Contacts of the helix formed by residues 41 - 64 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.2 6.1 - - + -
16A ALA* 4.0 20.0 - - + +
17A THR* 3.8 23.9 + - - +
20A THR* 2.8 31.2 + - - +
58A ARG* 4.9 5.7 + - - -
39B ALA 3.4 2.2 + - - -
40B LEU* 1.3 75.8 - - - +
42B TYR* 1.3 61.5 + - + +
43B PRO* 3.3 14.7 - - + +
44B GLY* 2.7 24.1 + - - -
45B GLN* 2.9 22.9 + - - +
47B ARG* 4.4 0.3 + - - -
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.1 50.5 + - + +
10A ILE 4.0 11.0 - - - -
11A GLU* 3.8 11.4 - - - +
12A VAL* 3.2 41.1 + - + -
41B ASP* 1.3 70.6 - - + +
43B PRO* 1.3 77.1 - - + +
45B GLN* 3.1 11.9 + - - +
46B ASP* 3.0 19.9 + - - +
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Residues in contact with PRO 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 3.3 17.7 - - + +
42B TYR* 1.3 94.6 - - + +
44B GLY* 1.3 60.5 + - - +
46B ASP* 3.1 11.4 + - + +
47B ARG* 3.0 44.8 + - - +
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Residues in contact with GLY 44 (chain B).
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* 4.4 0.2 - - - -
24A GLU* 4.7 0.9 - - - -
31B TYR* 4.2 2.6 - - - -
40B LEU* 3.5 26.0 - - - +
41B ASP* 2.7 24.3 + - - -
43B PRO* 1.3 74.3 - - - +
45B GLN* 1.3 56.1 + - - +
47B ARG* 3.1 21.7 + - - +
48B LEU* 2.9 24.3 + - - +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR 4.5 1.2 - - - +
9A GLN* 3.5 18.1 - - - +
10A ILE* 2.8 49.4 + - - +
12A VAL* 3.8 3.6 - - - +
35B SER* 3.9 14.0 + - - +
40B LEU* 2.8 40.7 + - + +
41B ASP 2.9 12.8 + - - +
42B TYR* 3.1 18.8 + - - +
44B GLY* 1.3 75.6 - - - +
46B ASP* 1.3 60.7 + - - +
48B LEU* 3.5 5.0 - - + +
49B HIS* 3.0 40.4 + - + -
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR 3.0 11.5 + - - +
43B PRO* 3.2 14.7 - - + +
44B GLY 3.0 0.2 - - - -
45B GLN* 1.3 75.2 - - - +
47B ARG* 1.3 61.9 + - - +
48B LEU 3.2 0.4 - - - -
49B HIS* 3.3 5.5 + - - +
50B ARG* 2.7 74.0 + - - +
53B ARG* 5.6 4.3 + - - -
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 3.8 4.4 - - - +
24A GLU* 2.8 47.4 + - - +
51A LEU* 5.5 6.3 - - - +
54A LYS* 5.9 9.7 - - - +
58A ARG* 3.4 23.5 - - - +
31B TYR* 4.7 9.8 - - + +
41B ASP* 4.4 2.0 + - - -
43B PRO* 3.0 30.7 + - - +
44B GLY* 3.6 19.4 - - - +
46B ASP* 1.3 76.3 - - - +
48B LEU* 1.3 65.8 + - - +
50B ARG* 3.9 10.4 - - - +
51B LEU* 3.0 25.3 + - - +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 3.4 21.0 - - + +
31B TYR* 3.6 33.5 - - + +
32B GLU* 3.6 39.5 - - + +
35B SER* 3.9 9.0 - - - +
40B LEU* 3.8 12.3 - - + -
44B GLY 2.9 13.4 + - - +
45B GLN* 3.5 11.7 - - + +
46B ASP 3.2 0.2 - - - -
47B ARG* 1.3 79.1 - - - +
49B HIS* 1.3 83.3 + - + +
51B LEU* 3.3 1.4 + - - +
52B LYS* 3.0 25.4 + - + -
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Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A THR* 3.6 39.5 + - + +
8A THR 3.7 21.7 + - - -
9A GLN* 4.8 2.7 - - + -
45B GLN* 3.0 29.8 + - + +
46B ASP* 3.3 5.5 + - - +
48B LEU* 1.3 98.8 - - + +
50B ARG* 1.3 65.7 + - - +
52B LYS* 3.4 12.7 + - + +
53B ARG* 3.1 48.6 + - - +
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Residues in contact with ARG 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 2.7 56.3 + - - +
47B ARG* 3.9 10.1 - - - +
49B HIS* 1.3 74.1 - - - +
51B LEU* 1.3 66.4 + - - +
53B ARG* 3.2 25.8 + - - +
54B LYS* 2.9 38.4 + - + +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 5.2 2.2 - - - +
47A ARG* 5.7 0.9 - - - +
24B GLU* 3.9 31.6 - - + +
27B ILE* 4.2 14.1 - - + -
28B LEU* 3.7 41.3 - - + +
31B TYR* 4.6 9.0 - - + -
47B ARG 3.0 19.3 + - - +
48B LEU 3.5 3.6 - - - +
50B ARG* 1.3 75.9 - - - +
52B LYS* 1.3 57.8 + - - +
54B LYS* 3.9 23.9 - - + +
55B LEU* 2.8 41.8 + - + +
58B ARG* 4.9 3.4 - - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A THR 6.2 0.9 - - - +
28B LEU* 3.8 22.0 - - + +
32B GLU* 4.1 21.4 + - - +
