Contacts of the helix formed by residues 46 - 67 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN 4.7 1.1 - - - +
43A TRP* 3.5 50.0 - - + +
45A TRP* 1.3 79.1 - - - +
47A TRP* 1.3 92.0 + - + +
48A GLY 3.2 0.2 - - - -
49A VAL* 3.1 17.5 + - + +
50A VAL* 3.1 21.7 + - + +
251A LYS* 5.4 3.4 - - + +
252A ASP* 4.5 7.2 - - - +
255A ALA* 3.6 30.3 - - + -
259A VAL* 4.6 7.2 - - + -
504A ANJ 4.3 13.9 - - - -
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Residues in contact with TRP 47 (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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43A TRP 3.7 6.0 + - - -
44A MET* 3.5 56.8 - - + +
45A TRP 3.3 1.0 - - - -
46A ILE* 1.3 94.2 - - + +
48A GLY* 1.3 62.2 + - - +
50A VAL* 3.1 30.3 + - + +
51A LEU* 2.8 26.8 + - - +
103A LEU* 5.9 1.8 - - + -
106A ILE* 5.4 2.2 - - + -
107A ALA* 4.3 15.4 - - - +
110A LEU* 3.4 43.2 - - + +
111A HIS* 4.2 24.5 - - + +
259A VAL* 5.1 6.7 - - + -
503A LOP 3.9 33.4 - - + -
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE 3.1 0.2 + - - -
47A TRP* 1.3 77.0 - - - +
49A VAL* 1.3 57.1 + - - +
51A LEU* 3.1 7.6 - - - +
52A ALA* 3.0 22.9 + - - +
111A HIS* 3.8 6.5 + - - -
501A HEM 2.8 59.0 + - - +
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Residues in contact with VAL 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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46A ILE* 3.1 10.0 + - + +
48A GLY* 1.3 70.8 - - - +
50A VAL* 1.3 69.6 + - + +
51A LEU 2.9 1.8 - - - -
52A ALA* 2.8 16.2 + - + +
53A PHE* 2.9 13.0 + - + +
252A ASP* 3.9 25.6 - - + +
256A LEU* 3.3 31.0 - - + -
501A HEM 4.1 1.4 + - - +
504A ANJ 3.3 57.4 + - + +
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Residues in contact with VAL 50 (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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46A ILE* 3.1 29.3 + - + +
47A TRP* 3.1 36.5 + - + +
49A VAL* 1.3 78.3 - - + +
51A LEU* 1.3 60.8 + - - +
53A PHE* 3.7 3.9 - - + +
54A CYS* 3.2 23.0 + - - -
103A LEU* 4.6 13.2 - - + -
107A ALA* 4.6 9.2 - - + -
255A ALA* 6.0 0.2 - - + -
256A LEU* 4.1 14.8 - - + -
259A VAL* 4.0 32.1 - - + -
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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
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47A TRP 2.8 15.0 + - - +
48A GLY* 3.1 7.0 - - - +
50A VAL* 1.3 74.7 - - - +
52A ALA* 1.3 68.7 + - - +
54A CYS* 2.9 16.9 + - - +
55A LEU* 2.9 11.3 + - - +
104A PHE* 3.5 45.1 - - + +
107A ALA* 3.6 12.6 - - + -
108A VAL* 3.7 11.0 - - + +
111A HIS* 3.4 36.3 - - + +
501A HEM 3.3 40.4 - - + +
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Residues in contact with ALA 52 (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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48A GLY 3.0 9.3 + - - +
49A VAL* 2.8 15.0 + - + +
51A LEU* 1.3 72.6 - - - +
53A PHE* 1.3 64.4 + - - +
55A LEU* 2.8 18.5 + - - +
56A VAL* 3.1 17.6 + - - +
209A VAL* 6.1 0.2 - - - -
501A HEM 3.6 9.5 - - - +
504A ANJ 3.1 44.8 - - + +
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Residues in contact with PHE 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 VAL* 2.9 7.6 + - + +
50A VAL* 3.7 12.1 - - + +
52A ALA* 1.3 77.7 - - - +
54A CYS* 1.3 63.0 + - - +
56A VAL* 3.1 9.6 + - + +
57A LEU* 2.7 69.2 + - + +
103A LEU* 4.9 4.0 - - + -
256A LEU* 4.1 31.2 - - + -
260A LEU* 3.3 46.2 - - + -
263A PHE* 5.2 0.7 - + - -
264A PHE* 5.6 4.3 - + - -
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Residues in contact with CYS 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 VAL* 3.2 19.5 + - - -
