Contacts of the helix formed by residues 2 - 25 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LYS* 5.3 2.8 - - - +
20E LEU* 3.7 31.8 - - + +
23E LYS* 6.5 0.2 - - + -
1G SER* 1.3 77.2 + - - +
3G LEU* 1.3 64.6 + - + +
5G GLU* 3.1 23.6 + - - +
6G LEU* 3.1 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 3 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 4.2 18.2 - - + -
24E TRP* 3.9 28.9 - - + -
21F LEU* 5.5 2.2 - - + -
1G SER 3.3 8.0 - - - +
2G LYS* 1.3 78.9 - - - +
4G LEU* 1.3 56.9 + - - +
6G LEU* 3.3 9.4 + - + +
7G LEU* 2.9 28.2 + - - +
3H LEU* 3.8 24.0 - - + -
4H LEU* 3.6 22.0 - - + -
7H LEU* 3.6 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 4 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G SER* 3.3 23.6 + - - +
2G LYS 3.3 1.0 - - - -
3G LEU* 1.3 72.8 - - - +
5G GLU* 1.3 67.2 + - - +
7G LEU* 3.1 28.0 + - + +
8G ARG* 2.9 21.7 + - - +
3H LEU* 4.1 17.0 - - + -
21I LEU 4.4 11.9 - - - +
22I GLU* 4.0 24.3 - - + +
25I GLY* 3.5 36.1 - - - +
26I NH2 4.0 2.9 - - - +
24J TRP* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 5 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LYS* 3.6 32.4 - - + +
1G SER* 3.3 18.5 + - - +
2G LYS* 3.1 12.8 + - - +
4G LEU* 1.3 77.4 - - + +
6G LEU* 1.3 64.5 + - - +
8G ARG* 2.9 39.3 + - - +
9G LYS* 3.0 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ALA* 3.6 30.7 - - + +
16E LYS* 4.3 13.6 - - + +
17E ALA* 4.4 9.9 - - + +
20E LEU* 4.1 13.9 - - + -
14F LEU* 4.8 3.6 - - + -
18F ILE* 4.8 7.2 - - + -
21F LEU* 4.0 26.9 - - + -
2G LYS 3.1 8.2 + - - +
3G LEU* 3.4 8.1 - - - +
5G GLU* 1.3 77.9 - - - +
7G LEU* 1.3 63.1 + - - +
9G LYS* 3.2 6.3 + - - +
10G LEU* 3.0 41.6 + - + +
7H LEU* 4.2 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G LEU 2.9 14.4 + - - +
4G LEU* 3.1 31.6 + - + +
6G LEU* 1.3 75.2 - - - +
8G ARG* 1.3 64.4 + - - +
10G LEU* 3.1 6.8 + - - +
11G GLY* 2.9 19.8 + - - -
3H LEU* 4.1 13.2 - - + -
6H LEU* 4.2 13.7 - - + -
7H LEU* 3.7 19.0 - - + +
10H LEU* 3.3 31.2 - - + -
18I ILE* 3.9 25.8 - - + +
21I LEU* 4.4 21.1 - - + -
22I GLU* 5.3 2.7 - - + -
24J TRP* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LYS* 4.7 6.5 - - - +
4G LEU 2.9 5.2 + - - +
5G GLU* 2.9 31.9 + - - +
7G LEU* 1.3 74.4 - - - +
9G LYS* 1.3 82.8 + - - +
11G GLY* 3.1 3.5 + - - -
12G GLU* 2.9 55.2 + - + +
18I ILE* 4.4 11.4 - - + +
22I GLU* 3.0 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LYS* 4.0 13.6 - - + +
12E GLU* 2.7 39.4 + - + +
13E ALA* 4.1 27.0 - - + +
16E LYS* 3.3 33.0 - - + +
5G GLU 3.0 13.8 + - - +
6G LEU 3.2 7.2 + - - +
8G ARG* 1.3 92.5 - - - +
10G LEU* 1.3 58.2 + - - +
12G GLU* 3.3 23.2 + - - +
13G ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ALA* 4.7 2.9 - - + -
14F LEU* 3.7 31.6 - - + -
18F ILE* 3.8 26.7 - - + -
6G LEU* 3.0 25.2 + - + +
7G LEU 3.5 5.6 - - - +
9G LYS* 1.3 75.0 - - - +
11G GLY* 1.3 57.3 + - - +
13G ALA* 3.5 4.5 + - - +
14G LEU* 2.9 32.8 + - - +
7H LEU* 3.8 37.2 - - + +
10H LEU* 4.5 16.8 - - + +
11H GLY* 4.7 7.4 - - - +
14H LEU* 3.8 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 11 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU 2.9 13.3 + - - -
8G ARG* 3.1 5.1 + - - -
10G LEU* 1.3 75.9 - - - +
12G GLU* 1.3 54.9 + - - +
14G LEU* 3.8 6.5 - - - +
15G HIS* 2.9 31.1 + - - +
10H LEU* 5.1 1.3 - - - +
15I HIS* 5.3 7.8 + - - -
18I ILE* 4.0 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LYS* 3.3 35.0 + - + +
8G ARG* 2.9 45.7 + - + +
9G LYS* 3.3 21.2 + - - +
11G GLY* 1.3 69.8 - - - +
13G ALA* 1.3 65.7 + - - +
15G HIS* 3.5 8.2 + - - +
16G LYS* 3.1 35.4 + - - +
15I HIS* 6.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 3.9 9.9 - - + +
9E LYS* 4.0 22.8 - - + +
10E LEU* 4.5 12.1 - - + +
13E ALA* 5.8 1.3 - - + -
9G LYS 2.9 17.2 + - - +
