Contacts of the helix formed by residues 46 - 67 (chain D) in PDB entry 2QJK
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 ILE 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D ASN 4.7 0.7 - - - +
43D TRP* 3.3 53.2 - - + +
45D TRP* 1.3 80.4 - - - +
47D TRP* 1.3 93.2 + - + +
48D GLY 3.2 0.2 - - - -
49D VAL* 3.0 19.6 + - + +
50D VAL* 3.1 20.6 + - + +
251D LYS* 5.2 2.7 - - - +
252D ASP* 5.4 5.2 - - - -
255D ALA* 3.7 26.7 - - + -
259D VAL* 4.7 6.7 - - + -
504D ANJ 4.3 13.0 - - - -
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Residues in contact with TRP 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP 3.8 5.6 + - - -
44D MET* 3.5 55.9 - - + +
45D TRP 3.3 1.0 - - - -
46D ILE* 1.3 93.5 - - + +
48D GLY* 1.3 63.9 + - - +
50D VAL* 3.1 29.6 + - + +
51D LEU* 2.9 27.1 + - - +
103D LEU* 5.9 2.0 - - + -
106D ILE* 5.7 1.6 - - + -
107D ALA* 4.2 16.1 - - - +
110D LEU* 3.4 44.8 - - + +
111D HIS* 4.2 25.1 - - + +
259D VAL* 5.2 10.1 - - + -
503D LOP 4.5 27.4 - - + -
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Residues in contact with GLY 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE 3.1 1.4 + - - -
47D TRP* 1.3 76.6 - - - +
49D VAL* 1.3 55.5 + - - +
51D LEU* 3.1 8.1 + - - +
52D ALA* 3.0 23.2 + - - +
111D HIS* 3.8 4.9 + - - -
501D HEM 3.5 60.2 + - - +
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ILE* 3.0 10.0 + - + +
48D GLY* 1.3 70.1 - - - +
50D VAL* 1.3 70.4 + - + +
51D LEU 2.9 2.0 - - - -
52D ALA* 2.8 20.2 + - + +
53D PHE* 2.9 13.1 + - + +
252D ASP* 2.8 43.3 - - + +
256D LEU* 3.4 29.6 - - + -
501D HEM 4.1 1.6 - - - +
504D ANJ 3.4 34.8 + - + +
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Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ILE* 3.1 29.5 + - + +
47D TRP* 3.1 36.5 + - + +
49D VAL* 1.3 77.0 - - + +
51D LEU* 1.3 61.7 + - - +
53D PHE* 3.7 4.1 - - + +
54D CYS* 3.2 22.2 + - - -
103D LEU* 4.5 13.2 - - + -
107D ALA* 4.5 9.0 - - + -
255D ALA* 6.0 0.4 - - + -
256D LEU* 4.1 15.9 - - + -
259D VAL* 4.0 31.6 - - + -
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D TRP 2.9 14.8 + - - +
48D GLY* 3.1 7.0 - - - +
50D VAL* 1.3 75.9 - - - +
52D ALA* 1.3 66.3 + - - +
54D CYS* 2.9 17.4 + - - +
55D LEU* 2.9 11.6 + - - +
104D PHE* 3.4 33.5 - - + +
107D ALA* 3.6 10.8 - - + -
108D VAL* 3.2 28.0 - - + -
111D HIS* 3.4 43.3 - - + +
501D HEM 3.3 31.9 - - + +
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLY 3.0 9.1 + - - +
49D VAL* 2.8 15.0 + - + +
51D LEU* 1.3 75.5 - - - +
53D PHE* 1.3 63.9 + - - +
55D LEU* 2.8 19.6 + - - +
56D VAL* 3.1 17.2 + - + +
501D HEM 3.4 9.5 - - - +
504D ANJ 3.2 42.8 - - + +
