Contacts of the helix formed by residues 2 - 25 (chain A) in PDB entry 3M6L
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 ASN 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 1.3 77.5 + - - +
3A ILE* 1.3 68.6 + - - +
4A GLN* 3.1 34.8 + - - +
5A ILE* 3.1 40.4 - - - +
6A LEU* 3.0 29.9 + - - +
289A ARG* 5.4 1.0 + - - -
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Residues in contact with ILE 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN* 1.3 78.3 - - - +
4A GLN* 1.3 73.0 + - + +
6A LEU* 4.5 7.2 - - + +
7A GLN* 2.9 41.6 + - - +
217A TYR* 4.2 38.8 - - + -
218A GLU* 5.0 17.5 - - + +
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Residues in contact with GLN 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN* 3.1 24.7 + - - +
3A ILE* 1.3 93.7 - - + +
5A ILE* 1.3 58.7 + - - +
7A GLN* 3.7 7.8 - - - +
8A GLU* 3.0 28.2 + - - +
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Residues in contact with ILE 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 4.4 0.7 - - - -
2A ASN* 3.1 41.7 - - - +
4A GLN* 1.3 77.3 - - - +
6A LEU* 1.3 64.5 + - + +
8A GLU* 3.3 6.3 + - + +
9A GLN* 2.8 47.0 + - + +
44A TYR* 4.0 4.9 - - - +
285A ALA* 3.8 42.2 - - + +
286A SER 4.2 2.5 - - - +
289A ARG* 3.9 34.5 - - + +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.2 30.3 - - + -
2A ASN* 3.0 30.5 + - - +
3A ILE* 4.2 4.9 - - + +
5A ILE* 1.3 81.1 - - + +
7A GLN* 1.4 56.1 + - - +
9A GLN* 3.3 6.5 + - - +
10A ALA* 2.9 31.0 + - - +
40A SER* 3.9 22.7 - - - +
41A VAL* 4.1 4.9 - - + +
44A TYR* 3.4 34.3 - - + +
217A TYR* 3.7 38.2 + - + -
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Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 2.9 35.7 + - - +
4A GLN* 3.7 6.7 - - - +
6A LEU* 1.4 68.0 - - - +
8A GLU* 1.3 61.2 + - - +
10A ALA* 3.3 1.0 + - - +
11A ASN* 2.9 53.1 + - - +
217A TYR* 3.5 21.5 + - + +
272A ALA* 4.9 8.1 - - - +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN 3.0 17.6 + - - +
5A ILE* 3.3 6.3 + - - +
7A GLN* 1.3 79.8 - - - +
9A GLN* 1.3 52.5 + - - +
11A ASN* 3.3 5.2 + - - +
12A THR* 2.7 37.1 + - - -
274A PHE* 4.2 8.4 - - + -
283A PRO* 3.5 29.8 - - + +
285A ALA* 3.2 16.5 - - - +
286A SER* 2.7 38.1 + - - +
633A PO4 4.2 7.1 + - - -
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Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 2.8 26.4 + - + +
6A LEU* 3.6 7.5 - - - +
8A GLU* 1.3 77.8 - - - +
10A ALA* 1.4 63.0 + - - +
12A THR* 3.1 4.6 + - - -
13A LEU* 3.0 27.0 + - - +
40A SER* 3.6 7.6 - - - +
43A SER* 4.3 0.4 + - - -
44A TYR* 2.6 31.6 + - - -
286A SER* 3.3 18.8 - - - +
289A ARG* 3.4 15.9 - - - +
290A PHE* 3.6 38.4 - - + -
2001A GOL 2.9 27.1 + - - -
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU 2.9 17.4 + - - +
7A GLN 3.8 1.3 - - - +
9A GLN* 1.4 76.1 - - - +
11A ASN* 1.3 60.2 + - - +
13A LEU* 3.2 2.1 + - - +
14A ARG* 2.9 37.2 + - - +
36A ALA* 3.5 13.3 - - - +
37A ASP* 3.1 29.8 - - - +
40A SER* 3.1 16.3 + - - +
217A TYR* 3.6 4.5 - - - +
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Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN* 2.9 43.1 + - - +
