Contacts of the helix formed by residues 9 - 27 (chain D) in PDB entry 3Q2P
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 GLY 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D ASP* 2.9 19.8 + - - +
8D ILE* 1.3 78.2 - - - +
10D PRO* 1.3 65.1 - - - +
11D PHE 3.4 2.7 - - - -
12D THR* 2.9 6.3 + - - -
13D GLN* 2.9 32.5 + - - +
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Residues in contact with PRO 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLY* 1.3 81.2 - - - +
11D PHE* 1.3 57.1 + - - +
13D GLN* 3.7 9.5 - - + +
14D ASN* 2.7 48.8 + - - +
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Residues in contact with PHE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 5.4 3.8 - - + -
7D ASP* 6.0 1.3 - - - +
9D GLY 3.4 1.0 - - - -
10D PRO* 1.3 78.8 - - - +
12D THR* 1.3 62.4 + - - +
14D ASN* 3.4 9.5 + - + +
15D LEU* 3.0 37.5 + - + +
43D LYS* 6.2 0.2 - - - -
60D TYR* 3.6 26.5 - + - -
77D GLU* 4.2 9.9 - - - -
84D ARG* 3.3 29.9 + - - -
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Residues in contact with THR 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.6 17.6 - - + +
7D ASP* 2.9 31.7 + - - +
8D ILE* 3.8 9.4 - - - -
9D GLY 2.9 10.4 + - - -
11D PHE* 1.3 79.1 - - - +
13D GLN* 1.3 65.8 + - - +
15D LEU* 3.1 11.1 + - + +
16D ALA* 3.0 20.6 + - - +
37D ALA* 4.2 9.2 - - + -
41D CYS* 4.1 26.9 - - + -
62D LEU* 4.0 7.1 - - + +
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Residues in contact with GLN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 3.0 26.9 + - - +
9D GLY 2.9 17.6 + - - +
10D PRO* 3.8 8.3 - - + +
12D THR* 1.3 75.2 - - - +
14D ASN* 1.3 60.0 + - - +
16D ALA* 3.1 5.9 + - - +
17D LYS* 2.8 30.5 + - - +
34D PHE* 3.7 14.3 - - + -
36D LYS* 3.6 13.3 - - - +
37D ALA* 2.8 47.7 + - - +
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Residues in contact with ASN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PRO* 2.7 38.0 + - - +
11D PHE* 3.6 10.0 - - + +
13D GLN* 1.3 74.8 - - - +
15D LEU* 1.3 60.3 + - - +
17D LYS* 3.9 12.3 - - - +
18D PHE* 3.1 22.9 + - - +
84D ARG* 4.1 9.9 + - - +
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 5.2 3.1 - - + -
11D PHE* 3.0 26.5 + - + +
12D THR* 3.3 14.8 - - + +
14D ASN* 1.3 76.6 - - - +
16D ALA* 1.3 56.7 + - - +
18D PHE* 3.2 7.2 + - + +
19D ALA 3.0 21.8 + - - -
60D TYR* 3.4 56.3 - - + -
62D LEU* 3.7 12.6 - - + -
75D ILE* 3.2 23.6 - - + +
77D GLU* 5.9 0.2 - - + -
84D ARG* 3.4 41.5 - - - +
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR 3.0 6.2 + - - +
13D GLN 3.1 6.5 + - - +
15D LEU* 1.3 73.1 - - - +
17D LYS* 1.3 66.8 + - - +
19D ALA* 3.0 8.5 + - - +
20D VAL* 3.0 24.9 + - - +
34D PHE* 3.7 13.2 - - + -
37D ALA* 3.7 30.5 - - + -
62D LEU* 3.4 15.4 - - + +
64D VAL* 3.7 12.7 - - + +
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLN 2.8 16.8 + - - +
14D ASN* 3.9 12.8 - - - +
16D ALA* 1.3 75.0 - - - +
18D PHE* 1.3 57.9 + - - +
20D VAL* 3.2 1.9 + - - +
21D ASP* 2.8 63.8 + - - +
34D PHE* 3.6 38.5 - - + -
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Residues in contact with PHE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASN 3.1 14.1 + - - +
15D LEU* 3.2 12.1 - - - +
