Contacts of the helix formed by residues 11 - 23 (chain Q) in PDB entry 2D2I
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 11 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193P ALA* 6.3 0.4 - - - -
9Q GLY 3.0 9.7 + - - -
10Q PHE* 1.3 75.4 - - - +
12Q ARG* 1.3 67.9 + - - -
13Q ILE 3.4 2.2 - - - -
14Q GLY 3.8 0.7 - - - -
15Q ARG* 2.8 36.9 + - - +
5341Q NAP 3.1 31.8 + - - -
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Residues in contact with ARG 12 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191P LEU* 4.4 17.4 - - + +
192P ASP* 3.4 30.4 - - - +
11Q GLY* 1.3 71.1 - - - +
13Q ILE* 1.3 59.0 + - + +
15Q ARG* 3.1 21.2 - - - +
16Q ASN* 2.8 46.0 + - - +
50Q ASP* 2.9 42.7 + - - -
52Q VAL* 4.1 10.7 - - - +
53Q LEU* 4.7 1.6 - - - +
186Q LEU* 3.9 9.4 - - + -
319Q GLU* 2.7 48.3 + - + +
5341Q NAP 2.9 40.9 + - - +
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Residues in contact with ILE 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q ARG* 1.3 72.9 - - - +
14Q GLY* 1.3 60.6 + - - +
17Q PHE* 2.8 38.0 + - + +
96Q ILE* 5.9 0.2 - - + -
98Q SER* 4.4 2.7 - - - -
122Q THR* 3.9 30.3 - - + +
319Q GLU* 4.1 13.5 - - + +
322Q TYR* 4.0 13.2 - - + -
323Q SER* 3.8 20.0 - - - +
326Q VAL* 4.8 3.8 - - + -
5341Q NAP 3.0 73.5 + - + +
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Residues in contact with GLY 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q ILE* 4.1 11.1 - - - +
9Q GLY 3.6 21.4 + - - -
10Q PHE* 4.0 9.0 - - - -
11Q GLY 3.3 6.4 + - - -
13Q ILE* 1.3 79.3 - - - +
15Q ARG* 1.3 55.6 + - - +
17Q PHE* 3.5 7.9 - - - +
18Q LEU* 3.1 25.5 + - - +
96Q ILE* 5.6 1.1 - - - -
98Q SER* 3.8 11.1 + - - -
5341Q NAP 4.8 0.2 + - - -
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Residues in contact with ARG 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192P ASP* 3.1 36.8 + - - +
193P ALA* 5.0 2.6 - - - +
194P SER 5.5 0.6 - - - +
10Q PHE* 2.9 59.2 + - + +
11Q GLY* 2.8 37.5 + - - +
12Q ARG* 3.1 26.1 - - - +
14Q GLY* 1.3 69.0 - - - +
16Q ASN* 1.3 66.7 + - - +
17Q PHE 3.1 1.3 - - - -
18Q LEU* 3.1 3.4 + - - +
19Q ARG* 2.9 28.3 + - + +
46Q LEU* 3.2 53.7 + - - +
47Q LEU* 4.0 8.1 - - + +
50Q ASP* 4.6 5.0 + - - +
53Q LEU* 5.6 0.9 - - + -
5341Q NAP 5.2 0.6 + - - -
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Residues in contact with ASN 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q ARG* 2.8 46.0 + - - +
13Q ILE* 4.3 0.4 - - - -
15Q ARG* 1.3 72.7 - - - +
17Q PHE* 1.3 52.4 + - - +
19Q ARG* 3.2 6.5 + - - +
20Q CYS* 2.7 41.2 + - - -
50Q ASP* 5.0 0.4 + - - -
53Q LEU* 3.6 25.3 - - - +
319Q GLU* 3.5 32.2 + - - +
320Q TRP* 3.6 24.1 + - + -
323Q SER* 3.3 20.4 - - - +
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Residues in contact with PHE 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q VAL* 4.8 2.9 - - + -
7Q ILE* 3.6 30.7 - - + -
13Q ILE* 2.8 25.5 + - + +
14Q GLY* 3.5 4.0 - - - +
16Q ASN* 1.3 69.9 - - - +
