Contacts of the helix formed by residues 47 - 71 (chain A) in PDB entry 1L8Z
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 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MET* 3.4 41.4 - - + +
45A GLU* 2.6 5.1 + - - +
46A LYS* 1.3 75.4 - - - +
48A GLU* 1.3 59.9 + - - +
51A MET* 2.6 42.9 - - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 5.2 4.3 - - - -
40A THR* 3.8 10.4 - - - +
41A TRP 3.8 5.8 - - - +
44A MET* 3.1 49.2 - - + +
45A GLU 3.0 1.8 + - - -
47A LYS* 1.3 83.2 - - - +
49A LYS* 1.3 59.3 - - - +
51A MET* 2.9 6.2 + - - +
52A TRP* 2.7 73.7 + - + +
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 2.7 68.6 - - + +
42A ASN* 3.1 39.1 + - - +
45A GLU* 3.3 28.9 - - - +
46A LYS* 3.9 3.6 - - - +
48A GLU* 1.3 80.4 - - - +
50A LEU* 1.3 68.2 + - + +
52A TRP* 3.0 11.8 + - - +
53A ILE* 3.1 16.8 + - + +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.0 51.7 + - + +
49A LYS* 1.3 80.9 - - + +
51A MET* 1.3 57.8 + - + +
53A ILE* 3.0 44.1 - - + +
54A LYS* 3.4 10.8 + - - +
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Residues in contact with MET 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS 4.3 2.0 - - - +
47A LYS* 2.6 34.1 + - - +
48A GLU* 2.9 5.0 + - - +
50A LEU* 1.3 73.9 - - + +
52A TRP* 1.3 69.9 + - + +
54A LYS* 3.2 10.2 + - - +
55A LYS* 3.1 22.1 + - - +
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Residues in contact with TRP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ARG 2.6 21.2 - - - +
10A ALA* 3.8 11.9 - - + +
13A ILE* 3.4 7.0 - - + +
14A TRP* 2.9 89.1 - + + +
37A MET* 3.6 13.7 - - + -
40A THR* 4.5 0.9 - - + -
41A TRP* 3.0 51.8 - + + -
48A GLU* 2.7 71.4 + - + +
49A LYS 3.0 7.6 + - - +
51A MET* 1.3 75.6 - - + +
53A ILE* 1.3 59.3 + - - +
55A LYS* 3.1 16.8 + - + +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.9 38.9 - - + +
10A ALA* 3.3 15.3 - - + +
41A TRP* 4.9 3.4 - - + -
49A LYS* 3.1 13.0 - - + +
50A LEU* 3.0 41.1 - - + +
52A TRP* 1.3 75.8 - - - +
54A LYS* 1.3 52.7 + - - +
55A LYS 3.0 1.0 + - - -
57A ALA* 2.5 41.6 + - + +
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.4 9.7 + - - +
51A MET* 3.2 11.7 + - - +
53A ILE* 1.3 80.0 - - - +
55A LYS* 1.3 55.7 + - - +
57A ALA* 3.5 11.2 - - + -
58A GLU* 2.5 52.4 + - + +
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 2.9 43.6 - - + +
14A TRP* 5.9 2.7 - - + -
51A MET 3.1 11.5 + - - +
52A TRP* 3.1 6.4 + - + +
53A ILE 3.0 0.8 + - - -
54A LYS* 1.3 80.0 - - - +
56A ALA* 1.3 59.1 + - - +
58A GLU* 3.6 5.4 - - - +
59A ASP* 3.1 23.2 + - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PRO* 3.2 8.1 - - + +
9A ARG* 2.8 38.6 - - - +
12A GLU* 3.7 5.8 - - + -
13A ILE* 3.2 29.6 - - + +
52A TRP 3.4 0.4 + - - -
53A ILE 3.1 1.8 + - - -
55A LYS* 1.3 77.7 - - - +
57A ALA* 1.3 54.7 + - - +
58A GLU 3.2 0.4 - - - -
59A ASP* 3.4 2.9 - - - -
60A GLN* 2.5 34.7 + - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ARG* 3.1 27.1 - - + +
53A ILE* 2.5 30.9 + - + +
54A LYS* 3.5 13.5 - - + -
56A ALA* 1.3 69.0 - - - +
58A GLU* 1.3 66.4 + - - +
59A ASP 3.1 0.4 - - - -
60A GLN* 3.4 22.5 + - - +
61A LYS* 3.8 5.4 + - - +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 2.5 39.4 + - + +
55A LYS* 3.6 5.8 - - - +
57A ALA* 1.3 76.0 - - - +
59A ASP* 1.3 61.4 + - - +
61A LYS* 3.6 26.9 + - + +
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PRO* 3.8 10.4 - - + +
13A ILE* 3.6 15.1 - - + +
55A LYS 3.1 18.6 + - - +
56A ALA* 3.4 11.0 - - - +
57A ALA 3.1 0.2 - - - -
58A GLU* 1.3 79.7 - - - +