8A GLU* 5.0 0.4 - - - +
10A ALA* 1.3 74.7 - - - +
12A THR* 1.3 59.7 + - - +
14A ARG* 3.1 32.4 + - - +
15A PHE* 3.0 44.7 + - + -
272A ALA* 3.6 27.1 + - - +
274A PHE* 3.7 21.4 - - + -
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Residues in contact with THR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU 2.7 22.2 + - - -
9A GLN* 3.3 11.0 - - - -
11A ASN* 1.3 75.3 - - - +
13A LEU* 1.3 65.3 + - - +
15A PHE* 3.3 1.6 + - - +
16A LEU* 3.0 29.6 + - + +
78A LEU* 3.9 22.2 - - + -
274A PHE* 3.9 8.0 - - - -
281A HIS 4.4 6.6 - - - +
282A ILE* 4.3 14.1 - - + -
283A PRO* 3.4 28.9 - - + +
286A SER* 3.4 14.8 + - - -
290A PHE* 4.8 0.4 - - - -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN 3.0 10.7 + - - +
10A ALA 3.6 5.6 - - - +
12A THR* 1.3 77.8 - - - +
14A ARG* 1.4 63.0 + - - +
16A LEU* 4.0 1.0 - - - +
17A SER* 2.9 28.8 + - - -
36A ALA* 4.0 10.3 - - + +
39A LEU* 4.2 15.5 - - + -
40A SER* 3.4 32.5 - - - +
71A LEU* 3.8 16.6 - - + -
74A SER* 3.9 8.7 + - - -
75A PHE* 3.8 28.3 - - + +
78A LEU* 3.5 23.6 - - + -
290A PHE* 3.8 18.4 - - + -
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Residues in contact with ARG 14 (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 ALA* 2.9 28.8 + - - +
11A ASN* 3.1 32.7 + - - +
13A LEU* 1.4 74.3 - - - +
15A PHE* 1.4 71.8 + - + +
17A SER* 3.4 2.3 + - - -
18A ALA* 2.9 29.6 + - - +
32A PRO 5.4 0.7 - - - -
33A LEU* 3.0 45.1 + - + +
36A ALA* 3.6 13.9 - - + +
37A ASP* 2.9 42.0 + - - +
215A HIS* 4.0 1.2 + - - -
217A TYR* 4.6 1.2 + - - -
244A LYS* 3.0 41.3 + - - +
245A GLY* 4.7 5.6 - - - -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.0 36.8 + - + +
12A THR 4.4 0.9 - - - +
14A ARG* 1.4 84.4 - - + +
16A LEU* 1.3 61.4 + - - +
18A ALA* 4.3 9.2 - - + -
19A ASP* 2.9 38.6 + - - +
33A LEU* 6.0 4.7 - - + -
245A GLY* 5.3 3.1 - - - -
265A ILE* 4.7 2.9 - - + -
268A ALA* 3.5 45.1 - - + -
269A LYS* 3.8 32.1 - - + -
272A ALA* 3.5 24.5 - - + -
274A PHE* 3.7 31.0 - + + -
281A HIS 5.9 2.0 - - - +
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Residues in contact with LEU 16 (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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12A THR* 3.0 21.4 + - + +
13A LEU 4.0 0.7 - - - +
15A PHE* 1.3 76.0 - - - +
17A SER* 1.3 62.8 - - - +
19A ASP* 3.7 2.6 - - - +
20A MSE 2.9 33.1 + - - +
74A SER* 3.4 22.4 - - - +
78A LEU* 3.9 37.5 - - + -
85A LEU* 4.4 6.7 - - + -
88A LEU* 4.2 13.7 - - + -
280A PHE* 3.8 43.1 - - + -
281A HIS 4.4 4.4 + - - +
282A ILE* 4.4 13.7 - - + -
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Residues in contact with SER 17 (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 2.9 22.2 + - - -
14A ARG* 3.6 4.5 - - - -
16A LEU* 1.3 77.7 - - - +
18A ALA* 1.4 62.4 + - - +
20A MSE 3.2 3.9 + - - +
21A VAL* 3.1 29.4 + - - +
29A PRO* 5.9 1.3 - - - -
32A PRO* 3.7 25.1 - - - +
33A LEU* 4.7 1.3 - - - -
70A ALA* 4.0 14.3 - - - +
71A LEU* 3.5 26.9 + - - +
74A SER* 3.6 4.1 + - - -
