Contacts of the helix formed by residues 3 - 27 (chain F) in PDB entry 2D2C
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 THR 3 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.1 41.9 - - + +
150B PRO* 4.7 9.0 - - + +
154B THR 5.8 4.8 - - - +
2F MET* 1.3 77.4 - - - +
4F GLU* 1.3 75.9 + - - +
5F GLU* 3.0 4.0 + - - -
6F MET* 3.3 10.6 + - + +
7F LEU* 3.0 42.1 + - + +
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Residues in contact with GLU 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 6.0 0.7 - - + -
33C GLU* 3.5 23.7 - - - +
35C GLU* 3.4 22.0 - - - +
51C LYS* 5.3 3.2 + - - -
2F MET 5.2 3.1 - - - +
3F THR* 1.3 83.7 + - - +
5F GLU* 1.3 90.4 + - + +
7F LEU* 3.3 13.4 - - - +
8F TYR* 3.3 20.3 + - - +
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Residues in contact with GLU 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU* 3.0 40.9 - - + +
2E ILE* 4.8 2.9 - - + +
2F MET* 3.5 37.0 - - - +
3F THR 3.0 1.2 + - - +
4F GLU* 1.3 103.7 - - + +
6F MET* 1.3 54.2 + - + +
8F TYR* 2.7 40.2 - - - -
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Residues in contact with MET 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 3.5 16.8 - - + +
2E ILE* 3.0 45.1 - - - +
4E GLY* 4.0 6.5 - - - -
5E ALA* 2.6 42.9 - - + +
8E TYR* 4.2 19.3 - - + -
2F MET 4.0 14.4 - - - +
3F THR* 3.6 11.9 - - - +
5F GLU* 1.3 73.1 - - + +
7F LEU* 1.3 75.0 + - - +
8F TYR 3.0 2.5 - - - -
9F ALA* 2.5 24.4 + - - +
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Residues in contact with LEU 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR* 5.1 23.6 - - + -
5E ALA* 4.1 2.9 - - - -
3F THR* 3.0 41.8 + - + +
4F GLU* 3.3 11.7 - - - +
6F MET* 1.3 87.4 - - - +
8F TYR* 1.3 60.6 + - + +
10F ALA* 3.3 11.4 - - - +
11F LEU* 3.1 26.2 - - + +
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Residues in contact with TYR 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ILE* 5.2 2.2 - - + -
4F GLU 3.3 8.0 + - - +
5F GLU 2.7 23.3 - - - -
6F MET 3.0 1.0 - - - -
7F LEU* 1.3 79.2 - - + +
9F ALA* 1.3 81.4 + - + +
10F ALA 3.1 4.9 - - - -
11F LEU* 2.7 20.5 - - + +
12F LEU* 2.6 42.0 - - + +
10G PHE* 5.6 6.9 - - - -
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Residues in contact with ALA 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ILE* 3.0 37.0 - - + -
5E ALA* 3.7 6.0 - - + +
6E VAL* 4.4 6.9 - - + -
6F MET 2.5 13.0 + - - +
8F TYR* 1.3 84.9 - - + +
10F ALA* 1.3 65.7 - - - +
12F LEU* 3.0 24.2 - - + +
13F SER* 3.3 11.4 + - - -
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Residues in contact with ALA 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ALA* 2.8 34.3 - - + +
8E TYR* 5.3 2.0 - - + -
9E ILE* 2.8 35.4 - - + +
6F MET 2.9 4.2 + - - -
7F LEU* 3.3 12.8 - - - +
8F TYR 3.1 0.4 - - - -
9F ALA* 1.3 80.2 - - - +
11F LEU* 1.3 58.7 + - + +
12F LEU 2.4 15.4 + - - -
13F SER* 2.9 5.9 + - - -
14F PHE 3.3 0.3 + - - -
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 3.2 20.2 - - + +
7F LEU* 3.1 26.0 - - + +
8F TYR* 2.7 38.6 - - + +
