Contacts of the helix formed by residues 49 - 72 (chain A) in PDB entry 5LUQ
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 ALA 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 1.3 77.9 - - + +
50A VAL* 1.3 66.2 + - + +
52A ALA* 3.4 7.2 - - - +
53A LEU* 2.8 42.7 + - + +
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 6.2 1.1 - - - -
48A PRO 2.5 7.2 + - - +
49A ALA* 1.3 83.2 - - + +
51A LEU* 1.3 82.7 + - + +
53A LEU* 3.9 1.7 - - - +
54A GLN* 3.0 31.5 + - + +
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Residues in contact with LEU 51 (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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44A LEU 5.1 0.2 - - - +
45A SER* 3.9 15.5 - - - -
46A SER* 3.1 35.4 - - - +
47A SER* 3.1 34.8 - - - +
48A PRO 3.1 1.2 + - - +
50A VAL* 1.3 86.5 - - + +
52A ALA* 1.3 49.6 + - - +
54A GLN* 3.6 19.0 + - - +
55A THR* 2.5 42.0 + - - +
96A MSE 5.8 0.2 - - - -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER 3.8 1.0 + - - -
48A PRO* 3.4 14.2 + - + -
49A ALA* 3.4 22.9 - - - +
50A VAL 3.1 0.6 - - - -
51A LEU* 1.3 78.7 - - - +
53A LEU* 1.3 58.7 + - + +
55A THR* 2.7 19.9 + - - -
56A SER* 2.9 20.8 + - - -
96A MSE 5.3 11.4 - - - +
99A LYS* 5.4 8.1 - - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 2.8 28.3 + - - +
50A VAL* 3.9 1.8 - - - +
52A ALA* 1.3 69.2 - - - +
54A GLN* 1.3 66.5 + - - +
56A SER* 2.8 23.6 + - - +
57A LEU* 3.8 20.1 - - + +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A CYS* 3.5 38.8 - - - +
12A LEU* 6.0 3.0 - - + +
50A VAL* 3.0 21.9 + - + +
51A LEU* 3.7 26.0 - - - +
53A LEU* 1.3 80.5 - - - +
55A THR* 1.3 65.2 + - + +
56A SER 3.3 0.3 + - - -
57A LEU* 3.8 7.7 + - - +
58A VAL* 3.4 22.7 + - + +
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.4 2.0 - - + -
42A CYS* 3.6 22.9 - - - +
45A SER* 3.0 31.6 - - - +
51A LEU* 2.5 24.3 + - - +
52A ALA* 2.7 17.7 + - - -
54A GLN* 1.3 77.1 - - + +
56A SER* 1.3 63.4 + - - +
57A LEU 3.5 0.2 - - - -
58A VAL* 3.7 7.8 - - - +
59A PHE* 2.9 40.0 + - + +
96A MSE 4.5 10.4 - - + +
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA 2.9 12.1 + - - -
53A LEU* 2.8 28.8 + - - +
55A THR* 1.3 76.5 + - - +
57A LEU* 1.3 72.1 + - - +
59A PHE* 3.9 4.0 - - - +
60A SER* 3.0 29.4 + - - -
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Residues in contact with LEU 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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13A LEU* 4.1 25.1 - - + -
53A LEU* 3.8 23.1 - - + +
54A GLN* 4.2 5.8 - - - +
55A THR 3.5 0.2 - - - -
56A SER* 1.3 80.1 - - - +
58A VAL* 1.3 63.5 + - - +
60A SER* 3.2 6.2 + - - -
61A ARG* 3.0 35.2 + - - +
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Residues in contact with VAL 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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10A CYS 5.0 4.0 - - - +
12A LEU* 3.6 43.3 - - + -
13A LEU* 3.8 23.8 - - + -
16A GLN* 3.6 14.3 + - - +
38A LEU* 5.0 5.8 - - + +
42A CYS* 3.9 17.5 - - + -
54A GLN 3.4 17.3 - - - +
55A THR* 3.5 8.7 + - - +
56A SER 3.2 0.6 - - - -
57A LEU* 1.3 77.5 - - + +
59A PHE* 1.3 66.9 + - + +
61A ARG 3.4 0.2 + - - -
62A ASP* 2.9 26.5 + - + +
