Contacts of the helix formed by residues 43 - 64 (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 PRO 43 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A C 3.5 42.5 + - + +
90A A 4.1 25.1 - - + +
91A G 4.0 13.5 - - - +
41W GLU* 3.6 17.2 - - + +
42W ASN* 1.3 86.4 - - - +
44W GLY* 1.3 62.9 + - - +
45W ARG 3.0 1.7 + - - -
46W ILE* 3.1 28.8 - - + +
47W LYS* 3.5 10.4 + - - +
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Residues in contact with GLY 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A G 3.3 9.0 + - - +
92A G 3.6 38.1 + - - -
42W ASN 2.5 8.6 + - - -
43W PRO* 1.3 74.5 - - - +
45W ARG* 1.3 56.3 + - - -
47W LYS* 3.7 9.1 - - - +
48W GLU* 3.0 30.3 + - - +
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Residues in contact with ARG 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A G 6.1 3.6 - - - +
1W THR* 6.4 0.9 - - + -
2W VAL* 4.8 21.9 - - + +
26W GLU* 4.0 25.3 + - - +
42W ASN* 2.7 27.1 + - + +
44W GLY* 1.3 70.5 - - - +
46W ILE* 1.3 56.2 + - - +
47W LYS 2.7 4.9 - - - -
48W GLU* 2.7 10.7 + - + +
49W LEU* 2.6 40.0 + - + +
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Residues in contact with ILE 46 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A C 3.8 26.9 - - - +
27W LEU* 3.8 19.2 - - + +
30W ALA* 4.3 23.6 - - + -
31W ARG* 4.5 13.5 - - + +
34W GLN* 4.0 30.3 - - + +
42W ASN 4.3 1.4 + - - -
43W PRO* 3.1 26.4 - - + +
45W ARG* 1.3 75.4 - - - +
47W LYS* 1.3 57.6 + - - +
49W LEU* 4.4 10.8 - - - -
50W ARG* 3.4 22.4 + - + +
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Residues in contact with LYS 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A C 3.8 27.4 - - - +
71A G 5.6 3.7 + - - -
83A C 3.6 29.9 + - - -
91A G 5.7 2.5 - - - +
92A G 5.8 1.6 - - - +
43W PRO 3.6 13.7 - - - +
44W GLY* 3.7 9.0 - - - +
45W ARG 2.7 0.2 - - - -
46W ILE* 1.3 81.1 - - - +
48W GLU* 1.3 73.4 + - - +
49W LEU 3.3 0.2 - - - -
50W ARG* 3.2 17.0 + - - +
51W LYS* 3.3 40.7 + - - +
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Residues in contact with GLU 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A G 4.3 7.3 + - - +
93A C 4.2 17.4 - - - +
1W THR* 3.4 44.6 + - + -
44W GLY 3.0 21.5 + - - +
45W ARG* 2.7 20.3 + - + +
47W LYS* 1.3 84.4 - - - +
49W LEU* 1.3 56.1 + - - +
51W LYS* 2.9 16.3 + - - +
52W ALA* 2.7 36.0 + - + +
55W ARG* 4.3 11.1 + - - -
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Residues in contact with LEU 49 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W LEU* 3.5 37.2 - - + +
26W GLU* 3.7 38.6 - - + +
27W LEU* 3.4 46.7 - - + +
30W ALA* 4.6 4.7 - - + -
45W ARG* 2.6 23.9 + - + +
46W ILE* 3.9 7.4 - - - +
48W GLU* 1.3 74.1 - - - +
50W ARG* 1.3 57.9 + - - +
52W ALA* 3.9 4.7 - - - +
53W ILE* 2.9 34.5 + - - +
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Residues in contact with ARG 50 (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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55A U 3.4 11.7 + - - -
56A G 3.0 44.2 + - - -
57A C 4.3 10.6 + - - -
68A U 4.4 1.6 - - - +
69A A 3.2 71.8 + - - +
70A A 3.6 11.5 + - - -
