Contacts of the helix formed by residues 15 - 37 (chain A) in PDB entry 3SDL
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 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY 3.1 1.8 + - - -
14A PRO* 1.3 80.5 - - - +
16A ALA* 1.3 60.3 + - - +
17A THR 3.3 0.7 - - - -
18A ASN* 4.0 6.3 + - - +
19A ALA* 3.4 20.4 + - - +
11C ALA* 5.1 4.2 - - - +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.8 24.0 - - + -
13A GLY 3.1 14.9 + - - +
14A PRO 3.0 1.2 + - - -
15A GLY* 1.3 77.3 - - - +
17A THR* 1.3 60.7 + - - +
19A ALA* 3.7 2.7 - - - -
20A THR* 2.9 35.8 + - - -
38B ARG 4.2 3.8 - - - +
39B ALA* 3.0 27.5 - - - +
41B ASP* 3.9 7.9 - - + +
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 4.7 0.4 + - - -
14A PRO* 3.3 13.0 + - - +
15A GLY 3.3 0.8 - - - -
16A ALA* 1.3 77.9 - - - +
18A ASN* 1.3 64.0 + - - +
20A THR* 3.2 4.0 + - - -
21A ILE* 3.1 33.6 + - + +
62A HIS* 4.3 21.1 - - + +
41B ASP* 3.8 22.8 + - - +
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Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 4.7 0.8 + - - +
15A GLY* 4.0 7.8 + - - +
17A THR* 1.3 79.2 - - - +
19A ALA* 1.3 59.8 + - - +
21A ILE* 3.7 6.0 + - - +
22A ASN* 2.8 44.0 + - - +
62A HIS* 2.9 40.8 + - + +
72A MET* 5.9 2.2 - - - -
77A ARG* 3.1 19.1 + - - +
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY 3.4 19.2 + - - +
16A ALA* 3.5 6.1 - - - +
17A THR 3.1 0.6 - - - -
18A ASN* 1.3 77.9 - - - +
20A THR* 1.3 60.3 + - - +
22A ASN* 3.3 5.6 + - - +
23A PHE* 2.9 29.6 + - - +
84A MET* 3.8 4.5 - - - +
34B PHE* 3.6 7.1 - - + -
39B ALA* 3.7 11.4 - - + +
11C ALA* 3.5 32.5 - - + +
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Residues in contact with THR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 2.9 16.7 + - - -
17A THR 3.2 0.9 + - - -
19A ALA* 1.3 73.4 - - - +
21A ILE* 1.3 61.5 + - - +
23A PHE* 3.7 0.2 - - - +
24A GLU* 2.8 54.6 + - + +
58A ARG* 4.3 2.0 - - - +
34B PHE* 4.2 7.9 - - + -
39B ALA 3.1 4.7 + - - -
40B LEU* 3.4 17.5 - - + -
41B ASP* 2.8 50.7 + - - +
47B ARG* 3.8 6.3 - - - +
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.1 22.7 + - + +
18A ASN* 3.8 7.6 - - - +
19A ALA 3.3 0.2 - - - -
20A THR* 1.3 76.7 - - - +
22A ASN* 1.3 56.9 + - - +
25A ALA* 3.1 25.5 + - - +
55A LEU* 3.8 11.5 - - + +
58A ARG* 4.0 34.8 - - + +
59A ILE* 3.6 30.3 - - + +
62A HIS* 3.7 43.3 - - + +
77A ARG* 3.9 14.8 - - - +
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Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 2.8 35.3 + - - +
19A ALA* 3.3 8.3 + - - +
21A ILE* 1.3 76.0 - - - +
23A PHE* 1.3 65.7 + - - +
25A ALA* 3.1 8.4 + - - +
26A GLY 3.1 17.3 + - - -
72A MET* 5.4 1.4 - - - -
77A ARG* 3.0 45.8 + - - +
80A ILE* 4.3 22.9 - - + +
81A GLY* 3.3 9.1 - - - -
84A MET* 3.8 13.2 - - + -
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Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 2.9 17.9 + - - +
20A THR 3.7 2.5 - - - +
22A ASN* 1.3 76.4 - - - +
24A GLU* 1.3 68.3 + - + +
26A GLY* 3.1 5.7 + - - -