48B LEU* 3.0 18.5 + - + +
49B HIS* 3.7 17.3 - - + +
50B ARG 3.2 0.2 - - - -
51B LEU* 1.3 77.6 - - - +
53B ARG* 1.3 58.6 + - + +
55B LEU* 3.9 1.1 - - - +
56B GLU* 2.9 33.6 + - + +
74B LEU* 4.5 18.1 - - + +
78B LYS* 5.7 1.6 - - - +
99C ARG* 5.4 7.5 - - - +
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A THR* 3.3 32.3 - - + +
46B ASP* 5.6 4.0 + - - -
49B HIS* 3.1 29.6 + - - +
50B ARG* 3.6 27.0 - - - +
52B LYS* 1.3 74.6 - - + +
54B LYS* 1.3 67.3 + - + +
56B GLU* 3.1 7.0 + - - +
57B SER* 3.1 22.9 + - - -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 3.7 32.0 - - - +
50B ARG* 2.9 33.8 + - + +
51B LEU* 3.9 21.2 - - + +
53B ARG* 1.3 76.7 - - + +
55B LEU* 1.3 62.1 + - - +
57B SER* 2.6 23.5 + - - -
58B ARG* 3.0 23.1 + - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.6 26.2 - - + +
24B GLU* 3.9 7.4 - - + +
25B ALA* 3.4 32.1 - - - +
28B LEU* 4.0 14.8 - - + -
51B LEU* 2.8 25.8 + - + +
52B LYS 3.9 2.7 - - - +
54B LYS* 1.3 73.4 - - - +
56B GLU* 1.3 58.1 + - - +
58B ARG* 3.0 40.8 + - - +
59B ILE* 3.0 35.5 + - + +
74B LEU* 3.6 22.9 - - + -
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS* 2.9 22.9 + - + +
53B ARG* 3.1 6.3 + - - +
55B LEU* 1.3 76.4 - - - +
57B SER* 1.3 61.2 + - - +
59B ILE* 3.6 12.4 + - - +
60B LYS* 3.4 38.6 + - + +
74B LEU* 3.2 37.4 + - + +
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ARG 3.1 9.1 + - - -
54B LYS* 2.6 27.2 + - - -
56B GLU* 1.3 75.1 - - - +
58B ARG* 1.3 65.7 + - - +
60B LYS* 3.5 8.1 + - - +
61B THR* 3.1 27.0 + - - -
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 4.6 7.3 + - - -
43A PRO* 6.2 0.2 - - - +
47A ARG* 3.3 20.9 - - - +
20B THR* 4.1 8.9 - - - +
21B ILE* 4.1 28.5 - - + +
24B GLU* 2.5 32.6 + - - +
51B LEU* 4.9 4.4 - - - +
54B LYS* 3.0 19.7 + - + +
55B LEU* 3.0 43.4 - - + +
57B SER* 1.3 80.1 + - - +
59B ILE* 1.3 55.7 + - + +
61B THR* 3.4 6.8 + - - -
62B HIS* 2.9 31.6 + - - +
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.8 22.2 - - + -
25B ALA* 5.7 0.2 - - + -
55B LEU* 3.0 20.4 + - + +
56B GLU* 3.8 13.0 - - - +
57B SER 3.3 0.2 - - - -
58B ARG* 1.3 74.9 - - - +
60B LYS* 1.3 63.4 + - + +
62B HIS* 3.8 4.0 - - - -
63B ASN* 2.9 36.0 + - - +
72B MET 3.5 21.5 - - - +
73B SER* 4.6 1.8 - - - -
74B LEU* 3.4 50.9 - - + +
77B ARG* 3.6 17.5 - - + +
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU* 3.4 29.0 + - + +
57B SER* 3.9 9.4 - - - +
58B ARG 3.4 0.2 - - - -
59B ILE* 1.3 81.1 - - + +
61B THR* 1.3 62.8 + - - +
63B ASN* 3.7 8.0 + - - +
64B LYS* 3.2 25.7 + - - +
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B SER* 3.1 18.2 + - - -
58B ARG* 3.7 7.6 - - - -
60B LYS* 1.3 79.1 - - - +
62B HIS* 1.3 60.3 + - - +
63B ASN 3.4 0.2 - - - -
64B LYS* 3.7 30.0 + - - +
65B SER* 4.4 5.7 + - - -
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Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 3.9 29.7 - - + +
18B ASN* 3.7 38.0 + - + +
21B ILE* 3.7 16.4 - - + +
58B ARG 2.9 17.8 + - - +
59B ILE* 4.0 3.1 - - - +
61B THR* 1.3 76.2 - - + +
63B ASN* 1.3 63.3 + - - +
64B LYS 3.3 0.9 - - - -
65B SER* 3.0 25.7 + - - -
66B GLU* 3.6 33.1 + - + +
77B ARG* 4.1 11.6 + - - +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 2.9 22.7 + - - +
60B LYS* 4.2 6.3 - - - +
61B THR 3.4 0.6 - - - -
62B HIS* 1.3 77.5 + - - +
64B LYS* 1.3 62.5 + - - +
65B SER 3.3 0.2 - - - -
66B GLU* 3.5 7.1 - - - +
71B ARG* 3.2 56.0 + - - +
72B MET 2.8 34.1 + - - +
73B SER* 4.8 1.8 - - - +
77B ARG* 2.9 26.5 + - - -
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS 3.2 16.2 - - - +
61B THR* 3.7 27.6 + - - +
62B HIS 3.3 0.8 - - - -
63B ASN* 1.3 78.5 - - - +
65B SER* 1.3 60.5 + - - +
66B GLU 3.6 3.6 + - - +
71B ARG* 5.7 2.2 - - - +
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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