27W LEU* 4.2 16.4 - - + -
31W ARG* 4.9 10.4 - - - +
46W ILE* 3.4 19.3 - - - +
47W LYS* 3.2 8.9 + - - +
48W GLU 3.0 0.8 + - - -
49W LEU* 1.3 75.6 - - - +
51W LYS* 1.3 65.3 + - + +
53W ILE* 3.3 10.5 + - - +
54W ALA* 3.0 16.8 + - - +
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Residues in contact with LYS 51 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A A 4.3 2.2 - - - +
71A G 3.3 41.6 + - - +
72A C 3.5 28.4 + - - +
47W LYS* 3.3 34.2 + - - +
48W GLU* 2.9 21.4 + - - +
50W ARG* 1.3 74.0 - - + +
52W ALA* 1.3 60.8 + - - +
54W ALA* 3.0 9.5 + - - +
55W ARG* 2.8 52.3 + - - +
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Residues in contact with ALA 52 (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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3W LEU* 4.4 16.2 - - + -
8W ILE* 4.8 0.2 - - - +
23W LEU* 3.7 25.4 - - + -
48W GLU* 2.7 19.5 + - + +
49W LEU* 3.9 6.5 - - - +
51W LYS* 1.3 71.7 - - - +
53W ILE* 1.3 63.9 + - - +
55W ARG* 3.2 21.1 + - - +
56W ILE* 3.0 27.9 + - - +
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Residues in contact with ILE 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A U 4.4 12.3 - - - -
20W LEU* 3.7 23.3 - - + +
23W LEU* 3.8 20.4 - - + +
24W LYS* 4.1 29.6 - - + +
27W LEU* 3.6 28.0 - - + -
49W LEU 2.9 24.3 + - - +
50W ARG* 3.5 6.5 - - - +
51W LYS 3.2 0.6 - - - -
52W ALA* 1.3 76.4 - - - +
54W ALA* 1.3 62.5 + - - +
56W ILE* 3.9 1.7 - - - +
57W LYS* 3.1 38.6 + - + +
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Residues in contact with ALA 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A U 3.4 41.6 + - - +
69A A 4.1 2.7 - - - +
71A G 5.8 0.9 - - + +
72A C 3.7 16.2 - - - +
50W ARG 3.0 12.2 + - - +
51W LYS* 3.0 11.1 + - - +
53W ILE* 1.3 75.3 - - - +
55W ARG* 1.3 67.3 + - - +
57W LYS* 3.0 4.5 + - - +
58W THR* 2.7 26.7 + - - -
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Residues in contact with ARG 55 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A C 3.2 31.9 + - - +
73A C 3.6 22.3 + - - -
1W THR 3.9 19.7 - - - +
3W LEU* 3.7 20.4 + - - +
4W HIS* 6.0 0.6 - - - +
5W VAL* 4.3 15.3 - - + +
8W ILE* 3.6 17.9 - - + -
48W GLU* 4.3 8.9 + - - -
51W LYS* 2.8 35.6 + - - +
52W ALA* 3.5 28.5 - - - +
54W ALA* 1.3 74.4 - - - +
56W ILE* 1.3 65.0 + - - +
58W THR* 2.9 4.9 + - - -
59W ILE* 2.8 29.9 + - + +
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Residues in contact with ILE 56 (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 3.8 - - + -
8W ILE* 4.0 26.2 - - + +
11W MET* 5.4 1.3 - - + -
16W ARG* 3.9 35.2 - - + +
19W GLU* 3.7 22.2 - - + -
20W LEU* 4.1 17.9 - - + +
23W LEU* 3.5 31.0 - - + -
52W ALA 3.0 13.6 + - - +
53W ILE 3.9 3.6 - - - +
55W ARG* 1.3 75.2 - - - +
57W LYS* 1.3 64.3 + - - +
59W ILE* 3.2 1.6 + - - +
60W GLN* 2.8 38.4 + - - +
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Residues in contact with LYS 57 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A U 3.4 73.8 + - + +
1T SER* 6.0 2.0 - - - +
20W LEU* 4.0 20.6 - - + +
24W LYS* 4.2 15.3 - - - +
53W ILE* 3.1 31.0 + - - +
54W ALA 3.0 5.0 + - - +
