Contacts of the helix formed by residues 46 - 67 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M ASN 4.7 1.3 - - - +
43M TRP* 3.4 48.2 - - + +
45M TRP* 1.3 79.6 - - - +
47M TRP* 1.3 95.7 + - + +
49M VAL* 3.0 20.0 + - + +
50M VAL* 3.1 21.2 + - + +
251M LYS* 5.3 3.8 - - + +
252M ASP* 5.4 6.3 - - - -
255M ALA* 3.7 31.0 - - + -
259M VAL* 4.7 6.3 - - + -
505M ANJ 4.2 13.9 - - - -
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Residues in contact with TRP 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M TRP 3.8 5.4 + - - -
44M MET* 3.5 48.0 - - + +
45M TRP 3.3 0.4 - - - -
46M ILE* 1.3 94.3 - - + +
48M GLY* 1.3 64.5 + - - +
50M VAL* 3.0 31.2 + - + +
51M LEU* 2.8 27.3 + - - +
103M LEU* 6.0 2.2 - - + -
106M ILE* 5.5 2.7 - - + -
107M ALA* 4.3 15.0 - - + +
110M LEU* 3.4 45.9 - - + +
111M HIS* 4.1 24.0 - - + +
259M VAL* 5.1 10.3 - - + -
504M LOP 4.1 37.5 - - + -
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Residues in contact with GLY 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M TRP 3.9 0.2 + - - -
46M ILE 3.1 1.4 + - - -
47M TRP* 1.3 76.0 - - - +
49M VAL* 1.3 57.9 + - - +
51M LEU* 3.1 7.5 - - - +
52M ALA* 2.9 22.9 + - - +
111M HIS* 3.7 7.8 + - - -
501M HEM 3.2 56.8 + - - +
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Residues in contact with VAL 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M ILE* 3.0 10.2 + - + +
48M GLY* 1.3 70.3 - - - +
50M VAL* 1.3 71.2 + - + +
51M LEU 2.9 1.8 - - - -
52M ALA* 2.8 20.4 + - + +
53M PHE* 2.9 12.7 + - + +
252M ASP* 2.8 42.0 - - + +
256M LEU* 3.3 31.0 - - + -
501M HEM 4.0 2.0 + - - +
505M ANJ 3.4 35.5 + - + +
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Residues in contact with VAL 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M ILE* 3.1 28.4 + - + +
47M TRP* 3.0 37.6 + - + +
49M VAL* 1.3 76.7 - - + +
51M LEU* 1.3 60.8 + - - +
53M PHE* 3.6 4.2 - - + +
54M CYS* 3.2 22.6 + - - -
103M LEU* 4.6 14.1 - - + -
107M ALA* 4.5 9.2 - - + -
256M LEU* 4.0 17.5 - - + +
259M VAL* 3.9 32.3 - - + -
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Residues in contact with LEU 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M TRP 2.8 14.4 + - - +
48M GLY* 3.1 6.3 - - - +
49M VAL 2.9 0.2 - - - -
50M VAL* 1.3 76.5 - - - +
52M ALA* 1.3 69.5 + - - +
54M CYS* 2.8 16.8 + - - +
55M LEU* 2.9 10.2 + - - +
104M PHE* 3.4 45.1 - - + +
107M ALA* 3.5 13.9 - - + -
108M VAL* 3.7 9.9 - - + +
111M HIS* 3.4 36.8 - - + +
501M HEM 3.2 40.4 - - + -
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Residues in contact with ALA 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M GLY 2.9 8.3 + - - +
49M VAL* 2.8 21.7 + - + +
51M LEU* 1.3 69.6 - - - +
53M PHE* 1.3 56.8 + - - +
55M LEU* 2.8 29.1 + - - +
56M VAL* 3.1 17.2 + - + +
209M VAL* 6.0 0.2 - - - -
501M HEM 3.4 8.9 - - - +
505M ANJ 3.2 42.1 - - + +
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Residues in contact with PHE 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M VAL* 2.9 6.6 + - + +
50M VAL* 3.6 11.2 - - + +