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Residues in contact with PHE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL 2.9 9.6 + - - +
50D VAL* 3.7 10.8 - - + +
52D ALA* 1.3 76.8 - - - +
54D CYS* 1.3 58.0 + - - +
56D VAL* 3.1 9.6 + - + +
57D LEU* 2.7 68.8 + - + +
103D LEU* 4.9 7.6 - - + -
256D LEU* 4.1 32.8 - - + -
260D LEU* 3.4 45.3 - - + -
263D PHE* 5.2 0.4 - + - -
264D PHE* 5.6 4.0 - + - -
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Residues in contact with CYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL* 3.2 19.9 + - - -
51D LEU* 2.9 10.4 + - - +
53D PHE* 1.3 82.0 - - - +
55D LEU* 1.3 55.5 + - - +
57D LEU* 3.5 6.0 - - - +
58D GLN* 2.8 40.1 + - - +
100D GLY* 4.2 4.3 - - - +
103D LEU* 3.5 40.4 - - - -
104D PHE* 3.6 38.8 - - + -
107D ALA* 5.2 0.7 - - - -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU 2.9 8.6 + - - +
52D ALA* 2.8 14.9 + - - +
54D CYS* 1.3 76.7 - - - +
56D VAL* 1.3 63.4 + - + +
58D GLN* 3.7 1.1 - - - +
59D ILE* 3.0 46.2 + - + +
104D PHE* 4.3 21.0 - - + -
202D PRO* 4.4 5.4 - - + +
205D ILE* 4.1 15.9 - - + -
206D ALA* 3.8 33.2 - - + +
209D VAL* 4.0 20.0 - - + -
501D HEM 4.9 3.1 - - + -
502D HEM 4.6 10.3 - - + -
504D ANJ 4.8 12.8 - - + -
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ALA 3.1 13.8 + - - +
53D PHE* 3.6 8.1 - - + +
55D LEU* 1.3 72.7 - - + +
57D LEU* 1.3 71.0 + - - +
59D ILE* 2.8 17.4 + - + +
60D VAL* 2.9 31.6 + - + +
504D ANJ 4.3 19.7 - - + -
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PHE* 2.7 45.6 + - + +
54D CYS* 3.5 7.0 - - - +
56D VAL* 1.3 76.2 - - - +
58D GLN* 1.3 59.9 + - - +
60D VAL* 3.2 7.1 + - + +
61D THR* 2.7 52.1 + - + +
96D LEU* 4.5 20.2 - - + +
100D GLY* 4.5 8.7 - - - -
103D LEU* 5.3 2.7 - - + -
263D PHE* 3.8 33.7 - - + -
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Residues in contact with GLN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D CYS 2.8 26.5 + - - +
55D LEU* 3.7 3.4 - - - +
57D LEU* 1.3 75.2 - - - +
59D ILE* 1.3 57.2 + - - +
61D THR* 3.6 3.1 - - - -
62D GLY* 2.8 23.7 + - - -
96D LEU 4.0 0.5 - - - +
97D HIS* 2.9 65.2 + - - +
100D GLY* 3.0 22.1 - - - +
101D ALA 3.9 6.9 - - - +
104D PHE* 4.3 11.4 - - + -
502D HEM 3.3 45.5 - - + +
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Residues in contact with ILE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 3.0 42.8 + - + +
56D VAL* 2.8 13.7 + - + +
58D GLN* 1.3 70.9 - - + +
60D VAL* 1.3 62.4 + - + +
62D GLY* 3.6 0.3 - - - -
63D ILE* 2.9 53.4 + - + +
202D PRO* 4.3 26.5 - - + +
203D PHE* 4.6 19.5 - - + -
206D ALA* 4.9 6.7 - - + -
502D HEM 4.1 11.3 - - + +
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 2.9 33.6 + - + +
57D LEU* 3.6 12.3 - - + +
59D ILE* 1.3 72.2 - - + +
