Contacts of the helix formed by residues 41 - 65 (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 ASP 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA 3.4 2.0 + - - -
40A LEU* 1.3 76.8 - - - +
42A TYR* 1.3 60.0 + - + +
43A PRO* 3.8 16.0 - - + +
44A GLY* 2.8 27.8 + - - -
45A GLN* 2.9 25.3 + - - +
47A ARG* 4.4 0.3 + - - -
12B VAL* 3.9 11.0 - - + -
16B ALA* 4.0 16.4 - - + -
17B THR* 3.8 21.0 - - - +
20B THR* 3.0 27.3 + - - +
58B ARG* 4.6 7.3 + - - -
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Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 1.3 70.2 - - + +
43A PRO* 1.3 76.2 - - + +
45A GLN* 3.1 28.2 + - - +
46A ASP* 2.8 22.5 + - - +
9B GLN* 6.0 4.7 - - + -
10B ILE 4.1 16.8 - - - -
11B GLU* 4.2 11.7 - - - +
12B VAL* 3.5 33.6 + - + +
13B GLY 5.1 0.2 + - - -
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Residues in contact with PRO 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.6 15.9 - - + +
42A TYR* 1.3 97.4 - - + +
44A GLY* 1.3 59.8 + - - +
46A ASP* 3.2 18.4 + - + +
47A ARG* 3.3 33.8 + - - +
58B ARG* 6.2 0.2 - - - +
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 4.0 3.5 - - - -
40A LEU* 3.7 23.5 - - - +
41A ASP* 2.8 23.5 + - - -
43A PRO* 1.3 74.4 - - - +
45A GLN* 1.3 64.9 + - - +
47A ARG* 3.4 24.2 + - - +
48A LEU* 3.2 15.9 + - - +
20B THR* 4.4 0.2 - - - -
24B GLU* 4.6 0.9 - - - -
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Residues in contact with GLN 45 (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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35A SER* 5.5 3.3 - - - -
40A LEU* 2.9 40.0 + - + +
41A ASP 2.9 14.3 + - - +
42A TYR* 3.1 18.6 + - - +
44A GLY* 1.3 74.3 - - - +
46A ASP* 1.3 60.6 + - - +
48A LEU* 3.2 5.2 + - + +
49A HIS* 2.8 46.1 + - + -
9B GLN* 4.2 14.7 - - - +
10B ILE* 2.9 52.9 + - + +
12B VAL* 3.2 7.1 - - - +
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Residues in contact with ASP 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 2.8 25.8 + - - +
43A PRO* 3.4 10.8 - - + +
44A GLY 3.2 0.4 - - - -
45A GLN* 1.3 76.6 - - - +
47A ARG* 1.3 60.1 + - + +
49A HIS* 3.2 7.9 + - - +
50A ARG* 2.9 32.7 + - - +
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 4.7 9.7 - - + +
41A ASP* 4.4 1.0 + - - -
43A PRO* 3.3 25.6 + - - +
44A GLY* 3.4 26.8 - - - +
46A ASP* 1.3 77.8 - - + +
48A LEU* 1.3 61.8 + - - +
50A ARG* 3.5 15.5 - - + +
51A LEU* 3.3 24.6 + - - +
20B THR* 4.0 2.4 - - - +
24B GLU* 2.6 46.0 + - - +
51B LEU* 5.7 1.5 - - - +
54B LYS* 3.7 31.2 - - - +
58B ARG* 3.3 21.5 - - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.7 18.8 - - + +
31A TYR* 3.8 42.8 - - + +
32A GLU* 3.9 17.5 - - + +
35A SER* 4.2 8.3 - - - +
40A LEU* 3.7 20.9 - - + -
44A GLY 3.2 13.1 + - - +
45A GLN* 3.3 11.0 - - + +
46A ASP 3.1 0.2 - - - -
47A ARG* 1.3 78.7 - - - +
49A HIS* 1.3 82.6 + - + +
51A LEU* 3.4 3.3 + - - +
52A LYS* 3.1 23.9 + - + +
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Residues in contact with HIS 49 (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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45A GLN* 2.8 42.4 + - + +
46A ASP* 3.2 6.9 + - - +
48A LEU* 1.3 93.0 - - + +
50A ARG* 1.3 58.5 + - - +
52A LYS* 3.6 10.4 + - + +
53A ARG* 3.1 40.8 + - - +
7B THR* 3.3 41.2 - - + +
8B THR 4.1 12.7 + - - -
9B GLN* 5.2 3.8 - - + -
10B ILE* 6.1 2.5 - - + -
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP 2.9 15.4 + - - +
47A ARG* 3.5 21.8 - - - +
49A HIS* 1.3 76.5 - - - +
51A LEU* 1.3 65.3 - - + +
53A ARG* 3.1 23.4 + - - +
54A LYS* 2.9 78.9 + - + +
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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
----------------------------------------------------------
24A GLU* 3.8 24.7 - - + +
27A ILE* 4.7 9.0 - - + -
28A LEU* 3.5 41.1 - - + +
31A TYR* 5.5 5.2 - - + -
47A ARG 3.3 16.4 + - - +
48A LEU* 3.9 2.7 - - - +
50A ARG* 1.3 84.7 - - + +
52A LYS* 1.3 57.5 + - - +
54A LYS* 4.1 7.0 - - - +
55A LEU* 2.8 37.8 + - + +
58A ARG* 5.4 3.5 + - - +
31B TYR* 4.3 17.7 - - - +
47B ARG* 5.5 7.0 - - - +
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.8 23.3 - - + -
32A GLU* 4.1 21.3 + - - +
48A LEU* 3.1 21.5 + - + +
49A HIS* 3.7 11.7 - - + +
51A LEU* 1.3 76.6 - - - +
53A ARG* 1.3 59.3 + - - +
55A LEU* 3.6 1.0 - - - +
56A GLU* 2.9 65.3 + - + +
74A LEU* 4.4 11.7 - - + -
78A LYS* 6.0 0.4 - - - +
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Residues in contact with ARG 53 (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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49A HIS* 3.1 30.0 + - - +
