Contacts of the helix formed by residues 24 - 41 (chain W) in PDB entry 1JJ2
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 24 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17270 G 5.6 3.2 + - - -
20440 G 4.1 4.1 + - - +
20W GLU* 3.4 26.7 + - + +
21W PRO* 2.9 23.0 + - + +
23W HIS* 1.3 117.5 - - + +
25W ARG* 1.3 65.6 + - - +
26W ALA 3.4 2.5 - - - -
27W ASP* 3.5 10.4 + - + +
28W LYS* 3.5 15.6 + - - +
63W ARG* 3.9 27.8 - - - +
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Residues in contact with ARG 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27270 A 5.2 6.1 + - - -
27280 C 4.2 17.4 + - - -
14W LEU 4.7 9.3 + - - -
15W ARG* 5.9 0.2 - - - +
17W ALA* 4.2 22.6 + - + +
18W ARG* 3.3 34.8 - - - +
20W GLU* 5.2 0.4 - - - -
21W PRO 3.7 1.9 + - - +
22W ASN* 3.5 29.7 + - - +
24W LYS* 1.3 75.0 - - - +
26W ALA* 1.3 65.8 + - - +
28W LYS* 2.7 10.2 + - - +
29W ALA* 2.7 22.6 + - - +
63W ARG 3.2 8.1 + - - +
64W ALA 3.0 25.1 + - - -
65W ASN* 4.5 2.4 + - - +
66W THR* 3.7 42.3 + - - +
67W PRO 5.3 2.4 + - - -
68W SER* 5.5 4.0 - - - +
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Residues in contact with ALA 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W ARG* 1.3 78.1 - - - +
27W ASP* 1.3 64.3 + - - +
29W ALA* 3.2 3.8 + - - +
30W MET* 2.9 27.5 + - - +
58W ALA* 4.5 3.6 - - - +
59W TRP* 3.3 43.3 - - + +
62W GLY 4.5 2.0 - - - +
63W ARG* 3.0 23.4 + - + +
66W THR* 3.5 14.0 + - - +
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Residues in contact with ASP 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13820 G 2.7 30.9 + - - +
13830 U 3.5 24.3 + - - +
24W LYS* 3.8 11.3 - - + +
25W ARG 3.0 0.6 + - - -
26W ALA* 1.3 75.0 - - - +
28W LYS* 1.3 64.0 + - - +
30W MET* 3.2 4.7 + - - +
31W ILE* 3.2 27.4 + - + +
59W TRP* 3.4 9.6 - - - -
63W ARG* 2.8 39.4 + - - +
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Residues in contact with LYS 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17280 G 4.1 23.9 + - - +
17290 A 2.7 35.0 + - - -
17310 C 5.3 1.8 - - - +
16W ASP 4.8 4.5 - - - +
17W ALA* 4.2 16.4 - - + -
20W GLU* 3.9 44.3 + - + +
24W LYS 3.5 1.2 + - - +
25W ARG 2.7 13.7 + - - +
27W ASP* 1.3 73.9 - - - +
29W ALA* 1.3 64.4 + - - +
31W ILE* 2.9 22.5 + - + +
32W LEU* 2.9 37.2 + - + +
35W GLU* 5.6 2.8 + - - -
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Residues in contact with ALA 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14W LEU* 4.6 11.0 - - + -
17W ALA* 4.3 10.0 - - + +
25W ARG 2.7 15.7 + - - +
26W ALA* 3.4 8.3 - - - +
28W LYS* 1.3 71.9 - - - +
30W MET* 1.3 64.3 + - - +
32W LEU* 2.9 20.6 + - - +
33W ILE* 3.0 19.4 + - + +
58W ALA* 4.7 8.3 - - + -
66W THR* 3.8 30.7 - - + +
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Residues in contact with MET 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13830 U 3.6 9.9 - - - +
13840 C 3.4 33.8 + - - +
26W ALA 2.9 11.3 + - - +
27W ASP* 3.5 11.2 - - - +
29W ALA* 1.3 76.1 - - - +
31W ILE* 1.3 61.0 + - + +
33W ILE* 3.9 7.2 + - - +
34W ARG* 3.5 19.6 + - - +
50W LEU* 4.0 9.6 - - + +
54W ILE* 4.2 16.4 - - - -
55W ASN* 3.1 37.0 - - - +
58W ALA* 3.2 35.0 - - + -
59W TRP* 3.3 14.6 - - + +
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Residues in contact with ILE 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13840 C 5.4 5.6 - - - +
17270 G 5.1 0.2 - - - +
17280 G 3.3 34.1 - - - +
27W ASP* 3.2 17.0 + - + +
28W LYS* 2.9 28.5 + - + +
30W MET* 1.3 78.8 - - + +
32W LEU* 1.3 65.3 + - + +
34W ARG* 3.1 12.1 + - + +
35W GLU* 3.0 49.7 + - + +
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Residues in contact with LEU 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W ILE* 5.0 1.6 - - + -
13W PRO 4.8 4.5 - - - +
14W LEU* 4.2 21.5 - - + -
16W ASP* 3.9 22.0 - - + +
17W ALA* 3.5 41.3 - - + +
28W LYS* 2.9 30.0 + - + +
29W ALA* 2.9 8.3 + - - +
31W ILE* 1.3 76.9 - - - +
33W ILE* 1.3 56.8 + - - +
35W GLU* 3.2 19.9 + - - +
36W HIS* 2.8 32.2 + - - +