18Q LEU* 1.3 71.3 + - - +
20Q CYS* 3.1 4.7 + - - +
21Q TRP* 2.9 27.4 + - + +
29Q LEU* 4.6 15.7 - - + -
31Q VAL* 4.2 16.4 - - + -
96Q ILE* 3.7 31.0 - - + -
323Q SER* 3.7 12.2 + - - +
326Q VAL* 3.1 35.4 - - + -
327Q VAL* 3.4 33.7 - - + +
330Q ALA* 4.6 1.3 - - + -
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Residues in contact with LEU 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q ILE* 4.1 14.1 - - + -
10Q PHE* 3.6 27.4 - - + -
14Q GLY 3.1 13.7 + - - +
15Q ARG* 3.1 7.8 + - - +
17Q PHE* 1.3 81.5 - - - +
19Q ARG* 1.3 64.1 + - - +
21Q TRP* 3.1 17.1 + - + +
22Q PHE* 3.0 52.1 + - + -
31Q VAL* 4.4 7.2 - - + -
34Q ILE* 4.3 4.0 - - + -
47Q LEU* 3.9 23.1 - - + -
67Q ILE* 5.8 0.2 - - + -
74Q MET* 4.1 24.9 - - + -
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Residues in contact with ARG 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q ARG* 2.9 15.3 + - - +
16Q ASN* 3.5 8.5 - - - +
18Q LEU* 1.3 73.5 - - - +
20Q CYS* 1.3 66.0 + - - +
22Q PHE* 3.3 2.4 + - - +
23Q GLY* 3.1 18.4 + - - -
47Q LEU* 3.5 22.3 + - + +
48Q GLU 3.8 1.2 + - - -
50Q ASP* 3.1 22.4 + - - +
53Q LEU* 3.5 32.4 + - + +
54Q GLY 2.8 29.5 + - - -
55Q ARG 3.8 3.8 + - - -
56Q PHE* 3.4 68.0 - - + +
320Q TRP* 4.0 16.9 - - + -
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Residues in contact with CYS 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q ASN 2.7 27.6 + - - +
17Q PHE 3.1 4.9 + - - +
19Q ARG* 1.3 71.5 - - - +
21Q TRP* 1.3 63.7 - - - +
23Q GLY* 3.1 12.3 + - - -
24Q ARG* 3.2 19.1 + - - +
320Q TRP* 3.6 34.5 - - - -
323Q SER* 3.7 20.4 - - - -
324Q GLN* 3.4 34.9 + - - +
327Q VAL* 3.9 10.1 - - + -
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Residues in contact with TRP 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q PHE* 2.9 17.1 + + + +
18Q LEU* 3.3 22.4 - - + +
20Q CYS* 1.3 74.4 - - - +
22Q PHE* 1.3 91.4 + + - +
24Q ARG* 2.8 34.2 + - + +
27Q THR* 2.8 38.1 + - + +
29Q LEU* 3.4 33.4 - - + +
30Q GLU* 3.7 7.4 - - - -
31Q VAL* 3.6 47.3 - - + -
72Q LYS* 3.4 33.2 - - + -
74Q MET* 4.9 1.1 - - - -
327Q VAL* 4.1 13.8 - - + +
331Q GLU* 4.4 4.9 - - - -
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Residues in contact with PHE 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q LEU* 3.0 50.5 + - + +
19Q ARG 3.9 6.3 - - - +
21Q TRP* 1.3 90.7 - + - +
23Q GLY* 1.3 60.7 + - - +
24Q ARG 3.3 5.9 + - - +
56Q PHE* 4.0 22.4 - + + -
69Q VAL* 3.1 52.7 - - + -
70Q ASN* 4.2 13.5 - - + +
72Q LYS* 3.7 31.2 - - + +
74Q MET* 4.1 10.8 - - + -
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Residues in contact with GLY 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q ARG 3.1 9.5 + - - -
20Q CYS 3.1 11.0 + - - -
21Q TRP 3.0 1.4 - - - -
22Q PHE* 1.3 77.2 - - - +
24Q ARG* 1.3 63.7 + - - +
25Q GLN* 3.6 3.1 + - - +
56Q PHE* 6.0 0.2 - - - -
320Q TRP* 6.2 1.3 - - - -
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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