27A ILE* 3.1 46.0 + - + +
81A GLY* 4.4 2.5 - - - +
84A MET* 3.3 13.8 - - + +
85A MET* 4.0 24.8 - - + +
88A LEU* 4.0 7.2 - - + -
30B CYS 3.4 29.4 - - - -
31B TYR* 3.8 25.8 - + - -
34B PHE* 3.5 51.8 - + + -
40B LEU* 4.7 2.7 - - + -
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 2.8 24.0 + - + +
23A PHE* 1.3 85.6 - - + +
25A ALA* 1.3 63.8 + - - +
27A ILE* 3.3 8.9 - - + +
28A LEU* 3.0 17.5 + - - +
51A LEU* 3.8 10.8 - - + +
55A LEU* 3.4 14.4 - - + +
58A ARG* 2.7 39.2 + - - +
31B TYR* 2.6 36.6 + - + +
44B GLY* 4.7 0.3 - - - -
47B ARG* 2.8 37.7 + - - -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE 3.1 16.5 + - - +
22A ASN 3.2 10.5 - - - +
24A GLU* 1.3 77.1 - - - +
26A GLY* 1.3 62.4 + - - +
28A LEU* 3.0 7.3 + - - +
29A GLU* 3.0 20.1 + - - +
55A LEU* 3.4 16.1 - - + +
59A ILE* 5.4 0.7 - - + -
74A LEU* 4.6 5.4 - - + +
77A ARG* 3.9 10.5 - - + -
78A LYS* 3.9 33.1 - - + +
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN 3.1 8.1 + - - -
23A PHE 3.1 5.4 + - - -
25A ALA* 1.3 79.0 - - - +
27A ILE* 1.3 61.7 + - - +
29A GLU* 3.2 8.3 + - - +
30A CYS* 3.1 27.9 + - - -
78A LYS* 4.2 5.3 - - - +
81A GLY* 4.0 22.8 - - - -
82A VAL* 4.1 5.2 - - - +
85A MET* 3.9 7.1 - - - +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.1 39.7 + - + +
24A GLU* 3.3 16.6 - - + +
25A ALA 3.2 0.4 - - - -
26A GLY* 1.3 76.1 - - - +
28A LEU* 1.3 63.9 + - - +
30A CYS* 3.1 5.6 + - - +
31A TYR* 3.0 45.2 + - + -
51A LEU* 4.7 9.0 - - + -
85A MET* 3.6 24.0 - - + -
27B ILE* 4.0 31.0 - - + -
30B CYS* 4.6 2.7 - - + -
31B TYR* 4.1 13.0 - - + +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU 3.0 8.0 + - - +
25A ALA 3.0 7.6 + - - +
27A ILE* 1.3 77.8 - - - +
29A GLU* 1.3 56.7 + - - +
31A TYR* 3.1 6.1 + - + +
32A GLU* 2.9 44.7 + - - +
48A LEU* 3.7 41.1 - - + +
51A LEU* 3.5 21.3 - - + -
52A LYS* 3.8 32.1 - - + -
55A LEU* 4.0 11.9 - - + -
74A LEU* 4.4 8.7 - - + -
78A LYS* 4.2 15.0 - - - -
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Residues in contact with GLU 29 (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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25A ALA 3.0 12.2 + - - +
26A GLY* 3.2 14.1 + - - +
28A LEU* 1.3 76.2 - - - +
30A CYS* 1.3 58.1 + - - +
32A GLU* 3.4 9.2 + - - +
33A ARG* 2.6 78.6 + - - +
36A TRP* 4.5 8.5 - - - -
75A GLU* 5.1 0.3 - - - +
78A LYS* 3.2 39.1 + - + +
82A VAL* 4.2 13.7 - - + -
89B LEU* 6.2 0.4 - - + -
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Residues in contact with CYS 30 (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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26A GLY 3.1 18.6 + - - -
27A ILE 3.5 7.4 - - - +
29A GLU* 1.3 77.5 - - - +
31A TYR* 1.3 66.4 + - - +
33A ARG* 3.3 7.5 + - - +
34A PHE* 2.8 26.0 + - - +
85A MET* 3.5 19.5 - - - -
23B PHE* 3.6 7.2 - - + -
27B ILE* 4.5 2.5 - - + -
85B MET* 4.0 20.9 - - - -
88B LEU* 3.9 5.5 - - + +
89B LEU* 3.5 35.7 - - - -
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Residues in contact with TYR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.0 42.2 + - + +