56W ILE* 1.3 76.4 - - - +
58W THR* 1.3 63.3 + - - +
60W GLN* 3.3 19.2 + - - +
61W GLY* 3.1 19.1 + - - -
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Residues in contact with THR 58 (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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68A U 3.5 21.2 + - - +
72A C 2.6 31.3 + - - +
73A C 3.5 27.1 - - - +
105A G 4.3 4.7 - - - +
106A A 4.9 9.2 + - - +
54W ALA 2.7 15.5 + - - -
55W ARG* 3.1 8.3 - - - -
57W LYS* 1.3 78.3 - - - +
59W ILE* 1.3 58.1 + - + +
61W GLY* 3.2 3.6 + - - -
62W GLU* 2.9 42.6 + - + +
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Residues in contact with ILE 59 (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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73A C 4.7 9.2 - - - -
5W VAL* 4.2 9.6 - - + -
8W ILE* 3.4 32.8 - - + -
9W ARG* 3.5 46.0 - - + +
16W ARG* 4.0 9.6 - - - +
55W ARG* 2.8 24.6 + - + +
56W ILE 3.7 1.3 - - - +
58W THR* 1.3 68.4 - - - +
60W GLN* 1.3 59.3 + - - +
61W GLY 2.9 2.0 - - - -
62W GLU* 2.7 34.7 + - - +
63W GLU* 2.8 34.4 + - + +
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Residues in contact with GLN 60 (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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13W PRO 5.0 0.2 - - - +
16W ARG* 4.2 15.6 - - + +
17W GLU* 3.7 26.2 + - - +
20W LEU* 3.2 30.9 - - - +
56W ILE* 2.8 31.6 + - + +
57W LYS* 3.5 25.8 - - - +
59W ILE* 1.3 74.9 - - - +
61W GLY* 1.3 61.4 + - - +
64W GLY 3.2 1.6 + - - -
65W ASP* 2.7 52.0 + - - +
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Residues in contact with GLY 61 (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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68A U 5.9 0.7 - - - -
106A A 5.5 5.6 - - - -
57W LYS 3.1 12.0 + - - -
58W THR 3.2 5.1 + - - -
59W ILE 2.9 1.0 - - - -
60W GLN* 1.3 77.2 - - - +
62W GLU* 1.3 64.7 + - - +
64W GLY* 3.5 9.9 + - - -
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Residues in contact with GLU 62 (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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73A C 2.9 32.7 + - - +
105A G 5.1 1.4 + - - +
106A A 6.4 2.0 - - - -
9W ARG* 2.8 28.4 + - - -
58W THR* 2.9 26.2 + - + +
59W ILE* 2.7 20.2 + - - +
61W GLY* 1.3 73.0 - - - +
63W GLU* 1.3 68.0 + - + +
64W GLY* 3.4 0.7 + - - -
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Residues in contact with GLU 63 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W ARG* 4.0 21.4 + - - +
13W PRO* 6.0 0.7 - - + -
16W ARG* 3.2 44.5 + - - +
59W ILE* 2.8 30.0 + - + +
62W GLU* 1.3 80.3 - - - +
64W GLY* 1.3 58.8 + - - +
65W ASP 4.3 2.9 - - - +
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Residues in contact with GLY 64 (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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60W GLN 3.2 4.3 + - - -
61W GLY 3.5 6.8 + - - -
62W GLU 3.3 3.8 - - - -
63W GLU* 1.3 79.8 - - - +
65W ASP* 1.3 81.1 + - - +
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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