10G LEU* 3.8 4.5 - - - +
12G GLU* 1.3 72.0 - - - +
14G LEU* 1.3 60.3 + - - +
16G LYS* 3.3 5.6 + - - +
17G ALA* 2.9 28.4 + - - +
14H LEU* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU 2.9 18.6 + - - +
11G GLY* 3.8 6.1 - - - +
13G ALA* 1.3 73.5 - - - +
15G HIS* 1.3 60.3 + - - +
17G ALA* 3.3 2.8 + - - +
18G ILE* 3.0 53.9 + - + +
10H LEU* 3.8 21.1 - - + +
13H ALA* 4.3 10.5 - - + +
14H LEU* 3.9 33.6 - - + +
17H ALA* 4.4 9.0 - - + -
14I LEU* 3.8 18.8 - - + -
6J LEU* 5.4 1.3 - - + -
10J LEU* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 15 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G GLY 2.9 20.2 + - - +
12G GLU* 3.5 9.4 - - - +
13G ALA 3.3 0.2 - - - -
14G LEU* 1.3 75.2 - - - +
16G LYS* 1.3 66.4 + - + +
18G ILE* 3.4 11.5 + - - +
19G GLU* 3.1 52.7 + - + +
11I GLY* 5.6 6.0 + - - -
12I GLU* 6.3 3.8 - - + -
15I HIS* 5.4 27.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LYS 5.6 0.7 - - - +
5E GLU* 4.2 16.9 - - + +
6E LEU* 4.2 26.7 - - + +
9E LYS* 3.7 42.0 - - + +
12G GLU* 3.1 22.3 + - - +
13G ALA 3.6 5.6 - - - +
15G HIS* 1.3 78.2 - - + +
17G ALA* 1.3 64.4 + - - +
19G GLU* 3.2 17.0 + - - +
20G LEU* 3.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 4.6 12.9 - - + +
13G ALA 2.9 16.6 + - - +
14G LEU* 3.5 8.3 - - - +
16G LYS* 1.3 76.5 - - - +
18G ILE* 1.3 56.7 + - - +
20G LEU* 3.4 5.4 + - - +
21G LEU* 3.0 32.1 + - - +
14H LEU* 4.4 8.5 - - + -
17H ALA* 4.3 21.3 - - + -
18H ILE* 5.1 2.5 - - + -
21H LEU* 4.1 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 3.0 45.2 + - + +
15G HIS* 3.7 9.2 - - - +
16G LYS 3.3 0.2 - - - -
17G ALA* 1.3 72.3 - - + +
19G GLU* 1.3 61.3 + - + +
21G LEU* 3.1 15.0 + - + +
22G GLU* 2.9 33.4 + - + +
17H ALA* 5.6 1.1 - - + -
7I LEU* 4.1 29.6 - - + +
8I ARG* 4.4 17.5 - - + +
11I GLY* 4.1 24.5 - - - +
6J LEU* 6.0 0.9 - - + -
10J LEU* 4.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G HIS* 3.1 46.1 + - + +
16G LYS* 3.5 19.7 - - - +
18G ILE* 1.3 76.6 - - + +
20G LEU* 1.3 65.2 + - + +
22G GLU* 3.3 10.9 + - - +
23G LYS* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LYS* 3.6 30.5 - - + +
3E LEU* 3.5 41.3 - - + +
6E LEU* 4.4 6.1 - - + -
16G LYS* 3.0 34.9 + - + +
17G ALA* 3.5 8.5 - - - +
19G GLU* 1.3 78.8 - - + +
21G LEU* 1.3 63.1 + - - +
23G LYS* 3.1 9.6 + - + +
24G TRP* 2.9 35.9 + - + +
21H LEU* 4.0 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ALA 3.0 18.5 + - - +
18G ILE* 3.1 16.4 + - + +
20G LEU* 1.3 74.9 - - - +
22G GLU* 1.3 53.2 - - - +
24G TRP* 4.9 1.8 - - - -
25G GLY* 2.8 33.0 + - - +
17H ALA* 4.1 17.9 - - + +
20H LEU* 3.7 28.7 - - + -
21H LEU* 3.9 26.0 - - + +
24H TRP* 3.5 23.0 - - + -
4I LEU* 3.8 4.0 - - - +
7I LEU* 4.4 14.8 - - + -
6J LEU* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ILE* 2.9 24.9 + - + +
19G GLU* 3.4 11.2 - - - +
20G LEU 3.2 0.2 - - - -
21G LEU* 1.3 72.8 - - - +
23G LYS* 1.3 67.3 + - - +
25G GLY 3.0 18.7 - - - +
4I LEU* 2.7 45.1 - - - +
5I GLU* 4.8 0.3 + - - -
7I LEU* 4.3 6.1 - - + +
8I ARG* 2.7 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLU 3.1 8.8 + - - +
20G LEU* 3.1 11.1 + - + +
22G GLU* 1.3 80.7 - - - +
24G TRP* 1.3 76.9 + - + +
25G GLY 3.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LEU* 3.9 27.2 - - + +
4F LEU* 4.1 19.7 - - + -
20G LEU* 2.9 22.1 + - + +
21G LEU* 4.4 2.0 - - - +
23G LYS* 1.3 94.2 - - + +
25G GLY* 1.3 64.8 + - - +
26G NH2 3.9 0.3 + - - -
21H LEU* 3.4 37.2 - - + -
24H TRP* 4.5 16.9 - - + +
25H GLY* 3.4 37.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU 2.8 23.9 + - - -
22G GLU 3.0 14.3 - - - +
23G LYS 3.8 3.6 - - - +
24G TRP* 1.3 75.4 - - - +
26G NH2 1.3 47.8 + - - -
24H TRP* 3.4 23.0 - - - -
4I LEU* 3.6 13.3 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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