50A ARG* 3.4 37.4 + - - +
52A LYS* 1.3 77.5 - - - +
54A LYS* 1.3 65.0 + - + +
56A GLU* 3.3 11.1 + - - +
57A SER* 3.0 21.9 + - - -
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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
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50A ARG* 2.9 60.4 + - + +
51A LEU* 4.1 5.6 - - - +
53A ARG* 1.3 75.3 - - + +
55A LEU* 1.3 52.8 + - - +
57A SER* 2.9 10.5 + - - -
58A ARG* 2.7 51.1 + - + +
47B ARG* 5.9 9.9 - - - +
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Residues in contact with LEU 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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21A ILE* 3.8 25.1 - - + +
24A GLU* 3.4 28.3 - - + +
25A ALA* 3.4 16.2 - - + -
28A LEU* 4.0 22.4 - - + -
51A LEU* 2.8 24.0 + - + +
52A LYS* 3.6 5.2 - - - +
54A LYS* 1.3 76.4 - - - +
56A GLU* 1.3 56.8 + - - +
58A ARG* 3.2 32.2 + - + +
59A ILE* 2.9 39.0 + - + +
74A LEU* 4.4 10.3 - - + -
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Residues in contact with GLU 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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52A LYS* 2.9 49.3 + - - +
53A ARG* 3.7 8.1 - - - +
55A LEU* 1.3 75.3 - - - +
57A SER* 1.3 57.4 - - - +
59A ILE* 4.1 7.0 - - - +
60A LYS* 3.1 30.0 + - - +
74A LEU* 4.0 25.6 - - + +
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Residues in contact with SER 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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53A ARG* 3.0 14.3 + - - -
54A LYS* 2.9 16.0 + - - -
56A GLU* 1.3 78.7 - - - +
58A ARG* 1.3 56.6 + - - +
60A LYS* 4.0 4.3 - - - +
61A THR* 3.0 32.1 + - - -
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Residues in contact with ARG 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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20A THR* 4.3 6.3 - - - +
21A ILE* 4.0 31.0 - - + +
24A GLU* 2.7 31.8 + - - +
51A LEU* 5.4 4.8 + - - +
54A LYS* 2.7 31.2 + - + +
55A LEU* 3.3 32.1 - - + +
57A SER* 1.3 74.8 - - - +
59A ILE* 1.3 60.5 + - - +
61A THR* 3.7 6.2 - - - +
62A HIS* 2.8 32.7 + - - +
41B ASP* 4.9 4.8 + - - -
47B ARG* 3.4 22.2 - - - +
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Residues in contact with ILE 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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21A ILE* 3.6 24.5 - - + +
25A ALA* 5.4 0.2 - - + -
55A LEU* 2.9 24.4 + - + +
56A GLU* 4.1 5.8 - - - +
58A ARG* 1.3 74.6 - - - +
60A LYS* 1.3 59.7 + - + +
62A HIS* 3.9 4.0 - - - +
63A ASN* 2.8 50.4 + - - +
72A MET 3.7 4.3 - - - +
73A SER* 5.1 0.4 - - - -
74A LEU* 3.8 41.7 - - + +
77A ARG* 3.5 31.4 - - + +
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Residues in contact with LYS 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 GLU 3.1 18.2 + - - +
57A SER* 4.0 6.1 - - - +
59A ILE* 1.3 80.8 - - + +
61A THR* 1.3 60.3 + - - +
63A ASN* 4.2 6.2 - - - +
64A LYS* 3.3 36.8 + - + +
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Residues in contact with THR 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 SER* 3.0 22.2 + - - -
58A ARG* 3.7 7.0 - - + +
59A ILE 3.2 0.4 - - - -
60A LYS* 1.3 78.7 - - - +
62A HIS* 1.3 62.4 + - - +
64A LYS* 3.9 14.7 + - - +
65A SER* 2.9 26.9 + - - +
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 4.3 15.6 - - + +
18A ASN* 2.9 48.0 + - + +
21A ILE* 3.7 18.7 - - + +
58A ARG 2.8 22.2 + - - +
59A ILE* 3.3 3.8 + - - +
61A THR* 1.3 74.2 - - - +
63A ASN* 1.3 66.2 + - - +
65A SER* 2.9 25.2 + - - -
66A GLU* 3.4 29.5 + - + +
77A ARG* 4.2 11.7 - - - +
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Residues in contact with ASN 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 ILE* 2.8 33.7 + - - +
60A LYS* 4.2 7.7 - - - +
62A HIS* 1.3 77.9 - - - +
64A LYS* 1.3 54.7 + - + +
66A GLU* 2.7 19.9 + - - +
71A ARG* 2.7 46.8 + - + +
72A MET 3.1 29.4 + - - -
73A SER* 5.1 0.8 - - - +
77A ARG* 2.8 26.1 + - - -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 3.3 27.2 + - + +
61A THR* 4.2 15.0 + - - +
62A HIS 3.3 1.0 - - - -
63A ASN* 1.3 77.6 - - + +
65A SER* 1.3 59.8 + - - +
66A GLU 3.1 2.1 + - - +
71A ARG* 3.6 22.4 + - - +
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 2.9 18.3 + - - +
62A HIS* 2.9 17.6 + - - -
64A LYS* 1.3 77.5 - - - +
66A GLU* 1.3 69.7 + - - +
67A PRO* 4.7 0.9 - - - +
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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
------------------------------------------------------------
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