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Residues in contact with PHE 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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38A LEU 5.2 0.4 - - - -
42A CYS* 3.3 34.5 - - + -
55A THR* 2.9 27.7 + - + +
56A SER* 3.9 4.0 - - - +
58A VAL* 1.3 75.0 - - + +
60A SER* 1.3 58.1 + - - +
62A ASP* 3.1 9.5 + - - +
63A PHE* 2.8 54.8 + + + -
89A LEU* 5.0 2.0 - - + -
92A PHE* 3.2 57.4 - + + -
93A LEU* 6.2 0.2 - - + -
96A MSE 3.4 37.2 - - + -
100A ILE* 5.1 6.3 - - + -
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Residues in contact with SER 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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56A SER* 3.0 21.3 + - - -
57A LEU* 3.6 6.5 - - - -
58A VAL 3.2 0.2 - - - -
59A PHE* 1.3 77.6 - - - +
61A ARG* 1.3 64.9 + - - +
62A ASP 3.0 1.2 + - - -
63A PHE* 3.2 5.2 + - - +
64A GLY* 3.1 19.9 + - - -
103A TYR* 3.1 50.6 + - - -
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Residues in contact with ARG 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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13A LEU* 3.3 43.3 - - - +
14A ARG* 5.5 2.0 - - - +
16A GLN* 2.9 23.1 - - - +
17A GLU* 2.4 40.8 + - - -
57A LEU* 3.0 20.9 + - - +
60A SER* 1.3 77.2 - - - +
62A ASP* 1.3 49.3 + - - +
64A GLY* 5.4 0.7 - - - -
65A LEU* 2.6 49.1 + - + +
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Residues in contact with ASP 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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16A GLN* 3.7 16.9 + - - +
38A LEU* 4.7 19.8 - - - +
58A VAL* 2.9 21.5 + - + +
59A PHE* 3.1 13.4 - - - +
60A SER 2.9 0.2 - - - -
61A ARG* 1.3 74.1 - - - +
63A PHE* 1.3 66.0 + - - +
65A LEU* 3.3 3.5 + - - +
66A LEU* 2.9 24.9 + - - +
85A ILE* 3.6 19.9 - - - +
89A LEU* 3.7 21.0 - - + +
92A PHE* 4.3 11.1 - - - -
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Residues in contact with PHE 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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59A PHE* 2.8 52.5 + + + -
60A SER* 3.2 3.6 + - - +
62A ASP* 1.3 74.5 - - - +
64A GLY* 1.3 66.7 + - - +
66A LEU* 3.0 12.1 - - - +
67A VAL* 3.0 24.6 + - + +
89A LEU* 3.4 43.5 - - + -
92A PHE* 5.7 1.3 - + + -
93A LEU* 4.0 20.2 - - + -
100A ILE* 3.8 20.0 - - + -
103A TYR* 3.7 24.7 - + + +
106A GLU* 6.1 1.6 - - + +
107A ILE* 3.5 35.0 - - + -
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Residues in contact with GLY 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 SER 3.1 10.5 + - - -
61A ARG* 4.4 0.7 - - - -
63A PHE* 1.3 78.4 - - - +
65A LEU* 1.3 63.3 + - - +
67A VAL* 3.0 18.9 + - - +
68A PHE* 3.0 28.8 + - - -
103A TYR* 5.7 1.2 - - - -
106A GLU* 6.1 0.9 - - - -
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Residues in contact with LEU 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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16A GLN* 3.9 29.6 - - + +
17A GLU* 4.9 5.4 - - + +
20A SER* 3.2 41.7 - - - +
24A ARG* 4.8 4.3 - - - +
61A ARG* 2.6 29.6 + - + +
62A ASP* 3.6 4.3 - - - +
64A GLY* 1.3 74.3 - - - +
66A LEU* 1.3 57.9 + - - +
68A PHE* 3.4 31.6 - - + -
69A VAL* 2.8 38.7 + - + +
