Contacts of the helix formed by residues 12 - 36 (chain W) in PDB entry 1KD1
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 12 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W MET* 1.3 76.0 - - - +
13W PRO* 1.3 71.1 - - - +
14W ALA* 3.3 16.3 + - + +
15W GLU* 2.5 70.4 + - + +
16W ARG* 3.1 10.0 + - - +
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Residues in contact with PRO 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W MET 4.1 1.3 - - - +
12W THR* 1.3 93.2 - - - +
14W ALA* 1.3 57.7 + - - +
16W ARG* 3.6 13.2 + - - +
17W GLU* 3.2 35.0 + - - +
63W GLU* 6.0 0.4 - - + -
65W ASP* 3.5 40.8 - - + +
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Residues in contact with ALA 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W THR* 2.7 17.4 + - + +
13W PRO* 1.3 78.4 - - - +
15W GLU* 1.3 56.1 + - + +
17W GLU* 3.6 9.3 + - - +
18W ALA* 3.0 27.0 + - - +
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Residues in contact with GLU 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W ASP 4.6 3.3 - - - +
11W MET* 3.6 22.9 - - + +
12W THR* 2.5 51.7 + - + +
14W ALA* 1.3 71.2 - - + +
16W ARG* 1.3 59.4 + - - +
18W ALA* 3.8 6.2 - - - +
19W GLU* 2.8 29.6 + - - +
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Residues in contact with ARG 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W ILE* 3.2 19.8 + - + +
9W ARG* 3.8 11.3 + - - +
11W MET* 3.5 38.8 + - + -
12W THR 3.1 7.5 + - - +
13W PRO* 3.8 16.8 - - - +
15W GLU* 1.3 75.3 - - - +
17W GLU* 1.3 53.2 + - - +
19W GLU* 2.9 3.0 + - - +
20W LEU* 2.5 39.2 + - - +
56W ILE* 3.9 19.0 - - + +
59W ILE* 4.0 8.9 - - - +
60W GLN* 4.2 19.1 - - + +
63W GLU* 3.2 45.4 + - - +
65W ASP 2.6 38.1 + - - -
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Residues in contact with GLU 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13W PRO* 3.2 23.0 + - - +
14W ALA* 3.8 8.4 - - - +
16W ARG* 1.3 77.9 - - - +
18W ALA* 1.3 57.2 + - - +
20W LEU* 3.4 10.4 - - + +
21W ASP* 3.0 40.5 + - - +
60W GLN* 3.7 18.4 - - - +
65W ASP* 5.5 5.5 - - - +
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Residues in contact with ALA 18 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14W ALA 3.0 17.7 + - - +
15W GLU* 3.9 7.0 - - - +
16W ARG 3.2 0.2 - - - -
17W GLU* 1.3 77.7 - - - +
19W GLU* 1.3 56.7 + - - +
21W ASP* 3.8 4.9 + - - +
22W ASP* 2.7 36.6 + - - +
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Residues in contact with GLU 19 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3W LEU* 4.0 12.7 - - + +
11W MET* 3.9 24.5 - - + -
15W GLU 2.8 19.9 + - - +
16W ARG* 3.3 4.3 - - - +
18W ALA* 1.3 73.8 - - - +
20W LEU* 1.3 66.0 + - - +
22W ASP* 3.2 14.2 + - - +
23W LEU* 2.9 48.2 + - - +
56W ILE* 3.7 18.4 - - + -
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Residues in contact with LEU 20 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16W ARG 2.5 20.6 + - - +
17W GLU* 3.4 9.4 - - + +
19W GLU* 1.3 72.6 - - - +
21W ASP* 1.3 61.7 + - - +
22W ASP 2.8 6.2 + - - -
23W LEU* 2.9 14.1 + - - +
24W LYS* 3.0 28.6 + - - +
53W ILE* 3.7 39.9 - - + +
56W ILE* 4.1 20.2 - - + +
57W LYS* 4.0 17.0 - - + +
60W GLN* 3.2 30.7 - - - +
