Contacts of the helix formed by residues 9 - 27 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ASP* 3.0 16.7 + - - -
8B ILE* 1.3 84.0 - - - +
10B PRO* 1.3 78.5 - - - +
11B PHE* 3.2 3.4 - - - -
12B THR* 3.0 12.5 + - - -
13B GLN* 3.1 8.7 + - - +
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Residues in contact with PRO 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLY* 1.3 83.6 - - - +
11B PHE* 1.3 52.9 + - - +
13B GLN* 3.1 9.9 + - + +
14B ASN* 2.8 49.9 + - - +
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.0 6.3 - - + -
9B GLY 3.1 2.1 + - - +
10B PRO* 1.3 80.0 - - - +
12B THR* 1.3 67.4 + - - +
14B ASN* 3.3 11.2 + - + +
15B LEU* 3.1 41.4 + - + +
60B TYR* 3.7 25.8 - + - -
77B GLU* 4.3 6.5 - - - -
84B ARG* 3.5 28.6 + - - -
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Residues in contact with THR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.9 14.1 - - + +
7B ASP* 2.7 28.6 + - - +
8B ILE* 3.8 6.8 - - - -
9B GLY 3.0 9.0 + - - -
11B PHE* 1.3 77.1 - - - +
13B GLN* 1.3 67.6 + - - +
15B LEU* 3.1 10.5 + - + +
16B ALA* 2.9 21.7 + - - +
37B ALA* 4.3 8.7 - - + -
41B CYS* 3.9 32.8 - - + -
62B LEU* 4.1 13.0 - - + -
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 2.9 24.6 + - - +
9B GLY 3.1 15.6 + - - +
10B PRO* 3.4 11.2 - - + +
12B THR* 1.3 76.9 - - - +
14B ASN* 1.3 59.1 + - - +
16B ALA* 3.2 3.1 + - - +
17B LYS* 2.9 29.2 + - - +
34B PHE* 3.6 18.7 - - + -
36B LYS* 3.6 12.8 - - - +
37B ALA* 2.8 50.8 + - - +
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 2.8 32.6 + - - +
11B PHE* 3.6 10.3 - - + +
12B THR 3.1 0.2 - - - -
13B GLN* 1.3 75.9 - - - +
15B LEU* 1.3 60.4 + - - +
17B LYS* 3.4 10.6 - - - +
18B PHE* 2.9 27.4 + - - +
84B ARG* 4.1 9.7 + - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.3 0.9 - - + -
11B PHE* 3.1 42.0 + - + +
12B THR* 3.4 12.6 - - + +
14B ASN* 1.3 73.2 - - - +
16B ALA* 1.3 66.9 + - - +
18B PHE* 2.9 14.3 + - + +
19B ALA 3.0 9.9 + - - -
60B TYR* 3.7 42.4 - - + -
62B LEU* 3.6 14.4 - - + -
75B ILE* 3.4 20.0 - - + +
77B GLU* 5.8 0.2 - - + -
84B ARG* 3.2 46.2 - - - +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR 2.9 11.5 + - - +
13B GLN 3.5 7.6 - - - +
15B LEU* 1.3 76.3 - - - +
17B LYS* 1.3 63.4 + - - +
19B ALA* 3.1 8.3 + - - +
20B VAL* 3.1 26.4 + - - +
34B PHE* 3.7 17.0 - - + -
37B ALA* 3.7 16.4 - - + -
62B LEU* 3.4 14.3 - - + +
64B VAL* 3.7 19.4 - - + +
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLN 2.9 16.5 + - - +
14B ASN* 3.4 13.7 - - - +
16B ALA* 1.3 74.2 - - - +
18B PHE* 1.3 65.3 + - - +
20B VAL* 3.2 4.0 + - - +
21B ASP* 2.9 62.8 + - - +
34B PHE* 3.7 40.0 - - + -
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Residues in contact with PHE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN 2.9 13.0 + - - +