61D THR* 1.3 88.7 + - + +
62D GLY 2.9 1.4 + - - -
63D ILE* 3.0 9.2 + - - +
64D VAL* 3.0 25.6 + - + +
34F LEU* 3.9 32.8 - - + -
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 2.7 42.1 + - + +
58D GLN* 3.6 0.5 - - - -
60D VAL* 1.3 88.5 - - + +
62D GLY* 1.3 58.2 + - - +
64D VAL* 3.4 7.8 - - - +
65D LEU* 2.9 36.0 + - - +
93D LEU* 4.1 24.9 - - + +
96D LEU* 4.5 15.0 - - + -
97D HIS* 3.2 27.6 + - - +
34F LEU* 4.9 2.7 - - + -
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Residues in contact with GLY 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLN 2.8 21.0 + - - -
59D ILE 3.6 0.9 - - - -
60D VAL 2.9 1.0 + - - -
61D THR* 1.3 75.2 + - - +
63D ILE* 1.3 53.8 + - - +
65D LEU* 2.8 6.8 + - - +
66D ALA* 2.7 34.1 + - - +
97D HIS* 3.7 6.1 - - - -
502D HEM 3.6 30.0 - - - +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A SER* 2.8 35.1 + - - +
197A LEU* 4.7 1.3 - - + -
200A LEU* 3.2 43.3 - - + -
59D ILE* 2.9 35.0 + - + +
60D VAL* 3.6 6.7 - - - +
62D GLY* 1.3 70.7 - - - +
64D VAL* 1.3 64.6 + - + +
66D ALA* 3.2 4.7 - - - +
67D MET* 3.1 18.7 - - + +
199D TYR* 3.7 7.6 - - - +
203D PHE* 4.9 2.0 - - + -
502D HEM 3.3 21.0 - - + +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL* 3.1 15.0 - - + +
61D THR* 3.4 8.7 - - - +
63D ILE* 1.3 75.5 - - + +
65D LEU* 1.3 59.6 + - + +
67D MET* 2.7 40.9 + - - +
68D HIS* 3.4 7.7 - - + -
93D LEU* 3.4 31.0 - - + -
34F LEU* 4.0 26.7 - - + +
37F GLN* 3.5 30.3 - - + +
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D THR 2.9 14.9 + - - +
62D GLY* 2.8 9.8 + - - +
64D VAL* 1.3 76.7 - - + +
66D ALA* 1.3 53.8 + - - +
68D HIS* 2.7 29.6 + - + +
69D TYR* 3.0 11.4 + - - +
83D ILE* 3.7 39.3 - - + +
93D LEU* 4.1 17.9 - - + +
94D ARG* 4.1 15.9 - - + +
97D HIS* 3.6 37.2 - - + +
502D HEM 4.1 31.2 - - + +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASN* 2.9 19.8 + - - +
195A PHE* 5.2 1.9 - - - -
196A SER* 3.3 17.3 + - - +
62D GLY 2.7 15.9 + - - +
63D ILE* 3.2 14.1 - - - +
65D LEU* 1.3 72.5 - - - +
67D MET* 1.3 55.0 + - - +
68D HIS 3.1 1.0 + - - -
69D TYR* 3.8 7.2 + - - +
195D PHE* 4.4 16.6 - - + -
199D TYR* 4.1 17.0 - - + -
502D HEM 4.0 18.3 - - + +
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Residues in contact with MET 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA* 4.5 3.3 - - - +
192A ASN* 3.0 34.4 + - - +
193A ARG* 3.7 25.6 + - + +
196A SER* 3.7 9.0 - - - +
197A LEU* 3.4 47.6 - - + -
63D ILE* 3.1 19.5 - - + +
64D VAL* 2.7 19.4 + - - +
66D ALA* 1.3 68.9 - - - +
68D HIS* 1.3 73.4 + - + +
37F GLN* 3.6 25.4 - - - -
38F MET* 4.1 15.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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