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Residues in contact with ASP 21 (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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17W GLU* 3.0 22.7 + - - +
18W ALA* 4.2 5.5 - - - +
20W LEU* 1.3 81.2 - - - +
22W ASP* 1.3 58.5 + - - +
24W LYS* 3.9 21.6 + - - +
25W THR* 3.1 26.0 + - - -
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Residues in contact with ASP 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W ALA* 2.7 25.5 + - - +
19W GLU* 3.2 22.3 + - - +
20W LEU 2.9 0.6 - - - -
21W ASP* 1.3 77.3 - - - +
23W LEU* 1.3 68.0 + - + +
25W THR* 3.2 8.8 + - - +
26W GLU* 3.1 19.6 + - - +
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Residues in contact with LEU 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3W LEU* 4.3 4.3 - - + -
19W GLU* 2.9 28.4 + - - +
20W LEU 2.9 6.3 + - - +
22W ASP* 1.3 72.3 - - + +
24W LYS* 1.3 67.7 + - - +
26W GLU* 2.8 12.1 + - - +
27W LEU* 2.8 24.1 + - - +
49W LEU* 3.5 24.4 - - + +
52W ALA* 3.7 26.7 - - + -
53W ILE* 3.8 21.8 - - + -
56W ILE* 3.5 32.1 - - + -
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Residues in contact with LYS 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A U 5.1 4.2 + - - -
1T SER 5.7 1.2 + - - -
3T ASP* 4.0 26.6 + - - +
44T GLN* 6.2 0.2 - - - -
20W LEU* 3.0 37.3 + - + +
21W ASP* 3.9 23.2 + - - +
23W LEU* 1.3 75.5 - - - +
25W THR* 1.3 59.3 + - - +
27W LEU* 3.2 6.0 + - + +
28W LEU* 2.8 30.5 + - - +
53W ILE* 4.1 21.0 - - + +
57W LYS* 4.2 23.9 - - - +
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Residues in contact with THR 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T GLN* 4.4 16.9 + - - +
21W ASP 3.1 13.5 + - - -
22W ASP* 3.2 11.5 + - - -
23W LEU 3.1 0.8 - - - -
24W LYS* 1.3 76.2 - - - +
26W GLU* 1.3 65.8 + - - +
28W LEU* 3.3 7.1 + - + +
29W ASN* 2.9 46.4 + - - +
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Residues in contact with GLU 26 (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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22W ASP 3.1 11.0 + - - +
23W LEU* 2.8 18.6 + - - +
25W THR* 1.3 74.1 - - - +
27W LEU* 1.3 65.0 + - - +
29W ASN* 3.2 8.4 + - - +
30W ALA* 2.8 22.1 + - + +
45W ARG* 4.0 28.1 + - - +
49W LEU* 3.7 29.7 - - + +
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Residues in contact with LEU 27 (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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23W LEU 2.8 10.6 + - - +
24W LYS* 3.3 10.5 - - + +
26W GLU* 1.3 76.3 - - - +
28W LEU* 1.3 55.5 + - - +
30W ALA* 2.5 26.4 + - - +
31W ARG* 2.9 47.0 + - - +
46W ILE* 3.8 33.9 - - + +
49W LEU* 3.4 21.9 - - + +
50W ARG* 4.2 13.0 - - + -
53W ILE* 3.6 25.6 - - + -
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Residues in contact with LEU 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T ILE* 4.2 22.2 - - + +
6T LYS 3.6 29.8 - - - +
7T HIS* 4.4 4.0 - - - +
8T PRO* 5.0 2.5 - - + +
44T GLN* 3.4 31.0 - - + +
45T TYR* 3.9 21.8 - - + +
24W LYS 2.8 20.6 + - - +
25W THR* 3.7 7.9 - - + +
27W LEU* 1.3 73.5 - - - +
29W ASN* 1.3 61.4 + - - +
31W ARG* 3.6 10.9 + - - +
32W ALA* 3.1 24.9 + - - +
