Contacts of the helix formed by residues 12 - 29 (chain A) in PDB entry 3AQ8
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLU 3.0 11.7 + - - -
10A LYS 3.2 1.0 - - - -
11A LEU* 1.3 81.0 - - - +
13A GLY* 1.3 66.6 + - - +
14A GLU 3.8 0.7 + - - -
15A ASN* 4.4 2.8 + - - +
16A ALA* 3.5 15.2 + - - +
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Residues in contact with GLY 13 (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 TYR* 2.9 39.6 + - - +
9A GLU* 4.0 5.4 + - - -
11A LEU* 3.8 1.3 - - - +
12A GLY* 1.3 77.2 - - - +
14A GLU* 1.3 67.0 + - - -
16A ALA* 3.2 2.1 + - - +
17A MET* 3.0 22.5 + - - +
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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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8A TYR* 3.1 24.0 + - + +
12A GLY 3.8 0.6 + - - -
13A GLY* 1.3 72.7 - - - -
15A ASN* 1.4 72.0 + - - +
17A MET* 3.1 3.9 + - + +
18A LYS* 2.9 57.7 + - + +
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Residues in contact with ASN 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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12A GLY 4.4 3.0 + - - +
13A GLY 3.4 0.6 - - - -
14A GLU* 1.4 90.7 - - - +
16A ALA* 1.4 61.7 + - - +
18A LYS* 3.6 14.6 + - - +
19A ALA* 3.2 22.0 + - - +
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Residues in contact with ALA 16 (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 LEU* 3.2 30.3 - - + +
12A GLY* 3.5 21.1 + - - +
13A GLY 3.2 1.3 + - - +
14A GLU 3.1 0.4 - - - -
15A ASN* 1.4 78.0 - - - +
17A MET* 1.3 60.6 + - - +
19A ALA* 3.2 6.3 + - - +
20A ALA* 2.9 30.5 + - - +
97A LEU* 5.1 1.4 - - - +
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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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8A TYR* 4.1 26.0 - - + +
11A LEU* 4.3 13.9 - - + +
13A GLY 3.0 13.1 + - - +
14A GLU* 3.1 7.2 + - - +
16A ALA* 1.3 77.5 - - - +
18A LYS* 1.3 64.4 + - - +
20A ALA* 4.3 9.0 - - - -
21A VAL* 3.0 41.7 + - + +
51A THR* 3.9 16.6 + - + +
54A LEU* 4.0 29.8 - - + +
55A THR* 3.6 18.8 - - - +
58A LEU* 4.2 17.0 - - + -
94A LEU* 6.3 0.7 - - - -
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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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14A GLU* 2.9 53.2 + - + +
15A ASN* 3.9 13.5 + - - +
17A MET* 1.3 77.1 - - - +
19A ALA* 1.3 57.3 + - - +
22A PRO* 3.0 25.8 - - - +
51A THR* 4.9 17.0 - - + -
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Residues in contact with ALA 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 ASN 3.2 16.5 + - - +
16A ALA* 3.8 6.1 - - - +
17A MET 3.2 0.6 - - - -
18A LYS* 1.3 79.0 - - - +
20A ALA* 1.3 65.4 + - - +
22A PRO* 3.5 4.4 - - - +
23A LEU* 3.4 20.8 + - - +
97A LEU* 4.4 18.1 - - + +
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Residues in contact with ALA 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 ALA 2.9 17.4 + - - +
17A MET* 3.8 14.6 - - - +
19A ALA* 1.3 79.7 - - - +
21A VAL* 1.3 60.2 + - + +
23A LEU 3.3 0.2 + - - -
24A PHE* 2.8 27.8 + - - +
90A LEU* 5.6 3.8 - - + -
93A THR* 3.2 10.1 - - + +
94A LEU* 4.1 21.3 - - + -
97A LEU* 3.6 22.2 - - + +
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Residues in contact with VAL 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* 3.0 34.2 + - - +
18A LYS 5.5 0.2 - - - -