10F ALA* 1.3 78.6 - - + +
12F LEU* 1.3 68.2 + - - +
14F PHE* 3.8 7.8 - - + +
15F GLY* 3.0 16.3 + - - -
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 2.6 43.5 + - + +
9F ALA* 3.0 28.0 - - + +
10F ALA 2.4 6.9 + - - -
11F LEU* 1.3 79.7 - - - +
13F SER* 1.3 66.4 + - - +
15F GLY* 3.0 4.0 + - - -
16F LEU* 2.9 33.9 - - + +
14G GLY* 6.0 4.3 - - - -
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Residues in contact with SER 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ALA 4.4 0.5 + - - -
6E VAL* 4.9 6.1 - - - -
9E ILE* 3.0 23.0 - - - +
10E VAL* 3.8 15.7 - - - +
9F ALA 3.5 6.6 + - - -
10F ALA 2.9 2.1 + - - -
12F LEU* 1.3 81.7 - - - +
14F PHE* 1.3 60.8 + - - -
15F GLY 2.7 1.4 + - - -
16F LEU* 2.6 42.1 + - - +
17F ILE* 3.2 12.4 - - - +
17G PHE* 5.3 9.2 - - - -
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Residues in contact with PHE 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 3.1 39.0 - - + -
10E VAL* 5.2 0.4 - - - +
12E ILE* 4.0 11.2 - - + -
13E ALA* 3.2 45.5 - - + -
16E PHE* 4.9 14.4 - + + -
101E BCR 5.0 0.2 - - + -
10F ALA 3.3 0.8 + - - -
11F LEU* 3.8 9.4 - - + +
13F SER* 1.3 81.2 + - - +
15F GLY* 1.3 62.0 + - - +
17F ILE* 2.8 26.9 - - - +
18F PHE* 3.9 35.6 - + - -
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Residues in contact with GLY 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU 3.0 13.0 + - - -
12F LEU 3.6 4.0 - - - -
13F SER 2.7 5.9 + - - -
14F PHE* 1.3 75.2 - - - +
16F LEU* 1.3 51.8 + - - +
17F ILE 2.7 16.5 + - - -
18F PHE* 2.7 27.0 + - - +
19F VAL* 3.2 12.4 + - - +
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Residues in contact with LEU 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 2.9 47.6 - - + +
13F SER* 2.6 16.9 + - - +
15F GLY* 1.3 70.3 - - - +
17F ILE* 1.3 62.3 + - + -
18F PHE 3.1 0.2 - - - -
19F VAL* 3.1 33.3 - - + +
20F GLY 3.1 18.2 + - - -
14G GLY* 4.1 28.3 - - - +
17G PHE* 4.8 9.5 - - + -
21G TYR* 3.6 14.5 + - - +
4H LEU* 6.1 2.0 - - + -
7H VAL* 4.5 16.6 - - + -
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Residues in contact with ILE 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 4.4 15.0 - - + -
13E ALA* 4.1 10.5 - - + -
101E BCR 3.6 45.8 - - + -
13F SER 3.2 15.9 - - - +
14F PHE* 2.8 33.2 - - - +
15F GLY 2.7 0.4 + - - -
16F LEU* 1.3 78.4 - - - +
18F PHE* 1.3 64.7 + - + +
21F TRP* 3.0 24.3 + - - +
17G PHE* 3.7 29.2 - - + -
24G TYR* 4.6 8.2 + - - +
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Residues in contact with PHE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PHE* 5.6 0.7 - + - -
101E BCR 3.3 50.9 - - + -
14F PHE* 3.9 36.6 - + - -
15F GLY* 2.7 12.9 + - - +
17F ILE* 1.3 84.4 - - + +
19F VAL* 1.3 71.0 + - - +
20F GLY 3.0 1.6 - - - -
21F TRP* 2.8 25.5 + + + -
22F GLY* 2.7 25.3 + - - -
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Residues in contact with VAL 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F GLY 3.6 5.6 - - - +
16F LEU* 3.1 50.0 - - + +
18F PHE* 1.3 78.1 - - - +
20F GLY* 1.3 61.2 + - - +
22F GLY* 4.0 0.9 + - - -
