Contacts of the helix formed by residues 37 - 58 (chain B) in PDB entry 2QE9
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 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU 3.6 3.3 - - - +
28B LEU* 3.4 24.9 + - - +
29B LYS 3.3 21.5 - - - +
30B ASN* 3.0 20.2 + - - +
31B ARG* 5.2 0.9 - - - -
35B VAL 3.0 11.5 + - - +
36B GLU* 1.3 71.4 - - - +
38B ILE* 1.3 60.4 - - - +
39B LEU* 3.5 7.1 + - - +
40B TYR* 2.8 41.9 + - - +
41B THR* 2.7 30.5 + - - -
66B PHE* 4.1 9.4 - - - -
135B TRP* 3.8 5.4 - - - -
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Residues in contact with ILE 38 (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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18B TRP* 4.2 11.0 - - + -
19B CYS* 3.7 29.4 - - - -
22B LEU* 3.6 27.4 - - + -
26B GLU 4.4 3.4 - - - +
27B LEU* 3.3 14.7 + - + +
29B LYS 4.8 1.0 + - - -
31B ARG* 4.1 15.0 - - - +
37B ASN* 1.3 73.2 - - - +
39B LEU* 1.3 63.6 + - - +
41B THR* 3.4 4.9 + - - -
42B LEU* 3.2 23.6 + - + +
132B LEU* 4.1 13.6 - - + +
135B TRP* 3.9 28.2 - - + -
139B LEU* 3.8 19.3 - - + -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 5.1 1.1 - - + -
27B LEU* 2.9 31.7 + - + +
28B LEU* 3.9 18.8 - - + -
37B ASN* 3.9 2.7 - - - +
38B ILE* 1.3 77.7 - - - +
40B TYR* 1.3 57.7 + - - +
42B LEU* 3.3 9.4 + - + +
43B PHE* 3.0 25.5 + - - +
66B PHE* 4.1 3.4 - - + -
69B TYR 4.1 2.5 - - - +
70B GLN* 3.4 37.2 - - - +
71B THR* 3.6 5.6 - - - +
72B LEU* 3.7 31.6 - - + +
75B VAL* 3.6 28.3 - - + +
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.5 42.4 - - + +
37B ASN* 2.8 31.2 + - - +
39B LEU* 1.3 70.4 - - - +
41B THR* 1.3 56.3 + - - +
43B PHE* 3.7 22.8 - + - -
44B HIS* 2.8 47.7 + - + +
66B PHE* 3.4 47.0 - + + -
201B CIT 5.7 0.8 + - - -
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.4 18.6 + - - +
37B ASN 2.7 22.2 + - - -
38B ILE 3.5 6.1 - - - -
40B TYR* 1.3 76.9 - - - +
42B LEU* 1.3 56.2 + - - +
44B HIS* 3.6 2.5 - - - +
45B ILE* 3.0 33.6 + - + +
128B HIS* 3.8 36.8 - - + +
131B GLN* 4.7 2.3 + - - +
132B LEU* 3.7 23.8 - - + -
135B TRP* 3.4 15.7 - - + -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 4.4 19.5 - - + -
15B TRP* 4.6 9.0 - - + +
16B PHE* 3.9 23.6 - - + -
19B CYS* 3.7 29.2 - - - -
38B ILE* 3.2 15.4 + - + +
39B LEU* 3.3 11.2 + - + +
41B THR* 1.3 73.8 - - - +
43B PHE* 1.3 63.9 + - - +
45B ILE* 3.3 9.4 + - + +
46B ILE* 3.1 29.9 + - - +
72B LEU* 4.8 4.5 - - + -
75B VAL* 4.0 11.0 - - + -
129B ILE* 4.3 13.9 - - + -
132B LEU* 4.1 22.0 - - + -
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Residues in contact with PHE 43 (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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39B LEU 3.0 14.4 + - - +
40B TYR* 3.6 25.6 - + - +
42B LEU* 1.3 74.3 - - - +
44B HIS* 1.3 56.4 + - - +
46B ILE* 3.3 5.6 + - - +
47B ASP* 2.7 57.7 + - + +
64B VAL* 3.5 32.1 - - + -
66B PHE* 3.4 49.1 - + + -
69B TYR* 3.8 17.9 - + + -
75B VAL* 3.9 13.3 - - + +
78B LEU* 3.5 31.0 - - + -
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Residues in contact with HIS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.9 14.7 - - + +
40B TYR* 2.8 36.3 + - + +
41B THR 3.6 3.6 - - - +
43B PHE* 1.3 74.8 - - - +
45B ILE* 1.3 65.5 + - - +
47B ASP* 4.2 8.8 + - - -
