Contacts of the helix formed by residues 9 - 27 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASP* 3.3 13.6 + - - +
8A ILE* 1.3 78.0 - - - +
10A PRO* 1.3 77.5 - - - +
11A PHE* 3.2 2.9 - - - -
12A THR* 2.9 12.9 + - - -
13A GLN* 3.0 14.1 + - - +
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Residues in contact with PRO 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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9A GLY* 1.3 82.1 - - - +
11A PHE* 1.3 63.4 + - - +
13A GLN* 3.2 9.2 + - + +
14A ASN* 2.9 35.3 + - - +
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Residues in contact with PHE 11 (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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6A ILE* 5.1 5.8 - - + -
9A GLY 3.2 1.0 - - - -
10A PRO* 1.3 81.1 - - - +
12A THR* 1.3 66.1 + - - +
14A ASN* 3.5 12.0 + - + +
15A LEU* 3.2 40.6 + - + +
43A LYS* 4.8 8.1 - - - -
60A TYR* 3.5 18.4 - + - -
77A GLU* 4.2 2.7 - - - -
84A ARG* 3.0 34.3 - - - -
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Residues in contact with THR 12 (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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6A ILE* 3.5 19.8 - - - +
7A ASP 3.0 21.4 + - - +
8A ILE* 3.9 9.9 - - - -
9A GLY 2.9 9.7 + - - -
11A PHE* 1.3 77.8 - - - +
13A GLN* 1.3 61.7 + - - +
15A LEU* 3.1 12.4 + - + +
16A ALA* 2.8 25.3 + - - +
37A ALA* 4.0 12.3 - - + -
41A CYS* 4.0 29.6 - - + -
62A LEU* 4.2 8.2 - - + +
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Residues in contact with GLN 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 ILE* 3.2 22.6 + - - +
9A GLY 3.0 19.5 + - - +
10A PRO* 3.2 9.6 + - + +
12A THR* 1.3 75.5 - - - +
14A ASN* 1.3 52.7 + - - +
16A ALA* 3.1 4.4 + - - +
17A LYS* 2.7 36.9 + - - +
34A PHE* 3.6 12.6 - - + -
36A LYS* 3.5 12.7 - - - +
37A ALA* 2.7 49.0 + - - +
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Residues in contact with ASN 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 PRO* 2.9 30.3 + - - +
11A PHE* 3.5 14.2 - - + +
13A GLN* 1.3 77.2 - - - +
15A LEU* 1.3 51.6 + - - +
17A LYS* 3.2 11.1 + - - +
18A PHE* 2.7 36.7 + - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.2 38.8 + - + +
12A THR* 3.1 14.2 + - - +
14A ASN* 1.3 76.2 - - + +
16A ALA* 1.3 59.6 + - - +
18A PHE* 3.1 5.9 + - - +
19A ALA 2.8 23.4 + - - -
60A TYR* 3.5 38.1 - - + -
62A LEU* 3.7 14.6 - - + -
75A ILE* 3.2 21.6 - - + +
84A ARG* 3.0 44.0 - - - +
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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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12A THR 2.8 7.9 + - - +
13A GLN 3.1 6.9 + - - +
15A LEU* 1.3 75.0 - - - +
17A LYS* 1.3 63.5 + - - +
19A ALA* 2.9 17.9 + - - +
20A VAL* 3.0 15.8 + - - +
34A PHE* 3.8 12.3 - - + -
37A ALA* 3.6 31.2 - - + -
62A LEU* 3.8 12.3 - - + +
64A VAL* 3.9 15.3 - - + +
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Residues in contact with LYS 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 GLN 2.7 20.0 + - - +
14A ASN* 3.6 11.4 - - - +
16A ALA* 1.3 73.5 - - - +
18A PHE* 1.3 57.5 + - - +
20A VAL* 3.1 2.4 + - - +
21A ASP* 2.8 63.9 + - - +
34A PHE* 3.5 38.5 - - + +
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Residues in contact with PHE 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 ASN 2.7 18.4 + - - +
15A LEU* 3.3 13.9 - - - +
17A LYS* 1.3 74.2 - - - +