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Residues in contact with ALA 18 (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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14A ARG 2.9 17.1 + - - +
15A PHE* 4.0 12.6 - - + +
17A SER* 1.4 76.1 - - - +
19A ASP* 1.3 58.8 + - - +
21A VAL* 3.5 6.6 + - - +
22A GLN* 2.9 30.5 + - - +
29A PRO* 5.1 3.6 - - - -
33A LEU* 4.5 7.1 - - + +
260A LEU* 4.1 20.5 + - + +
265A ILE* 3.8 23.1 - - + +
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Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 2.9 27.1 + - - +
16A LEU 3.7 3.8 - - - +
18A ALA* 1.3 79.0 - - - +
20A MSE 1.3 56.0 + - - +
22A GLN* 3.4 5.9 + - - +
23A LYS* 3.0 30.7 + - - +
265A ILE* 3.9 10.9 - - - +
269A LYS* 3.0 29.7 + - - -
279A SER* 3.4 14.7 - - - -
280A PHE* 2.8 46.8 + - + +
281A HIS 4.6 1.0 + - - -
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Residues in contact with MSE 20 (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 LEU 2.9 23.7 + - - +
17A SER 3.2 3.8 + - - +
19A ASP* 1.3 73.2 - - - +
21A VAL* 1.3 61.4 + - - +
23A LYS* 3.4 2.9 + - - +
24A ALA* 3.0 30.0 + - - +
70A ALA* 3.8 22.4 - - + +
73A TYR* 4.2 9.2 - - + -
74A SER* 3.6 24.9 - - - -
88A LEU* 3.6 43.5 - - + +
91A PHE* 3.6 40.0 - - + +
98A THR* 5.1 0.4 - - + -
280A PHE* 3.6 17.9 - - + -
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 3.1 16.5 + - - +
18A ALA* 3.8 5.6 - - - +
20A MSE 1.3 78.4 - - - +
22A GLN* 1.3 63.7 + - - +
24A ALA 3.4 0.7 + - - -
25A ASN* 2.9 18.9 + - - -
26A SER 3.3 23.6 + - - +
27A GLY 3.9 11.2 - - - +
28A HIS 3.7 31.0 - - - +
29A PRO* 4.1 10.8 - - + -
70A ALA* 4.4 5.6 - - + -
91A PHE* 3.9 14.1 - - + -
259A PRO* 3.7 26.8 - - + +
260A LEU 5.1 0.7 - - - +
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Residues in contact with GLN 22 (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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18A ALA 2.9 18.2 + - - +
19A ASP* 3.8 5.8 - - - +
20A MSE 3.3 0.2 - - - -
21A VAL* 1.3 78.0 - - - +
23A LYS* 1.3 62.3 + - - +
25A ASN* 3.0 21.0 + - - +
259A PRO* 3.4 21.0 - - - +
260A LEU 3.5 3.5 + - - -
261A GLY* 2.8 41.0 + - - -
262A GLU* 4.1 21.2 + - + +
265A ILE* 3.7 16.7 - - + +
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Residues in contact with LYS 23 (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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19A ASP 3.0 17.8 + - - +
20A MSE 3.9 3.4 - - - +
22A GLN* 1.3 76.5 - - - +
24A ALA* 1.3 60.6 + - - +
25A ASN* 3.4 1.9 + - - +
89A LYS* 2.9 43.7 + - + +
90A ASN* 5.1 4.6 - - - +
280A PHE* 3.8 26.2 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MSE 3.0 17.0 + - - +
23A LYS* 1.3 77.6 - - - +
25A ASN* 1.4 65.7 + - - +
26A SER* 3.2 23.3 + - - +
91A PHE* 3.4 30.7 - - + +
92A ARG* 4.1 6.5 - - + -
93A GLN* 3.9 13.9 - - - +
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL 2.9 8.8 + - - -
22A GLN* 3.0 18.0 + - - +
23A LYS 3.2 2.0 - - - +
24A ALA* 1.4 78.3 - - - +
26A SER* 1.3 59.5 + - - +
259A PRO* 3.5 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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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