28A LEU* 3.4 11.4 - - + +
30A CYS* 1.3 75.9 - - - +
32A GLU* 1.3 59.0 + - - +
34A PHE* 3.2 2.9 + - - +
35A SER* 2.9 28.6 + - - -
40A LEU* 4.1 15.9 - - + +
44A GLY 4.0 11.4 - - - -
47A ARG* 4.6 7.9 + - + +
48A LEU* 3.8 39.4 - - + +
51A LEU* 5.5 5.8 - - + -
23B PHE* 3.6 25.5 - + - -
24B GLU* 2.6 42.7 + - + +
27B ILE* 4.0 12.8 - - + +
51B LEU* 5.2 3.8 - - - +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 2.9 33.1 + - + +
29A GLU* 3.4 12.8 - - - +
30A CYS 3.2 0.2 - - - -
31A TYR* 1.3 76.7 - - - +
33A ARG* 1.3 61.7 + - - +
35A SER* 2.5 25.8 + - - +
36A TRP* 3.1 27.9 - - + +
48A LEU* 4.0 20.0 - - + +
52A LYS* 4.1 20.1 + - - +
78A LYS* 3.0 30.7 + - - -
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 2.6 52.6 + - - +
30A CYS* 3.9 5.2 - - - +
32A GLU* 1.3 74.4 - - - +
34A PHE* 1.3 59.4 + - - +
36A TRP* 3.3 35.3 + - + +
37A GLN* 2.7 29.8 + - - -
82A VAL* 4.7 11.8 - - - +
88B LEU* 3.1 31.9 + - + -
89B LEU* 3.1 32.7 + - - +
91B MET* 3.6 24.3 - - - +
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Residues in contact with PHE 34 (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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30A CYS 2.8 17.1 + - - +
31A TYR 3.3 3.8 - - - +
33A ARG* 1.3 75.2 - - - +
35A SER* 1.3 59.7 + - - +
37A GLN* 2.9 28.3 + - - +
38A ARG 3.6 2.1 + - - -
39A ALA* 3.3 47.1 + - + -
40A LEU* 3.7 28.0 - - + -
19B ALA* 3.5 21.3 - - + -
20B THR* 4.0 4.0 - - - -
23B PHE* 3.5 43.1 - + + -
84B MET* 4.0 10.3 - - + -
88B LEU* 3.7 6.6 - - + +
10D LEU* 3.5 26.2 - - + -
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR 2.9 12.6 + - - -
32A GLU* 2.5 25.4 + - - +
34A PHE* 1.3 77.5 - - - +
36A TRP* 1.3 63.5 + - - +
38A ARG* 2.9 20.6 + - - +
40A LEU* 4.0 28.3 - - - -
45A GLN* 5.5 2.7 - - - -
48A LEU* 4.2 7.5 - - - +
10B ILE* 3.9 31.7 - - - +
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Residues in contact with TRP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 4.5 8.7 - - - -
32A GLU* 3.1 33.8 + - + +
33A ARG* 3.3 42.0 - - + +
34A PHE 3.1 0.2 - - - -
35A SER* 1.3 82.4 + - - +
37A GLN* 1.3 65.5 + - - +
38A ARG* 3.1 13.5 + - - +
10B ILE* 5.9 2.5 - - + -
91B MET* 4.3 4.7 - - + -
38D VAL* 5.7 0.3 - - - +
75D VAL* 3.6 38.9 - - + +
76D ASP* 3.6 13.7 - - - -
77D LYS* 3.4 61.7 - - + +
78D CYS 4.9 1.6 - - - -
79D ASP* 5.4 6.1 - - + -
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Residues in contact with GLN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG 2.7 22.6 + - - +
34A PHE 2.9 14.0 + - - +
36A TRP* 1.3 76.3 - - - +
38A ARG* 1.3 72.0 + - - +
39A ALA* 3.3 7.5 + - + +
88B LEU* 3.9 9.7 - - + +
91B MET* 4.1 2.6 - - - +
9D MET* 3.7 22.4 - - + +
10D LEU* 3.5 42.6 - - + +
11D ALA* 5.4 1.1 + - - +
13D ASN* 5.2 4.0 - - - +
73D LEU 4.4 2.9 - - - +
74D VAL* 3.7 9.4 - - - -
75D VAL* 2.8 52.1 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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