3 58.7 + - - +
29A GLN* 3.6 18.3 - - - +
30A ALA* 3.7 5.5 + - - +
36A GLN* 5.3 2.3 + - - +
40A THR* 2.9 41.5 + - + +
43A LEU* 4.4 16.8 - - - +
44A ALA* 4.9 1.6 - - - +
47A GLN* 5.4 6.3 + - - -
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Residues in contact with VAL 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 ILE* 2.7 36.1 + - + +
24A LYS 3.6 2.7 - - - +
25A GLN 2.6 4.4 + - - -
26A GLU* 1.3 72.5 - - - +
28A SER* 1.3 56.2 + - - +
29A GLN 2.8 4.9 - - - -
30A ALA* 2.6 36.4 + - + +
37A PHE* 3.4 26.9 - - + -
40A THR* 3.3 27.1 - - + -
41A ILE* 4.2 7.4 - - + -
62A LEU* 3.6 25.8 - - + -
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Residues in contact with SER 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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24A LYS* 2.7 22.4 + - - +
25A GLN* 2.5 18.0 + - - -
27A VAL* 1.3 72.5 - - - +
29A GLN* 1.3 57.8 + - - -
30A ALA 3.6 5.6 - - - +
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Residues in contact with GLN 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 GLN 3.1 6.5 + - - +
26A GLU* 3.6 14.0 - - - +
27A VAL 2.8 0.8 - - - -
28A SER* 1.3 76.2 - - - +
30A ALA* 1.3 71.2 + - - +
31A ALA* 5.0 0.9 - - - +
36A GLN* 5.0 3.8 - - + +
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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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26A GLU 3.7 2.8 + - - +
27A VAL* 2.6 24.9 + - - +
28A SER 3.6 7.1 - - - +
29A GLN* 1.3 85.4 - - - +
31A ALA* 1.3 61.1 + - - +
32A PRO* 4.7 0.9 - - - +
36A GLN* 3.6 19.0 - - + +
37A PHE* 3.2 44.0 - - + +
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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