19A ALA* 1.3 63.5 + - - +
21A ASP* 3.5 8.6 + - + +
22A GLU* 3.1 59.7 + - + +
75A ILE* 4.1 22.0 - - + -
84A ARG* 3.7 52.5 - - + -
85A LYS* 4.1 10.3 - - - -
86A LEU* 4.1 2.2 - - - -
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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 LEU 2.8 12.2 + - - +
16A ALA* 2.9 11.9 + - - +
18A PHE* 1.3 78.8 - - - +
20A VAL* 1.3 58.8 + - - +
22A GLU* 3.6 0.6 + - - -
23A GLU* 3.1 27.9 + - - +
62A LEU* 5.5 0.2 - - + -
64A VAL* 5.0 2.5 - - + -
73A ALA* 3.7 29.8 - - + -
75A ILE* 3.9 7.6 - - + -
86A LEU* 3.7 20.1 - - + +
89A PHE* 4.0 6.8 - - + -
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Residues in contact with VAL 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 3.0 14.6 + - - +
17A LYS 3.7 6.5 - - - +
19A ALA* 1.3 73.7 - - - +
21A ASP* 1.3 69.8 + - - +
23A GLU* 3.4 5.4 + - - +
24A ASN* 3.0 38.0 + - - +
32A LEU* 4.1 11.2 - - + +
34A PHE* 3.7 35.7 - - + +
64A VAL* 3.9 22.7 - - + -
66A ALA* 3.9 17.0 - - + -
89A PHE* 4.6 10.5 - - + -
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Residues in contact with ASP 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 LYS* 2.8 57.3 + - - +
18A PHE* 3.9 10.3 - - + +
20A VAL* 1.3 83.2 - - - +
22A GLU* 1.3 66.2 + - - +
24A ASN* 3.5 11.3 + - - +
25A LYS* 3.3 27.2 + - - +
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Residues in contact with GLU 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 PHE* 3.1 54.7 + - + +
21A ASP* 1.3 75.6 - - - +
23A GLU* 1.3 61.1 + - - +
25A LYS* 3.0 41.1 + - - +
26A ILE* 3.0 29.2 + - + +
85A LYS* 5.5 1.2 - - - -
86A LEU* 3.7 30.5 + - + +
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Residues in contact with GLU 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 3.1 18.4 + - - +
20A VAL* 3.8 4.3 - - - +
21A ASP 3.3 0.2 - - - -
22A GLU* 1.3 73.5 - - - +
24A ASN* 1.3 56.1 + - - +
26A ILE* 2.9 17.4 + - - +
27A GLY* 2.7 32.2 + - - -
28A GLN* 3.5 20.6 + - - +
29A TYR* 3.3 20.4 - - + +
30A GLY 5.3 1.6 - - - +
32A LEU* 4.0 14.4 - - + -
86A LEU* 3.6 8.4 - - + +
89A PHE* 3.1 54.6 - - + +
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Residues in contact with ASN 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 VAL* 3.0 26.6 + - - +
21A ASP* 3.7 12.7 + - - +
22A GLU 3.3 0.2 - - - -
23A GLU* 1.3 72.4 - - - +
25A LYS* 1.3 66.7 + - - +
26A ILE 3.3 0.3 + - - -
27A GLY* 3.3 11.3 + - - +
30A GLY 3.7 8.4 - - - +
31A ARG* 3.8 38.3 + - - +
32A LEU* 2.9 51.8 + - - +
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Residues in contact with LYS 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 ASP* 3.3 14.1 + - - +
22A GLU* 3.0 43.2 + - - +
24A ASN* 1.3 81.1 - - - +
26A ILE* 1.3 62.6 + - + +
27A GLY* 4.4 0.2 - - - -
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Residues in contact with ILE 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 GLU* 3.0 14.3 + - + +
23A GLU* 2.9 29.9 + - - +
25A LYS* 1.3 80.2 - - + +
27A GLY* 1.3 59.8 + - - +
28A GLN* 3.6 19.9 + - + +
86A LEU* 3.9 18.8 - - + +
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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 GLU 2.7 16.4 + - - -
24A ASN 3.3 10.6 + - - -
25A LYS 4.4 0.4 - - - -
26A ILE* 1.3 74.3 - - - +
28A GLN* 1.3 62.7 + - - +
29A TYR 3.2 3.1 - - - -
30A GLY* 3.2 21.5 + - - -
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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