15B LEU* 2.9 12.8 + - - +
17B LYS* 1.3 77.6 - - - +
19B ALA* 1.3 60.8 + - - +
21B ASP* 3.3 9.9 + - + +
22B GLU* 2.9 64.6 + - + +
75B ILE* 4.1 15.9 - - + -
84B ARG* 3.4 57.4 - - + +
85B LYS* 3.9 3.8 - - - -
86B LEU* 3.9 16.8 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU 3.0 5.2 + - - +
16B ALA* 3.1 10.7 + - - +
18B PHE* 1.3 82.7 - - - +
20B VAL* 1.3 57.6 + - - +
22B GLU* 3.4 1.6 + - - -
23B GLU* 2.8 30.0 + - - +
64B VAL* 5.8 0.2 - - + -
73B ALA* 3.9 22.2 - - + -
75B ILE* 3.7 23.8 - - + -
86B LEU* 3.5 18.5 - - + +
89B PHE* 4.0 5.8 - - + -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 3.1 13.3 + - - +
17B LYS 3.2 6.9 + - - +
19B ALA* 1.3 74.7 - - - +
21B ASP* 1.3 63.2 + - - +
23B GLU* 3.2 2.9 + - - +
24B ASN* 2.8 36.3 + - - +
32B LEU* 3.9 24.6 - - + +
34B PHE* 4.0 29.8 - - + +
64B VAL* 4.1 13.2 - - + -
66B ALA* 4.1 17.3 - - + -
89B PHE* 4.0 21.3 - - + -
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 2.9 52.6 + - - +
18B PHE* 3.6 10.1 - - + +
20B VAL* 1.3 78.8 - - - +
22B GLU* 1.3 68.4 + - - +
24B ASN* 3.3 15.3 + - - +
25B LYS* 3.3 27.4 + - - +
34B PHE* 5.9 0.9 - - - +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 2.9 58.0 + - + +
19B ALA 3.7 4.3 - - - +
21B ASP* 1.3 76.9 - - - +
23B GLU* 1.3 63.3 + - - +
25B LYS* 2.6 57.3 + - - +
26B ILE* 3.3 15.9 + - + +
85B LYS* 6.0 0.2 - - - -
86B LEU* 3.7 23.7 + - + +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA 2.8 18.2 + - - +
20B VAL* 3.2 4.9 + - - +
22B GLU* 1.3 77.0 - - - +
24B ASN* 1.3 57.7 + - - +
26B ILE* 3.0 17.0 + - - +
27B GLY* 2.8 25.8 + - - -
28B GLN* 3.1 38.5 + - - +
29B TYR* 3.3 20.0 - - + -
30B GLY 4.9 0.6 - - - +
32B LEU* 4.0 9.2 - - + -
86B LEU* 3.7 8.8 - - + +
89B PHE* 3.3 47.2 - - + +
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Residues in contact with ASN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 2.8 27.3 + - - +
21B ASP* 3.6 12.8 + - - +
22B GLU 3.2 0.2 - - - -
23B GLU* 1.3 78.3 - - - +
25B LYS* 1.3 61.2 + - - +
27B GLY* 3.3 11.0 + - - +
30B GLY 3.3 11.8 - - - +
31B ARG* 3.5 29.9 + - - +
32B LEU* 2.7 52.6 + - - +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP* 3.3 17.2 + - - +
22B GLU* 2.6 45.8 + - - +
24B ASN* 1.3 75.4 - - + +
26B ILE* 1.3 64.0 + - + +
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU* 3.3 13.2 + - + +
23B GLU* 3.0 24.5 + - - +
25B LYS* 1.3 81.9 - - + +
27B GLY* 1.3 58.8 + - - +
28B GLN* 3.3 25.0 + - + +
86B LEU* 4.7 11.2 - - + +
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 2.8 12.8 + - - -
24B ASN 3.3 11.5 + - - -
26B ILE* 1.3 75.5 - - - +
28B GLN* 1.3 56.8 + - - -
29B TYR 2.8 13.0 + - - -
30B GLY* 2.9 22.8 + - - -
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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