48B VAL* 2.9 48.6 + - + +
124B HIS* 3.1 5.8 + + - -
128B HIS* 3.2 21.3 - + - -
200B NI 2.1 44.7 - - + +
201B CIT 3.0 22.9 + - - -
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Residues in contact with ILE 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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12B ARG* 3.9 11.7 - - - +
41B THR* 3.0 27.8 + - + +
42B LEU* 3.5 12.6 - - + +
44B HIS* 1.3 75.2 - - - +
46B ILE* 1.3 61.9 + - - +
48B VAL* 4.0 1.0 - - - +
49B GLU* 3.0 25.0 + - + +
124B HIS* 4.4 9.3 + - - +
125B GLU* 3.3 44.6 - - + +
128B HIS* 3.8 32.3 - - + -
129B ILE* 3.8 31.4 - - + -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 3.8 27.6 - - - +
16B PHE* 3.9 7.0 - - + -
42B LEU 3.1 16.0 + - - +
43B PHE* 3.5 7.6 - - - +
45B ILE* 1.3 76.3 - - - +
47B ASP* 1.3 63.7 + - - +
49B GLU* 3.5 6.2 + - - +
50B TYR* 3.1 24.3 + - - +
75B VAL* 3.5 39.5 - - + +
78B LEU* 4.0 19.7 - - + -
79B SER* 3.6 19.7 - - - -
82B PHE* 3.9 22.7 - - + -
86B ILE* 5.5 0.3 - - - +
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Residues in contact with ASP 47 (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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43B PHE* 2.7 47.4 + - + +
44B HIS* 3.6 9.0 + - - +
46B ILE* 1.3 74.6 - - - +
48B VAL* 1.3 59.2 + - + +
50B TYR* 3.8 4.5 - - - +
51B SER* 2.6 47.5 + - - -
63B ALA* 5.0 5.9 - - - +
64B VAL* 4.4 19.9 + - + +
78B LEU* 5.8 1.1 - - - +
82B PHE* 5.6 3.6 - - - -
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Residues in contact with VAL 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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44B HIS* 2.9 50.3 + - + +
47B ASP* 1.3 72.1 - - + +
49B GLU* 1.3 68.4 + - - +
51B SER* 3.4 5.1 + - - -
52B TRP* 3.2 46.4 + - + +
120B HIS* 4.9 4.7 - - + +
121B ILE* 5.8 2.2 - - + -
124B HIS* 3.5 34.1 - - + +
201B CIT 4.6 1.6 - - - +
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Residues in contact with GLU 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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5B PHE* 3.8 15.3 - - + -
8B ASN* 5.9 0.3 - - - +
9B TRP* 3.0 26.4 + - - -
12B ARG* 3.1 29.0 + - - +
45B ILE* 3.0 19.6 + - + +
46B ILE* 3.8 4.1 - - - +
48B VAL* 1.3 79.1 - - - +
50B TYR* 1.3 61.8 + - - +
52B TRP* 3.5 2.4 + - - +
53B ILE* 3.1 32.4 + - + +
83B ARG* 5.4 0.5 + - - -
86B ILE* 3.4 27.8 - - + +
121B ILE* 4.0 27.4 - - + +
125B GLU* 4.3 4.4 - - - +
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Residues in contact with TYR 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 ILE 3.1 15.6 + - - +
47B ASP* 3.9 3.1 - - - +
49B GLU* 1.3 76.7 - - - +
51B SER* 1.3 62.5 + - - +
53B ILE* 3.3 3.4 + - + -
54B ARG* 2.9 70.4 + - + +
57B GLN* 5.4 0.2 - - - -
61B ASP 5.9 0.4 - - - -
62B ILE 5.5 7.2 - - - -
64B VAL* 6.0 0.9 - - + -
82B PHE* 3.4 65.3 - + + -
85B GLU* 2.6 41.7 + - + -
86B ILE* 4.1 17.7 - - + +
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 2.6 36.0 + - - -
48B VAL* 3.9 6.0 - - - -
49B GLU 3.4 0.2 - - - -
50B TYR* 1.3 78.9 - - - +
52B TRP* 1.3 59.1 + - - +
54B ARG* 3.4 8.0 + - - +
55B ALA 3.1 21.1 + - - -
61B ASP* 4.7 8.7 + - - +
63B ALA* 5.9 2.4 - - - +
106B TRP* 3.7 31.1 - - - -
