Contacts of the helix formed by residues 29 - 45 (chain C) in PDB entry 1LK7
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 GLY 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ASP* 3.1 22.7 - - - -
28C THR* 1.3 77.3 - - - +
30C SER* 1.3 60.4 + - - -
31C THR 3.5 2.0 + - - -
32C THR 3.6 0.7 + - - -
33C ALA* 3.0 29.5 + - - +
59C GLN* 2.7 19.1 + - - +
1003C DER 3.8 9.0 - - - -
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Residues in contact with SER 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLU* 5.1 4.3 - - - -
7C LYS* 2.8 32.4 + - - -
29C GLY* 1.3 69.1 - - - -
31C THR* 1.3 64.9 + - - +
33C ALA* 3.2 19.6 + - - +
34C TYR* 3.5 17.7 + - - -
100C ARG* 4.9 2.8 - - - +
1003C DER 2.4 32.4 + - - -
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Residues in contact with THR 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 3.4 44.9 - - + +
10C ALA* 4.8 0.7 - - + -
11C ALA* 4.1 5.4 - - - +
30C SER* 1.3 76.6 + - - +
32C THR* 1.3 63.7 + - - +
34C TYR* 3.2 26.6 + - - +
35C PHE* 3.6 3.1 + - - +
86C GLY* 5.1 0.2 - - - -
120C LEU* 3.4 43.8 + - + +
121C VAL* 4.2 5.5 - - - +
122C ASP* 4.9 0.5 + - - -
125C LYS* 4.5 4.2 + - - -
1003C DER 2.8 21.6 + - - -
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 3.4 42.8 - - - +
28C THR 4.0 2.9 + - - -
29C GLY 3.6 6.3 + - - -
30C SER 3.4 0.2 - - - -
31C THR* 1.3 77.0 - - - +
33C ALA* 1.3 60.1 + - - +
35C PHE* 2.8 33.5 + - + +
36C ILE* 2.9 20.7 + - + +
84C VAL* 3.7 10.5 - - + +
85C ASP* 3.3 5.9 + - - -
86C GLY* 3.1 27.7 + - - -
120C LEU* 4.4 5.4 - - - +
1003C DER 4.6 0.2 + - - -
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY 3.0 16.0 + - - +
30C SER* 3.2 14.6 + - - +
32C THR* 1.3 76.5 - - - +
34C TYR* 1.3 62.4 + - + +
36C ILE* 3.4 3.0 + - - -
37C LYS* 3.1 36.7 + - - +
59C GLN* 4.2 6.5 - - - +
63C LEU* 3.6 25.7 - - + +
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLU* 2.7 35.3 + - - +
7C LYS* 3.7 33.2 - - + -
8C LYS* 3.0 50.3 + - + -
11C ALA* 3.6 13.7 - - + -
30C SER* 3.5 20.6 + - - -
31C THR 3.2 7.5 + - - +
32C THR 3.1 0.6 - - - -
33C ALA* 1.3 78.4 - - + +
35C PHE* 1.3 58.9 + - - +
37C LYS* 3.4 14.4 + - + +
38C LEU* 2.9 39.2 + - + +
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 3.6 23.7 - - + +
14C ALA* 3.9 21.5 - - + -
15C LEU* 3.8 20.0 - - + -
18C ILE* 3.9 23.1 - - + -
24C ILE* 4.4 3.6 - - + -
26C LEU* 4.2 19.7 - - + -
31C THR 3.6 0.8 + - - -
32C THR* 2.8 14.8 + - + +
34C TYR* 1.3 80.3 - - - +
36C ILE* 1.3 65.0 + - + +
38C LEU* 3.4 4.0 + - - +
39C LEU* 2.9 39.7 + - + +
84C VAL* 3.7 35.9 - - + -
120C LEU* 3.9 18.2 - - + -
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 4.3 24.0 - - + -
27C GLY 4.0 20.9 - - - +
32C THR* 2.9 17.2 + - + +
33C ALA* 3.8 8.1 - - - +
35C PHE* 1.3 82.7 - - + +
37C LYS* 1.3 57.2 + - - +
39C LEU* 3.3 4.1 + - - +
40C GLY* 2.9 24.4 + - - -
59C GLN* 4.8 1.3 - - - +
60C ALA* 4.2 21.3 - - + +
63C LEU* 3.9 31.6 - - + +
64C ALA* 4.1 12.8 - - + +
67C HIS* 4.6 1.6 - - + +
