Contacts of the helix formed by residues 2 - 25 (chain Q) in PDB entry 6C4Z
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 LYS 2 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q SER* 1.3 90.1 + - - +
3Q LEU* 1.3 70.3 + - + +
4Q LEU 3.3 0.9 - - - -
5Q GLU* 3.7 19.4 + - - +
6Q LEU* 3.2 21.7 + - - +
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Residues in contact with LEU 3 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1Q SER 4.2 5.8 - - - +
2Q LYS* 1.3 89.1 - - + +
4Q LEU* 1.3 56.8 + - + +
5Q GLU 3.3 0.2 - - - -
6Q LEU* 3.5 11.9 - - + +
7Q LEU* 2.6 34.7 + - - +
3R LEU* 4.4 22.2 - - + +
4R LEU* 3.4 33.4 - - + -
7R LEU* 4.1 13.5 - - + +
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Residues in contact with LEU 4 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O LEU 4.2 5.8 - - - +
22O GLU* 2.8 37.5 - - + +
25O GLY* 3.6 37.0 - - - +
26O NH2 4.0 2.0 - - - +
24P TRP* 4.3 11.0 - - + -
1Q SER* 4.1 25.4 - - - +
2Q LYS 3.3 0.2 - - - -
3Q LEU* 1.3 75.1 - - + +
5Q GLU* 1.3 64.9 + - + +
7Q LEU* 3.5 14.8 - - + +
8Q ARG 3.0 17.5 + - - -
3R LEU* 3.6 29.2 - - + -
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Residues in contact with GLU 5 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O GLU* 4.3 4.0 - - - +
1Q SER 3.8 16.5 + - - +
2Q LYS* 3.7 23.0 + - - +
4Q LEU* 1.3 77.6 - - - +
6Q LEU* 1.3 63.0 + - - +
8Q ARG* 3.1 9.8 + - - +
9Q LYS* 3.0 31.0 + - + +
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Residues in contact with LEU 6 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q LYS 3.2 12.6 + - - +
3Q LEU* 3.5 13.0 - - + +
4Q LEU 3.3 0.2 - - - -
5Q GLU* 1.3 79.3 - - - +
7Q LEU* 1.3 62.8 + - - +
9Q LYS* 3.3 11.1 + - + +
10Q LEU* 3.1 39.8 + - + +
7R LEU* 4.1 28.7 - - + -
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Residues in contact with LEU 7 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O ILE* 4.0 26.9 - - + +
21O LEU* 4.0 28.7 - - + -
22O GLU* 5.4 2.7 - - + +
20P LEU* 5.9 0.4 - - + -
3Q LEU 2.6 21.4 + - - +
4Q LEU* 3.5 19.1 - - + +
6Q LEU* 1.3 72.6 - - - +
8Q ARG* 1.3 64.7 + - - +
10Q LEU* 3.2 7.0 + - - +
11Q GLY* 3.0 18.4 + - - -
3R LEU* 4.7 7.9 - - + -
6R LEU* 3.9 17.5 - - + -
7R LEU* 3.7 20.2 - - + -
10R LEU* 3.3 31.6 - - + +
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Residues in contact with ARG 8 (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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15O HIS* 5.1 7.7 - - - -
18O ILE* 4.3 16.0 - - + +
19O GLU* 4.5 28.1 + - - +
22O GLU* 3.2 45.0 + - + +
4Q LEU 3.0 13.7 + - - +
5Q GLU* 3.3 11.0 - - - +
7Q LEU* 1.3 75.4 - - - +
9Q LYS* 1.3 60.1 + - + +
11Q GLY* 2.8 5.4 + - - -
12Q GLU* 2.7 62.9 + - + +
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Residues in contact with LYS 9 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q GLU* 3.0 23.4 + - + +
6Q LEU* 3.3 13.2 + - + +
8Q ARG* 1.3 79.1 - - + +
10Q LEU* 1.3 58.8 + - + +
12Q GLU* 3.2 25.7 + - - +
13Q ALA* 2.8 31.8 + - - +
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Residues in contact with LEU 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q LEU* 3.1 31.7 + - + +