60A GLN* 1.3 57.1 + - - +
61A LYS 3.0 10.1 + - - -
62A ARG* 3.1 26.6 + - - +
63A TYR* 4.0 0.7 + - - +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PRO* 3.1 20.9 - - + -
9A ARG* 3.1 37.8 + - - +
56A ALA 2.5 20.2 + - - +
57A ALA* 3.4 18.8 + - - +
58A GLU 3.4 0.2 - - - -
59A ASP* 1.3 70.2 - - - +
61A LYS* 1.2 64.0 + - - +
62A ARG 3.2 0.2 - - - -
63A TYR* 2.8 36.6 - - + -
64A GLU* 2.4 50.3 + - - +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA 3.8 4.8 + - - +
58A GLU* 3.6 27.5 + - + +
60A GLN* 1.2 86.4 - - - +
62A ARG* 1.3 67.9 + - + +
63A TYR 3.1 0.2 + - - -
64A GLU* 3.2 10.6 + - + +
65A ARG* 3.0 22.7 + - - +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 3.1 17.6 + - - +
61A LYS* 1.3 85.4 - - + +
63A TYR* 1.2 66.2 + - + +
65A ARG* 3.3 18.1 - - - +
66A GLU* 3.2 27.5 + - - +
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.5 0.7 - - - -
4A PRO* 2.8 27.4 - - + +
5A GLU* 2.7 46.8 + - + +
6A SER* 2.4 37.2 + - - -
7A PRO* 2.7 28.3 - - + -
59A ASP 4.3 0.2 - - - +
60A GLN* 2.8 29.8 - - + +
62A ARG* 1.2 86.1 - - + +
64A GLU* 1.3 55.0 + - - -
65A ARG 3.0 2.0 - - - -
66A GLU* 2.9 11.4 - - - +
67A LEU* 2.8 28.4 - - + +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 2.4 54.6 + - - +
61A LYS* 3.5 10.3 - - - +
63A TYR* 1.3 72.5 - - - +
65A ARG* 1.2 57.1 + - + +
67A LEU* 2.8 22.8 - - + +
68A SER* 2.7 41.8 + - - -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS 3.0 18.2 - - - +
62A ARG* 3.3 15.8 - - - +
64A GLU* 1.2 78.6 - - + +
66A GLU* 1.3 65.8 + - - +
67A LEU 3.0 1.1 - - - -
68A SER* 4.2 5.6 - - - -
69A GLU* 2.6 51.7 + - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 2.8 27.0 - - - +
4A PRO* 2.6 42.2 - - + -
62A ARG* 3.2 24.6 + - - +
63A TYR* 2.9 4.4 + - - +
65A ARG* 1.3 85.3 - - - +
67A LEU* 1.3 62.6 + - - +
69A GLU* 3.0 19.2 - - - +
70A MET* 3.8 0.9 + - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 2.8 8.2 - - - +
2A LYS* 2.8 43.5 - - + +
3A LEU* 5.2 0.2 - - - -
4A PRO* 3.7 10.1 - - + -
63A TYR* 2.8 32.3 - - + +
64A GLU* 2.8 48.3 + - + +
65A ARG 3.0 0.2 - - - -
66A GLU* 1.3 77.8 - - - +
68A SER* 1.3 70.4 + - - +
69A GLU 2.8 2.0 - - - -
70A MET* 2.5 26.5 + - - +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 4.0 7.0 - - - +
64A GLU* 2.7 23.8 + - - -
65A ARG* 4.2 4.0 - - - -
67A LEU* 1.3 77.2 - - - +
69A GLU* 1.4 48.2 - - - -
71A ARG* 2.2 25.2 + - - -
72A ALA* 2.2 38.9 - - - +
75A ALA* 3.3 12.1 + - - +
79A SER* 5.1 1.4 + - - -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 2.6 44.2 + - + +
66A GLU* 3.0 17.4 - - - +
67A LEU 2.6 1.4 + - - -
68A SER* 1.4 71.8 - - - +
70A MET* 1.3 58.7 + - - +
72A ALA* 2.5 37.3 - - - +
73A PRO* 2.9 4.5 - - - +
75A ALA 4.7 1.5 + - - -
76A ALA* 4.3 7.8 - - - +
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Residues in contact with MET 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 3.4 17.3 - - - +
2A LYS* 3.5 27.1 - - + -
3A LEU* 5.6 2.0 - - - -
66A GLU 4.3 0.7 - - - +
67A LEU 2.5 16.4 + - - +
69A GLU* 1.3 78.7 - - + +
71A ARG* 1.2 64.0 + - + +
73A PRO* 2.8 21.8 - - - +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 3.1 30.0 + - - +
68A SER* 2.2 11.8 + - - +
70A MET* 1.2 77.9 - - - +
72A ALA* 1.2 51.5 + - + +
73A PRO* 2.5 13.8 - - + +
74A PRO* 3.8 2.4 - - - +
75A ALA* 2.4 25.3 - - + +
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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
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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