69C ILE* 3.4 23.7 - - + +
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA* 3.1 27.2 + - - +
34C TYR* 3.6 15.5 - - + +
36C ILE* 1.3 76.7 - - - +
38C LEU* 1.3 63.8 + - + +
40C GLY* 3.3 2.4 + - - -
41C GLU* 3.0 34.5 + - - +
63C LEU* 3.9 21.3 - - + +
66C GLU* 4.2 5.1 + - - -
67C HIS* 3.3 45.9 + - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 4.6 4.5 - - + +
11C ALA* 4.2 6.5 - - + -
12C LYS* 4.1 34.1 - - + +
15C LEU* 3.6 19.3 - - + -
34C TYR* 2.9 29.2 + - + +
35C PHE 3.9 2.0 - - - +
37C LYS* 1.3 73.1 - - + +
39C LEU* 1.3 61.8 + - - +
41C GLU* 3.3 25.5 + - - +
42C LYS* 2.9 32.1 + - - +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 4.1 19.0 - - + +
18C ILE* 4.3 17.5 - - + -
24C ILE* 4.0 13.9 - - + -
26C LEU* 4.2 22.2 - - + -
35C PHE* 2.9 28.1 + - + +
36C ILE* 3.5 5.4 - - - +
37C LYS 3.3 0.2 - - - -
38C LEU* 1.3 75.4 - - - +
40C GLY* 1.3 62.8 + - - +
42C LYS* 3.2 4.1 + - + +
43C LEU* 3.0 21.7 + - - +
48C ILE* 4.4 8.7 - - + -
51C ILE* 3.3 35.0 - - + -
69C ILE* 4.4 15.3 - - + -
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE 2.9 14.4 + - - -
37C LYS 3.7 3.8 - - - -
38C LEU 3.2 0.4 - - - -
39C LEU* 1.3 77.3 - - - +
41C GLU* 1.3 55.9 + - - +
43C LEU* 3.2 4.4 + - - +
44C LYS* 2.9 30.7 + - - +
67C HIS* 3.7 27.3 - - - +
69C ILE* 3.8 12.1 - - - +
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LYS* 3.0 27.4 + - - +
38C LEU* 3.3 27.8 + - - +
40C GLY* 1.3 72.3 - - - +
42C LYS* 1.3 65.8 + - - +
44C LYS* 3.4 11.6 + - + +
45C ARG* 3.0 58.0 + - - +
67C HIS* 5.5 6.3 - - + -
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Residues in contact with LYS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 4.1 44.7 + - + +
18C ILE 5.2 1.2 + - - -
38C LEU 2.9 17.3 + - - +
39C LEU* 3.2 9.6 + - + +
41C GLU* 1.3 75.9 - - - +
43C LEU* 1.3 62.6 + - - +
45C ARG* 3.3 5.8 + - - +
46C GLY 3.1 4.2 + - - -
47C GLU* 2.9 76.1 + - - +
48C ILE* 4.0 21.6 - - + +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU 3.0 13.2 + - - +
40C GLY* 3.5 8.7 - - - +
42C LYS* 1.3 77.8 - - - +
44C LYS* 1.3 62.1 + - - +
46C GLY* 3.1 13.3 + - - -
48C ILE* 3.4 29.1 - - + +
49C SER* 3.9 13.9 - - - -
50C ASP 4.5 3.4 - - - +
51C ILE* 4.0 18.6 - - + +
68C ASP 4.0 11.9 - - - +
69C ILE* 4.1 11.7 - - + -
70C PRO* 3.7 31.0 - - + -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLY 2.9 16.0 + - - +
41C GLU* 3.6 12.8 - - + +
43C LEU* 1.3 76.3 - - - +
45C ARG* 1.3 60.0 + - + +
46C GLY 3.5 1.0 + - - -
67C HIS 6.0 0.2 - - - +
68C ASP* 6.2 1.6 - - + +
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Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLU* 3.0 60.7 + - - +
42C LYS* 3.6 7.9 - - - +
43C LEU 3.2 0.2 - - - -
44C LYS* 1.3 76.2 - - + +
46C GLY* 1.3 60.3 + - - +
47C GLU* 3.0 38.9 + - + +
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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
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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