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Residues in contact with LEU 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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62A ASP* 2.9 24.3 + - - +
63A PHE* 3.0 14.6 - - - +
65A LEU* 1.3 76.7 - - - +
67A VAL* 1.3 76.7 + - + +
69A VAL* 3.8 8.9 - - + +
70A ARG* 3.0 22.3 + - - +
82A ARG* 4.9 10.8 - - + +
85A ILE* 3.4 37.5 - - + -
86A LEU* 4.1 30.5 - - + -
89A LEU* 3.4 30.3 - - + -
110A THR* 4.5 6.1 - - + -
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Residues in contact with VAL 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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63A PHE* 3.0 25.4 + - + +
64A GLY* 3.0 13.1 + - - +
66A LEU* 1.3 87.1 - - + +
68A PHE* 1.3 63.9 + - + +
71A LYS* 2.7 41.1 + - + +
106A GLU* 5.4 4.0 - - + +
107A ILE* 5.6 4.3 - - + -
110A THR* 3.4 40.8 - - + +
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Residues in contact with PHE 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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24A ARG* 3.0 36.6 - - - -
64A GLY* 3.0 25.2 + - - -
65A LEU* 3.4 38.4 - - + -
67A VAL* 1.3 81.8 - - + +
69A VAL* 1.3 62.2 + - + +
71A LYS* 3.7 8.7 - - - -
72A SER* 2.2 40.4 + - - +
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Residues in contact with VAL 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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20A SER* 3.8 26.0 - - - +
23A ASP* 3.2 25.6 - - - +
24A ARG* 4.5 9.0 - - + +
65A LEU* 2.8 34.8 + - + +
66A LEU* 3.5 7.9 - - - +
67A VAL 3.1 0.4 - - - -
68A PHE* 1.3 95.0 - - + +
70A ARG* 1.3 69.6 + - + +
72A SER* 3.0 5.6 + - - -
73A LEU* 3.0 30.5 - - + +
78A PHE* 6.1 0.2 - - + -
82A ARG* 6.3 0.9 - - + -
85A ILE* 6.1 2.9 - - + -
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Residues in contact with ARG 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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66A LEU 3.0 9.3 + - - +
69A VAL* 1.3 83.9 - - + +
71A LYS* 1.3 87.7 + - - +
73A LEU* 3.1 15.8 + - - -
74A ASN* 3.8 19.3 + - - +
78A PHE* 3.8 24.7 - - + -
79A ARG* 4.3 5.6 - - - +
82A ARG* 3.3 59.0 - - + +
113A SER* 5.0 1.6 + - - -
114A VAL* 4.8 8.7 - - - +
117A LYS* 3.3 53.2 - - - +
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Residues in contact with LYS 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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67A VAL* 2.7 39.8 + - + +
68A PHE* 3.7 9.0 - - - -
70A ARG* 1.3 95.3 + - - +
72A SER* 1.3 57.7 + - - +
73A LEU 3.9 0.3 + - - -
109A ASN* 5.9 2.2 - - - +
110A THR* 5.5 7.5 + - + +
113A SER* 3.8 32.9 + - - -
117A LYS* 3.9 25.9 + - - +
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Residues in contact with SER 72 (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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24A ARG* 6.1 0.5 - - - +
68A PHE* 2.2 32.8 + - - +
69A VAL* 3.0 3.9 + - - -
71A LYS* 1.3 76.4 - - - +
73A LEU* 1.3 69.3 + - - +
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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
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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