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Residues in contact with TRP 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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149A ILE* 4.8 8.1 - - + -
48B VAL* 3.2 39.6 + - + +
51B SER* 1.3 76.5 - - - +
53B ILE* 1.3 58.7 + - - +
55B ALA* 3.2 10.0 + - + +
56B ILE* 2.9 33.3 + - - +
102B VAL* 5.5 0.2 - - + -
104B VAL* 4.1 13.0 - - + -
106B TRP* 3.8 34.8 - + - -
107B GLU* 5.2 0.9 - - - -
112B TYR* 3.6 32.5 - + - -
117B ILE* 3.7 49.4 - - + -
120B HIS* 3.8 28.8 + + - -
121B ILE* 3.8 14.1 - - + -
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Residues in contact with ILE 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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5B PHE* 5.2 1.1 - - + -
49B GLU* 3.1 21.0 + - + +
50B TYR* 3.8 7.2 - - + +
52B TRP* 1.3 74.0 - - - +
54B ARG* 1.3 57.2 + - - +
56B ILE* 3.3 16.5 + - + +
57B GLN* 3.1 28.5 + - - +
85B GLU* 5.0 0.4 - - + -
86B ILE* 3.9 34.5 - - + +
89B VAL* 3.5 32.9 - - + +
90B LEU* 3.8 33.4 - - + -
121B ILE* 4.0 18.6 - - + -
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Residues in contact with ARG 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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50B TYR* 2.9 61.6 + - + +
51B SER* 3.6 7.4 - - - +
53B ILE* 1.3 74.8 - - - +
55B ALA* 1.3 59.5 + - - +
57B GLN* 3.3 9.7 + - - +
58B GLY 3.0 6.9 + - - -
59B LYS* 2.9 63.3 + - + +
60B GLU* 3.3 29.1 + - - +
61B ASP* 4.3 12.9 + - - +
62B ILE* 4.5 10.3 - - - +
85B GLU* 3.5 18.1 + - - -
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Residues in contact with ALA 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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51B SER 3.1 14.1 + - - +
52B TRP* 3.5 19.3 - - + +
54B ARG* 1.3 72.7 - - - +
56B ILE* 1.3 62.2 + - - +
58B GLY* 3.0 21.1 + - - +
59B LYS 4.9 3.6 - - - -
102B VAL* 3.2 25.1 - - + +
103B SER 4.0 13.9 + - - +
105B PRO* 4.3 15.9 - - + -
106B TRP* 4.3 6.9 - - + -
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Residues in contact with ILE 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 TRP 2.9 15.2 + - - +
53B ILE* 3.5 20.4 - - + +
54B ARG 3.3 0.2 - - - -
55B ALA* 1.3 75.2 - - - +
57B GLN* 1.3 59.9 + - - +
58B GLY* 3.3 0.9 + - - -
89B VAL* 3.8 11.2 - - + -
90B LEU* 5.7 0.4 - - + -
93B HIS* 3.6 45.4 - - + +
100B GLU* 4.8 4.5 - - - +
102B VAL* 3.9 23.7 - - + +
114B ARG* 4.8 10.3 - - + -
117B ILE* 3.8 30.3 - - + -
118B LEU* 4.1 21.5 - - + -
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Residues in contact with GLN 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 ILE* 3.1 9.7 + - - +
54B ARG* 3.5 28.1 - - - +
55B ALA 3.3 0.2 - - - -
56B ILE* 1.3 73.1 - - - +
58B GLY* 1.3 59.9 + - - +
59B LYS* 2.9 37.5 + - + +
85B GLU* 2.7 27.3 + - - +
89B VAL* 3.3 37.6 - - + +
93B HIS* 4.7 7.4 - - + +
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Residues in contact with GLY 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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54B ARG 3.0 3.6 + - - -
55B ALA* 3.0 16.0 + - - -
56B ILE 3.2 0.9 - - - -
57B GLN* 1.3 78.7 - - - +
59B LYS* 1.3 64.8 + - - +
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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