52M ALA* 1.3 77.6 - - - +
54M CYS* 1.3 57.5 + - - +
56M VAL* 3.2 9.7 + - + +
57M LEU* 2.7 67.8 + - + +
103M LEU* 4.9 7.6 - - + -
256M LEU* 4.1 32.3 - - + -
260M LEU* 3.3 46.4 - - + -
263M PHE* 5.2 0.4 - + - -
264M PHE* 5.6 4.9 - + - -
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Residues in contact with CYS 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M VAL* 3.2 17.4 + - - -
51M LEU* 2.8 15.9 + - - +
53M PHE* 1.3 78.5 - - - +
55M LEU* 1.3 62.7 + - - +
57M LEU* 3.5 6.0 - - - +
58M GLN* 2.8 31.7 + - + +
100M GLY* 4.1 3.8 - - - +
103M LEU* 3.4 42.6 - - - -
104M PHE* 3.5 38.1 - - + -
107M ALA* 5.2 0.4 - - - -
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Residues in contact with LEU 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU 2.9 7.9 + - - +
52M ALA* 2.8 19.2 + - - +
54M CYS* 1.3 71.1 - - - +
56M VAL* 1.3 65.6 + - + +
58M GLN* 3.6 1.7 - - - +
59M ILE* 2.9 45.4 + - + +
104M PHE* 4.2 21.9 - - + -
202M PRO* 4.5 5.2 - - + +
205M ILE* 4.1 16.6 - - + -
206M ALA* 3.7 34.3 - - + +
209M VAL* 3.9 19.1 - - + -
501M HEM 5.2 3.6 - - + -
502M HEM 4.7 9.4 - - + -
505M ANJ 4.9 12.8 - - + -
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Residues in contact with VAL 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M ALA 3.1 14.0 + - - +
53M PHE* 3.6 8.1 - - + +
55M LEU* 1.3 73.2 - - + +
57M LEU* 1.3 69.0 + - - +
59M ILE* 2.8 19.0 + - + -
60M VAL* 2.9 31.4 + - + +
505M ANJ 4.2 22.4 - - + -
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Residues in contact with LEU 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M PHE* 2.7 47.4 + - + +
54M CYS* 3.5 7.2 - - - +
56M VAL* 1.3 73.9 - - - +
58M GLN* 1.3 61.6 + - - +
60M VAL* 3.3 8.8 + - + +
61M THR* 2.5 55.2 + - + +
96M LEU* 4.5 15.7 - - + +
100M GLY* 4.5 12.6 - - - -
103M LEU* 5.3 3.4 - - + -
263M PHE* 3.8 33.0 - - + -
264M PHE* 6.5 0.4 - - + -
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Residues in contact with GLN 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M CYS* 2.8 26.2 + - - +
55M LEU 3.6 2.7 - - - +
57M LEU* 1.3 77.9 - - - +
59M ILE* 1.3 57.1 + - - +
61M THR* 3.5 2.5 - - - -
62M GLY* 2.8 27.7 + - - -
96M LEU 3.9 0.9 - - - +
97M HIS* 2.9 66.4 + - - +
100M GLY* 3.1 20.7 - - - -
101M ALA 3.9 6.9 - - - +
104M PHE* 4.3 8.1 - - + -
502M HEM 3.1 51.4 - - + +
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Residues in contact with ILE 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M LEU* 3.1 38.1 - - + +
56M VAL* 2.8 17.5 + - + +
58M GLN* 1.3 71.2 - - + +
60M VAL* 1.3 61.4 + - + +
62M GLY* 3.6 0.2 - - - -
63M ILE* 2.9 53.0 + - + +
202M PRO* 4.3 19.5 - - + +
203M PHE* 4.6 18.6 - - + -
206M ALA* 4.9 6.1 - - + -
502M HEM 3.9 20.1 - - + +
505M ANJ 6.2 2.0 - - + -
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Residues in contact with VAL 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M VAL* 2.9 35.4 + - + +
57M LEU* 3.6 12.1 - - + +
59M ILE* 1.3 70.2 - - + +
61M THR* 1.3 87.6 + - + +
62M GLY 2.9 2.2 + - - -
63M ILE* 3.1 9.0 + - - +