7Q LEU* 3.2 6.3 + - - +
9Q LYS* 1.3 75.8 - - + +
11Q GLY* 1.3 53.0 + - - +
13Q ALA* 3.2 6.9 + - + +
14Q LEU* 2.8 35.3 + - - +
7R LEU* 3.9 36.6 - - + +
10R LEU* 4.3 26.9 - - + -
11R GLY* 4.6 9.9 - - - +
14R LEU* 4.2 23.0 - - + +
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Residues in contact with GLY 11 (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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14O LEU* 6.2 0.4 - - - -
15O HIS* 5.9 4.6 + - - -
18O ILE* 4.0 22.6 - - - +
7Q LEU 3.0 9.3 + - - -
8Q ARG* 2.8 7.4 + - - -
10Q LEU* 1.3 73.2 - - - +
12Q GLU* 1.3 64.0 + - - +
14Q LEU* 3.3 7.7 + - - +
15Q HIS* 3.0 24.1 + - - +
10R LEU* 5.2 4.0 - - - +
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Residues in contact with GLU 12 (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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15O HIS* 6.4 2.2 - - + -
8Q ARG* 2.7 52.3 + - + +
9Q LYS* 3.5 28.5 + - - +
11Q GLY* 1.3 71.0 - - - +
13Q ALA* 1.3 61.0 + - - +
15Q HIS* 3.4 8.9 + - - +
16Q LYS* 3.3 30.9 + - - +
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Residues in contact with ALA 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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9Q LYS 2.8 17.7 + - - +
10Q LEU* 3.6 5.2 - - + +
12Q GLU* 1.3 74.9 - - - +
14Q LEU* 1.3 66.5 + - - +
16Q LYS* 3.7 7.6 + - - +
17Q ALA* 3.3 13.3 + - - +
14R LEU* 3.7 26.8 - - + +
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Residues in contact with LEU 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O GLY* 6.4 0.2 - - - -
14O LEU* 3.8 17.9 - - + -
6P LEU* 5.1 1.6 - - + -
10P LEU* 3.4 33.4 - - + -
10Q LEU 2.8 16.3 + - - +
11Q GLY* 3.6 7.0 - - - +
13Q ALA* 1.3 74.4 - - - +
15Q HIS* 1.3 69.4 + - - +
17Q ALA* 2.8 15.6 + - - +
18Q ILE* 2.9 22.1 + - + +
10R LEU* 4.0 18.6 - - + +
13R ALA* 4.4 10.3 - - + -
14R LEU* 4.0 31.8 - - + +
17R ALA* 4.5 11.9 - - + -
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Residues in contact with HIS 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O GLY* 5.5 11.9 - - - -
12O GLU* 6.3 2.2 - - + -
15O HIS* 5.7 13.5 - + + +
11Q GLY 3.0 10.6 + - - +
12Q GLU* 3.4 14.4 + - - +
14Q LEU* 1.3 75.4 - - - +
16Q LYS* 1.3 64.5 + - - +
18Q ILE* 2.8 35.8 + - + +
19Q GLU* 2.9 42.7 + - + +
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Residues in contact with LYS 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 GLU* 3.3 20.3 + - - +
13Q ALA* 4.0 8.3 - - - +
14Q LEU 3.2 0.6 - - - -
15Q HIS* 1.3 88.6 - - - +
17Q ALA* 1.3 62.8 + - - +
19Q GLU* 3.4 11.7 + - - +
20Q LEU* 3.2 22.7 + - - +
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Residues in contact with ALA 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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13Q ALA 3.3 10.0 + - - +
14Q LEU* 2.8 10.8 + - - +
16Q LYS* 1.3 79.4 - - - +
18Q ILE* 1.3 61.3 + - - +
20Q LEU* 3.2 6.7 + - - +
21Q LEU* 3.0 27.9 + - - +
14R LEU* 4.5 8.3 - - + -
17R ALA* 3.9 26.2 - - + -
18R ILE* 5.1 3.6 - - + +
21R LEU* 4.2 17.6 - - + +
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Residues in contact with ILE 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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7O LEU* 3.9 25.2 - - + +