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Residues in contact with ASN 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80T ARG 5.8 0.7 - - - -
81T ILE* 3.1 30.4 - - + +
25W THR* 2.9 43.4 + - - +
26W GLU* 3.7 8.3 - - + +
28W LEU* 1.3 78.9 - - - +
30W ALA* 1.3 65.8 + - - +
32W ALA* 3.8 7.1 - - - +
33W VAL* 3.1 29.9 + - + +
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Residues in contact with ALA 30 (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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26W GLU* 2.8 12.1 + - + +
27W LEU* 2.5 23.4 + - - +
29W ASN* 1.3 71.4 - - - +
31W ARG* 1.3 54.8 + - - +
33W VAL* 3.0 9.9 + - - +
34W GLN* 2.9 27.9 + - - +
46W ILE* 4.3 26.6 - - + +
49W LEU* 4.6 5.6 - - + -
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Residues in contact with ARG 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A G 5.7 2.4 + - - -
3T ASP* 5.5 4.4 + - - -
5T ILE 5.6 1.0 + - - -
6T LYS* 3.8 23.8 + - - +
7T HIS* 4.1 18.1 - - + +
27W LEU* 2.9 46.5 + - + +
28W LEU* 3.8 15.6 - - - +
30W ALA* 1.3 74.4 - - - +
32W ALA* 1.3 53.5 + - - +
34W GLN* 3.2 14.5 + - - +
35W ALA* 2.6 36.5 + - - +
46W ILE* 4.5 14.0 - - + +
50W ARG* 4.9 13.7 - - - +
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Residues in contact with ALA 32 (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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8T PRO* 3.6 38.4 - - + +
10T VAL* 5.0 0.7 - - - +
81T ILE* 4.1 25.4 - - + -
28W LEU 3.1 15.4 + - - +
29W ASN* 3.8 7.0 - - - +
31W ARG* 1.3 75.6 - - - +
33W VAL* 1.3 63.2 + - - +
35W ALA* 3.1 3.2 + - - +
36W ALA* 2.9 25.3 + - - +
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Residues in contact with VAL 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T ILE 4.6 16.8 - - - -
29W ASN* 3.1 15.2 + - + +
30W ALA* 3.0 11.3 + - - +
32W ALA* 1.3 76.2 - - - +
34W GLN* 1.3 55.0 - - - +
36W ALA* 3.4 7.2 + - - +
38W GLY* 2.7 54.4 + - - +
40W PRO* 4.1 20.6 - - + -
41W GLU* 4.8 8.1 - - + +
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Residues in contact with GLN 34 (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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57A C 3.1 45.8 + - - -
58A C 4.1 9.6 + - - -
30W ALA 2.9 12.9 + - - +
31W ARG* 3.4 13.8 - - - +
33W VAL* 1.3 76.5 - - - +
35W ALA* 1.3 56.7 + - - +
36W ALA 3.0 4.7 - - - -
37W GLY* 2.8 21.7 + - - -
38W GLY 4.5 0.9 - - - +
41W GLU* 3.8 22.9 + - + +
46W ILE* 4.0 20.6 - - + +
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Residues in contact with ALA 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T HIS* 3.6 20.2 - - + +
8T PRO 3.3 23.8 - - - +
10T VAL* 2.7 24.8 - - + +
31W ARG 2.6 21.0 + - - +
32W ALA* 3.1 7.8 + - - +
34W GLN* 1.3 72.2 - - - +
36W ALA* 1.3 51.9 + - - +
37W GLY 3.2 2.7 + - - -
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Residues in contact with ALA 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T VAL* 3.4 22.2 - - + +
81T ILE 6.5 0.7 - - - -
32W ALA 2.9 15.0 + - - +
33W VAL* 3.9 6.3 - - - +
34W GLN 3.0 0.6 - - - -
35W ALA* 1.3 76.8 - - - +
37W GLY* 1.3 56.1 + - - +
38W GLY* 2.9 12.1 + - - +
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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