64M VAL* 3.0 26.6 + - + +
34O LEU* 4.0 32.1 - - + -
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Residues in contact with THR 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M LEU* 2.5 43.0 + - + +
58M GLN* 3.2 5.2 + - - -
60M VAL* 1.3 87.7 - - + +
62M GLY* 1.3 58.6 + - - +
64M VAL* 3.4 8.6 - - - +
65M LEU* 3.0 35.2 + - - +
93M LEU* 4.2 25.5 - - + +
96M LEU* 4.4 15.3 - - + -
97M HIS* 3.3 22.2 + - - +
34O LEU* 5.1 1.8 - - + -
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Residues in contact with GLY 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M GLN 2.8 21.6 + - - -
59M ILE 3.6 0.7 - - - -
60M VAL 2.9 0.2 - - - -
61M THR* 1.3 75.1 + - - +
63M ILE* 1.3 54.7 + - - +
65M LEU* 2.9 6.9 + - - +
66M ALA* 2.7 34.1 + - - +
97M HIS* 3.8 13.9 - - - -
502M HEM 3.3 21.5 - - - +
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Residues in contact with ILE 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ILE* 2.9 35.8 + - + +
60M VAL* 3.7 6.7 - - - +
62M GLY* 1.3 69.3 - - - +
64M VAL* 1.3 64.8 + - + +
66M ALA* 3.1 6.8 - - - +
67M MET* 3.2 17.2 - - + +
199M TYR* 3.7 7.6 - - + +
203M PHE* 4.9 2.5 - - + -
502M HEM 3.0 19.6 - - + +
196P SER* 2.9 33.2 + - - +
197P LEU* 4.9 1.1 - - + -
200P LEU* 3.3 44.0 - - + -
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Residues in contact with VAL 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M VAL* 3.0 18.8 + - + +
61M THR* 3.4 9.2 - - - +
63M ILE* 1.3 76.7 - - + +
65M LEU* 1.3 57.6 + - + +
67M MET* 2.7 40.7 + - - +
68M HIS* 3.3 11.1 - - + -
93M LEU* 3.4 31.9 - - + -
34O LEU* 4.0 22.9 - - + +
37O GLN* 3.6 29.6 - - + +
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Residues in contact with LEU 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M THR 3.0 15.1 + - - +
62M GLY* 2.9 7.7 + - - +
64M VAL* 1.3 81.2 - - + +
66M ALA* 1.3 55.2 + - - +
68M HIS* 2.8 29.1 + - + +
69M TYR* 3.0 11.4 + - - +
83M ILE* 3.6 39.9 - - + +
93M LEU* 4.1 18.8 - - + +
94M ARG* 4.2 15.9 - - + +
97M HIS* 3.6 35.2 - - + -
502M HEM 4.1 30.5 - - + +
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Residues in contact with ALA 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M GLY 2.7 14.8 + - - +
63M ILE* 3.1 17.5 - - - +
65M LEU* 1.3 73.1 - - - +
67M MET* 1.3 53.7 + - - +
68M HIS 3.2 0.6 + - - -
69M TYR* 3.6 8.0 + - - +
195M PHE* 4.4 15.8 - - + -
199M TYR* 4.2 14.8 - - + -
502M HEM 4.0 19.0 - - + +
192P ASN* 3.0 17.5 + - - +
195P PHE* 5.4 1.9 - - - -
196P SER* 3.3 19.7 + - - +
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Residues in contact with MET 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M ILE* 3.2 16.4 - - + +
64M VAL* 2.7 18.1 + - - +
66M ALA* 1.3 72.4 - - - +
68M HIS* 1.3 72.3 + - + +
37O GLN* 3.7 25.4 - - - -
38O MET* 4.2 16.4 - - - +
189P ALA* 4.4 3.1 - - - +
192P ASN* 2.9 36.0 + - - +
193P ARG* 3.8 23.5 + - + +
196P SER* 3.7 8.5 - - - +
197P LEU* 3.5 44.6 - - + -
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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