8O ARG* 4.3 25.6 - - + +
11O GLY* 4.1 23.1 - - - -
6P LEU* 5.5 1.8 - - + -
10P LEU* 4.0 25.1 - - + -
14Q LEU* 2.9 31.8 + - + +
15Q HIS* 2.8 21.6 + - + +
17Q ALA* 1.3 72.6 - - + +
19Q GLU* 1.3 65.8 + - + +
21Q LEU* 3.4 11.6 + - + +
22Q GLU* 3.1 25.8 + - - +
17R ALA* 5.8 0.4 - - + -
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Residues in contact with GLU 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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8O ARG* 5.2 15.1 + - - +
15Q HIS* 2.9 46.6 + - + +
16Q LYS* 3.7 15.3 - - - +
17Q ALA 3.3 0.2 - - - -
18Q ILE* 1.3 74.3 - - + +
20Q LEU* 1.3 63.3 + - - +
22Q GLU* 3.2 11.1 + - - +
23Q LYS* 3.1 21.2 + - - +
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Residues in contact with LEU 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 LYS 3.2 10.9 + - - +
17Q ALA* 3.4 9.2 - - - +
19Q GLU* 1.3 78.8 - - - +
21Q LEU* 1.3 63.7 + - - +
23Q LYS* 3.1 10.2 + - + +
24Q TRP* 3.0 58.4 + - + +
21R LEU* 3.4 33.9 - - + -
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Residues in contact with LEU 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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4O LEU* 4.3 3.0 - - + +
7O LEU* 4.3 15.7 - - + -
6P LEU* 3.9 27.6 - - + -
17Q ALA 3.0 21.0 + - - +
18Q ILE* 3.7 7.2 - - + +
20Q LEU* 1.3 75.6 - - - +
22Q GLU* 1.3 53.2 + - - +
24Q TRP* 4.7 2.0 - - - +
25Q GLY* 2.7 34.3 + - - -
17R ALA* 4.1 18.2 - - + +
20R LEU* 3.6 26.0 - - + -
21R LEU* 3.7 34.3 - - + +
24R TRP* 3.5 21.4 - - + -
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Residues in contact with GLU 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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4O LEU* 3.6 45.2 - - + +
5O GLU* 3.7 5.9 + - - -
7O LEU* 5.8 1.3 - - + +
8O ARG* 2.8 55.6 + - - +
18Q ILE* 3.1 16.8 + - + +
19Q GLU* 3.4 12.2 - - - +
20Q LEU 3.2 0.2 - - - -
21Q LEU* 1.3 76.5 - - - +
23Q LYS* 1.3 63.1 + - - +
25Q GLY 3.0 18.2 - - - +
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Residues in contact with LYS 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 GLU 3.1 11.0 + - - +
20Q LEU* 3.1 14.4 + - + +
22Q GLU* 1.3 77.4 - - - +
24Q TRP* 1.3 69.5 + - + +
25Q GLY 3.8 3.3 - - - +
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Residues in contact with TRP 24 (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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20Q LEU* 3.0 44.8 + - + +
21Q LEU* 4.0 2.9 - - - +
23Q LYS* 1.3 81.6 - - + +
25Q GLY* 1.3 64.6 + - - +
21R LEU* 3.5 38.6 - - + -
24R TRP* 4.3 15.9 - - + -
25R GLY* 3.3 38.4 - - - -
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Residues in contact with GLY 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4O LEU* 3.8 12.9 - - - +
21Q LEU 2.7 22.5 + - - -
22Q GLU 3.0 14.2 + - - +
23Q LYS 3.8 3.3 - - - +
24Q TRP* 1.3 75.7 - - - +
26Q NH2 1.3 48.2 + - - -
24R TRP* 3.4 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
------------------------------------------------------------
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