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Residues in contact with ILE 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W ILE* 4.4 16.1 - - + +
14W LEU* 3.9 18.4 - - + -
29W ALA 3.0 18.5 + - - +
30W MET* 3.9 15.9 - - - +
32W LEU* 1.3 75.6 - - - +
34W ARG* 1.3 62.1 + - - +
36W HIS* 3.6 1.2 + - - +
37W LEU* 3.2 31.6 + - + +
50W LEU* 3.8 24.9 - - + -
54W ILE* 3.8 28.3 - - + -
58W ALA* 4.8 7.2 - - + -
70W ILE* 4.2 23.6 - - + -
72W VAL* 5.2 3.8 - - + -
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Residues in contact with ARG 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13840 C 3.8 22.2 + - - -
13850 G 2.9 30.1 + - - -
30W MET 3.5 11.8 + - - +
31W ILE* 3.1 14.3 + - - +
33W ILE* 1.3 78.3 - - - +
35W GLU* 1.3 62.6 + - + +
37W LEU* 4.1 0.2 - - - +
38W ALA* 3.1 26.7 + - - +
45W GLU* 3.0 41.1 + - + +
46W ASP* 4.9 1.4 + - - +
48W VAL* 2.5 42.8 + - + +
50W LEU* 4.2 14.5 - - + +
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Residues in contact with GLU 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17280 G 5.6 0.2 + - - -
17290 A 5.5 4.6 + - - -
28W LYS* 5.6 2.9 + - - -
31W ILE* 3.0 33.3 + - + +
32W LEU* 3.7 22.1 - - - +
34W ARG* 1.3 75.9 - - + +
36W HIS* 1.3 64.7 + - - +
38W ALA* 3.4 2.8 + - - +
39W LYS* 3.1 25.5 + - - +
45W GLU* 3.7 32.0 - - - +
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Residues in contact with HIS 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28550 G 4.1 9.2 + - - -
10W VAL* 3.4 19.3 - - + +
11W THR 4.3 2.0 + - - -
12W ILE* 3.0 48.3 - - + +
13W PRO* 3.9 19.1 - - + +
32W LEU 2.8 17.3 + - - +
33W ILE 3.8 3.1 - - - +
35W GLU* 1.3 74.4 - - - +
37W LEU* 1.3 68.1 + - - +
39W LYS* 3.2 3.8 + - - +
40W HIS* 2.9 64.9 + + + +
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Residues in contact with LEU 37 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W VAL* 5.3 1.3 - - + -
12W ILE* 4.4 10.3 - - + -
33W ILE* 3.2 24.5 + - + +
34W ARG 4.1 0.2 - - - +
36W HIS* 1.3 77.0 - - - +
38W ALA* 1.3 63.5 + - - +
41W PHE* 3.0 56.5 + - + +
43W VAL* 5.2 0.2 - - - +
48W VAL* 3.7 15.9 - - + +
50W LEU* 3.5 20.6 - - + -
72W VAL* 3.6 24.2 - - + -
74W ALA* 4.0 6.5 - - + -
83W ALA* 5.2 2.0 - - + -
85W VAL* 3.1 31.9 - - + -
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Residues in contact with ALA 38 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W ARG 3.1 18.9 + - - +
35W GLU* 3.6 6.1 - - - +
37W LEU* 1.3 76.9 - - - +
39W LYS* 1.3 59.8 + - - +
42W SER* 3.3 2.1 + - - -
43W VAL* 2.8 47.1 + - - +
45W GLU* 4.0 30.5 - - + +
48W VAL* 3.9 9.1 - - + +
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Residues in contact with LYS 39 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28340 G 3.1 49.8 + - - +
28350 C 3.4 16.8 + - - -
29050 A 3.4 34.1 - - - +
35W GLU 3.1 17.0 + - - +
36W HIS* 3.7 3.1 - - - +
38W ALA* 1.3 76.6 - - - +
40W HIS* 1.3 84.3 + - + +
42W SER* 3.2 15.3 + - - +
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Residues in contact with HIS 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28540 A 5.3 4.3 - + - -
28550 G 5.2 10.8 + - - -
29040 U 2.8 45.1 + - - +
29050 A 3.3 34.4 + - - +
8W ARG* 3.8 18.3 + - - +
10W VAL* 5.8 3.4 - - + -
36W HIS* 2.9 66.1 + + + +
39W LYS* 1.3 90.1 - - + +
41W PHE* 1.3 69.1 + - + +
42W SER 3.4 1.1 - - - -
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Residues in contact with PHE 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W GLU* 5.0 4.3 - - - -
8W ARG* 3.6 48.5 - - + +
10W VAL* 4.3 13.7 - - + -
37W LEU* 3.0 46.8 + - + +
40W HIS* 1.3 85.5 - - + +
42W SER* 1.3 71.0 + - - +
43W VAL* 3.1 16.5 - - + +
74W ALA* 3.7 33.7 - - + -
75W ALA 4.8 1.3 - - - -
76W ARG* 3.3 40.1 + - + +
83W ALA* 4.7 10.3 - - + -
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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
------------------------------------------------------------
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