20A ALA* 1.3 76.0 - - + +
22A PRO* 1.3 63.3 - - + +
24A PHE* 3.2 8.4 + - + +
25A TYR* 2.9 50.7 + - + -
47A THR* 3.8 15.3 - - + +
50A GLN* 4.0 8.3 - - + -
51A THR* 3.6 33.0 - - - +
54A LEU* 4.2 16.8 - - + -
90A LEU* 6.3 0.7 - - + -
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Residues in contact with PRO 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 3.0 28.7 - - - +
19A ALA* 3.5 6.7 - - - +
21A VAL* 1.3 91.0 - - + +
23A LEU* 1.3 56.3 + - - +
25A TYR* 3.4 8.3 + - + +
26A LYS* 2.9 26.7 + - - +
47A THR* 4.3 17.9 - - + +
51A THR* 5.5 0.2 - - - +
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Residues in contact with LEU 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 ALA 3.4 15.1 + - - +
20A ALA* 3.3 1.4 + - - -
21A VAL 3.3 0.4 - - - -
22A PRO* 1.3 75.7 - - - +
24A PHE* 1.3 67.1 + - - +
26A LYS* 3.1 31.0 + - + +
27A LYS* 3.0 33.1 + - - +
93A THR* 3.7 19.3 - - + +
96A GLU* 4.0 31.0 - - + +
97A LEU* 3.7 35.4 - - + -
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Residues in contact with PHE 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 ALA 2.8 18.6 + - - +
21A VAL* 3.4 10.5 - - - +
23A LEU* 1.3 77.8 - - - +
25A TYR* 1.3 93.8 + + - +
27A LYS* 3.2 3.1 + - - +
28A VAL* 2.9 49.5 + - + +
50A GLN* 4.4 17.9 - - + -
54A LEU* 5.6 3.8 - - + -
86A ILE* 3.6 46.0 - - + -
89A ASN 3.9 0.9 - - - -
90A LEU* 3.6 39.9 - - + -
93A THR* 3.2 19.2 + - + +
144A HEM 6.4 0.2 - + - -
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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 VAL* 2.9 48.0 + - + +
22A PRO* 3.4 7.8 + - + +
24A PHE* 1.3 89.8 - + - +
26A LYS* 1.3 67.7 + - - +
28A VAL* 4.2 11.2 - - + -
29A LEU* 2.8 35.0 + - + +
38A PHE* 4.0 20.6 - + - -
43A MET* 3.4 29.6 - - + -
46A GLU* 2.4 35.6 + - + -
47A THR* 3.9 20.6 - - - +
50A GLN* 3.1 26.3 + - + +
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Residues in contact with LYS 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 PRO 2.9 15.6 + - - +
23A LEU* 3.1 30.5 + - + +
25A TYR* 1.3 76.5 - - - +
27A LYS* 1.3 66.6 + - + +
29A LEU* 3.6 6.3 + - - +
30A ALA* 3.3 20.3 + - - +
96A GLU* 5.7 2.6 + - - -
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Residues in contact with LYS 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 LEU* 3.0 24.9 + - + +
24A PHE 3.7 5.4 - - - +
25A TYR 3.1 0.2 - - - -
26A LYS* 1.3 78.1 - - + +
28A VAL* 1.3 66.4 + - - +
30A ALA* 3.0 15.7 + - - +
31A ASP* 3.2 13.9 + - - +
89A ASN* 3.4 22.8 - - + +
92A ALA* 3.9 17.9 - - + +
93A THR* 3.5 38.6 - - - +
96A GLU* 2.4 31.5 + - - -
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Residues in contact with VAL 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 PHE* 2.9 53.5 + - + +
25A TYR* 3.8 12.3 - - + +
27A LYS* 1.3 77.2 - - - +
29A LEU* 1.4 57.9 + - + +
31A ASP* 3.1 19.3 + - - +
34A VAL* 3.8 9.5 - - + +
35A LYS* 3.4 12.1 + - - +
38A PHE* 3.6 37.7 - - + -
86A ILE* 4.1 11.0 - - + -
89A ASN* 3.9 17.9 - - + +
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Residues in contact with LEU 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 TYR* 2.8 32.0 + - + +
26A LYS* 4.0 5.2 - - - +
28A VAL* 1.4 74.5 - - + +
30A ALA* 1.3 57.6 + - - +
35A LYS* 3.3 29.2 - - + +
38A PHE* 3.5 38.6 - - + +
43A MET* 3.9 34.3 - - + -
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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