23F LEU* 3.4 24.9 + - + +
21G TYR* 3.9 11.9 - - + +
4H LEU* 6.2 4.0 - - + -
7H VAL* 4.8 12.8 - - + -
11H VAL* 5.7 2.5 - - + -
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Residues in contact with GLY 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LEU 3.1 6.7 + - - -
18F PHE 2.8 2.8 + - - -
19F VAL* 1.3 76.8 - - - +
21F TRP* 1.3 67.2 + - - +
22F GLY 2.8 4.2 + - - -
23F LEU* 2.8 16.2 + - - +
24F GLY 2.9 11.1 + - - -
21G TYR* 3.4 36.9 - - - -
24G TYR* 3.2 6.9 - - - -
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Residues in contact with TRP 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ILE* 5.2 6.3 - - + -
101E BCR 3.5 49.8 - - + -
17F ILE 3.0 22.5 + - - +
18F PHE* 2.8 29.4 + + + +
20F GLY* 1.3 70.6 - - - +
22F GLY* 1.3 69.4 + - - +
24F GLY* 3.4 2.4 + - - -
25F VAL* 3.1 26.8 + - + +
24G TYR* 3.1 27.3 - + + -
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Residues in contact with GLY 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PHE 2.7 17.5 + - - -
19F VAL 4.5 1.8 - - - -
20F GLY 2.8 1.8 + - - -
21F TRP* 1.3 72.3 - - - +
23F LEU* 1.3 52.6 + - - -
25F VAL* 2.4 37.8 + - - +
26F LEU* 2.9 10.2 + - - -
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F VAL* 3.4 22.2 - - + +
20F GLY* 2.8 6.5 + - - +
22F GLY* 1.3 68.7 - - - -
24F GLY* 1.3 65.6 + - - +
26F LEU* 2.6 37.6 + - + +
27F LEU* 2.6 29.2 + - + +
18G TYR* 6.2 1.8 - - + -
21G TYR* 4.3 23.1 - - + -
11H VAL* 4.5 18.2 - - + -
12H VAL* 6.3 1.8 - - + -
15H TRP* 4.4 21.5 - - + +
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Residues in contact with GLY 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F GLY 2.9 9.7 + - - -
21F TRP 3.7 1.8 - - - -
22F GLY 2.9 2.8 + - - -
23F LEU* 1.3 74.7 - - - +
25F VAL* 1.3 59.9 + - - +
27F LEU* 3.2 20.8 + - - +
28F LEU* 3.5 14.5 - - - +
21G TYR* 3.8 3.2 + - - +
24G TYR* 3.4 35.6 - - - +
25G LYS* 3.6 8.4 + - - +
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Residues in contact with VAL 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F TRP* 3.1 35.9 - - + +
22F GLY* 2.4 18.2 + - - +
24F GLY* 1.3 68.7 - - - -
26F LEU* 1.3 56.1 + - - +
27F LEU 3.0 2.2 - - - -
28F LEU* 2.4 54.1 + - + +
29F LYS* 3.5 2.6 + - - +
24G TYR* 5.8 0.9 - - + -
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F GLY 2.9 6.4 + - - +
23F LEU* 2.6 33.9 + - + +
25F VAL* 1.3 73.1 - - - +
27F LEU* 1.3 57.6 + - - +
28F LEU 2.9 4.3 + - - -
29F LYS* 3.3 16.6 + - + +
30F ILE* 3.5 15.9 - - + +
15H TRP* 3.2 40.8 - - + -
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 2.6 36.4 + - + +
24F GLY* 3.2 22.7 - - - +
26F LEU* 1.3 72.5 - - - +
28F LEU* 1.3 59.7 + - - +
30F ILE* 3.4 22.8 - - + +
31F GLN* 3.3 16.4 + - - +
21G TYR* 4.5 5.4 - - + +
22G GLN* 5.8 2.5 - - - +
25G LYS* 3.1 36.4 + - + +
15H TRP* 2.7 48.2 - - + +
18H ALA* 6.3 1.8 - - + -
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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
------------------------------------------------------------
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