16D ALA 3.2 0.2 - - - -
17D LYS* 1.3 78.4 - - - +
19D ALA* 1.3 59.5 + - - +
21D ASP* 3.4 8.7 + - + +
22D GLU* 2.9 61.7 + - + +
75D ILE* 3.7 28.0 - - + -
84D ARG* 3.4 56.5 - - + +
85D LYS* 3.8 13.0 - - - -
86D LEU* 3.9 4.7 - - - -
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU 3.0 11.3 + - - +
16D ALA* 3.0 13.3 + - - +
18D PHE* 1.3 84.6 - - - +
20D VAL* 1.3 57.1 + - - +
22D GLU* 3.4 3.3 + - - +
23D GLU* 2.9 28.6 + - - +
64D VAL* 4.9 2.0 - - + -
73D ALA* 3.8 29.2 - - + -
75D ILE* 3.8 9.9 - - + -
86D LEU* 3.7 12.1 - - + +
89D PHE* 4.1 8.5 - - + -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA 3.0 16.7 + - - +
17D LYS 3.2 5.1 + - - +
19D ALA* 1.3 73.3 - - - +
21D ASP* 1.3 61.3 + - - +
23D GLU* 3.0 7.1 + - - +
24D ASN* 2.8 43.2 + - - +
32D LEU* 4.0 26.2 - - + +
34D PHE* 3.8 35.9 - - + +
64D VAL* 3.8 15.7 - - + -
66D ALA* 4.0 11.7 - - + -
89D PHE* 4.4 9.0 - - + -
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Residues in contact with ASP 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 2.8 58.8 + - - +
18D PHE* 3.7 8.8 - - + +
20D VAL* 1.3 72.7 - - - +
22D GLU* 1.3 66.1 - - - +
24D ASN* 3.3 20.7 + - - +
25D LYS* 3.4 18.1 + - - +
34D PHE* 5.8 1.2 - - - +
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Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 2.9 56.4 + - + +
19D ALA 3.6 4.3 - - - +
21D ASP* 1.3 78.0 - - - +
23D GLU* 1.3 63.0 + - - +
25D LYS* 3.0 52.1 + - - +
26D ILE* 3.3 14.8 + - + +
85D LYS* 6.0 0.3 - - - -
86D LEU* 3.8 24.1 + - + +
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA 2.9 18.0 + - - +
20D VAL 3.0 5.1 + - - +
22D GLU* 1.3 76.2 - - - +
24D ASN* 1.3 57.0 + - - +
26D ILE* 3.4 17.2 + - - +
27D GLY* 2.8 26.0 + - - -
28D GLN* 3.2 32.0 + - - +
29D TYR* 3.6 16.5 - - + -
30D GLY 5.0 0.9 - - - +
32D LEU* 3.6 20.4 - - + -
86D LEU* 3.9 3.6 - - + +
89D PHE* 3.3 46.4 - - + +
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Residues in contact with ASN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 2.8 22.1 + - - +
21D ASP* 3.6 15.7 + - - +
22D GLU 3.1 0.4 - - - -
23D GLU* 1.3 76.5 - - - +
25D LYS* 1.3 64.2 + - + +
27D GLY* 3.6 9.6 + - - -
30D GLY 3.7 8.6 - - - +
31D ARG* 3.9 3.2 - - - -
32D LEU* 3.0 50.4 + - - +
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Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASP* 3.6 13.9 - - - +
22D GLU* 3.0 39.7 + - - +
24D ASN* 1.3 76.1 - - + +
26D ILE* 1.3 69.9 + - + +
27D GLY* 3.3 0.9 + - - -
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Residues in contact with ILE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLU* 3.3 14.8 + - + +
23D GLU* 3.7 26.5 - - - +
25D LYS* 1.3 78.4 - - + +
27D GLY* 1.3 62.1 + - - +
28D GLN* 3.5 12.9 + - + +
86D LEU* 4.2 18.6 - - + +
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Residues in contact with GLY 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLU 2.8 15.6 + - - -
24D ASN 3.9 10.1 - - - -
25D LYS 3.2 2.3 - - - -
26D ILE* 1.3 77.8 - - - +
28D GLN* 1.3 57.6 + - - +
29D TYR 3.1 7.0 + - - -
30D GLY* 3.7 19.5 + - - -
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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