51A LEU* 2.9 10.1 + - - +
53A PHE* 1.3 81.6 - - - +
55A LEU* 1.3 58.4 + - - +
57A LEU* 3.6 5.8 - - - +
58A GLN* 2.8 37.7 + - - +
100A GLY 4.2 3.6 - - - +
103A LEU* 3.4 41.1 - - - -
104A PHE* 3.6 39.0 - - + -
107A ALA* 5.2 0.7 - - - -
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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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51A LEU 2.9 8.4 + - - +
52A ALA* 2.8 19.9 + - - +
54A CYS* 1.3 72.1 - - - +
56A VAL* 1.3 64.6 + - + +
58A GLN* 3.4 1.6 + - - +
59A ILE* 2.9 46.6 + - + +
104A PHE* 4.3 18.3 - - + -
202A PRO* 4.4 4.3 - - + +
205A ILE* 4.1 15.0 - - + -
206A ALA* 3.7 33.0 - - + +
209A VAL* 4.0 20.0 - - + -
501A HEM 5.2 3.8 - - + -
502A HEM 4.3 14.6 - - + -
504A ANJ 5.1 10.8 - - + -
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Residues in contact with VAL 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 ALA 3.1 8.6 + - - +
53A PHE* 3.6 7.6 - - + +
55A LEU* 1.3 74.1 - - + +
57A LEU* 1.3 68.4 + - - +
59A ILE* 2.8 18.9 + - + -
60A VAL* 2.9 31.4 + - + +
504A ANJ 3.5 31.2 - - + -
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Residues in contact with LEU 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 PHE* 2.7 47.6 + - + +
54A CYS* 3.6 6.7 - - - +
56A VAL* 1.3 73.9 - - - +
58A GLN* 1.3 61.0 + - - +
60A VAL* 3.6 6.8 - - + +
61A THR* 2.6 52.8 + - + +
96A LEU* 4.5 19.3 - - + +
100A GLY* 4.6 8.5 - - - -
103A LEU* 5.3 2.9 - - + -
263A PHE* 3.8 33.4 - - + -
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Residues in contact with GLN 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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54A CYS* 2.8 26.4 + - - +
55A LEU 3.6 2.5 - - - +
57A LEU* 1.3 77.2 - - - +
59A ILE* 1.3 57.9 + - - +
61A THR* 3.6 3.1 - - - -
62A GLY* 2.8 24.3 + - - -
96A LEU 3.9 0.5 - - - +
97A HIS* 2.8 70.0 + - - +
100A GLY* 3.0 21.0 - - - -
101A ALA 3.9 6.7 - - - +
104A PHE* 4.3 8.3 - - + -
502A HEM 3.3 49.1 - - + +
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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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55A LEU* 2.9 43.6 + - + +
56A VAL* 2.8 14.5 + - + +
58A GLN* 1.3 69.3 - - + +
60A VAL* 1.3 62.5 + - + +
62A GLY* 3.3 0.3 + - - -
63A ILE* 2.9 53.1 + - + +
202A PRO* 4.3 20.4 - - + +
203A PHE* 4.6 17.9 - - + -
206A ALA* 4.9 6.5 - - + -
502A HEM 3.8 21.0 - - + +
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Residues in contact with VAL 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 VAL* 2.9 34.8 + - + +
57A LEU* 3.6 11.4 - - + +
59A ILE* 1.3 72.2 - - + +
61A THR* 1.3 87.3 + - + +
62A GLY 2.9 1.4 + - - -
63A ILE* 3.1 9.0 + - - +
64A VAL* 3.1 26.4 + - + +
34C LEU* 4.1 31.4 - - + -
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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 LEU* 2.6 41.4 + - + +
58A GLN* 3.3 0.9 + - - -
60A VAL* 1.3 88.0 - - + +
62A GLY* 1.3 57.5 + - - +
64A VAL* 3.4 8.6 - - - +
65A LEU* 2.9 35.5 + - - +
93A LEU* 4.1 25.5 - - + +
96A LEU* 4.5 14.6 - - + -
97A HIS* 3.2 27.6 + - - +
34C LEU* 5.1 2.2 - - + -
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Residues in contact with GLY 62 (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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58A GLN 2.8 20.9 + - - -
60A VAL 2.9 0.4 - - - -
61A THR* 1.3 75.5 + - - +
63A ILE* 1.3 54.7 + - - +
65A LEU* 2.9 6.9 + - - +
66A ALA* 2.7 34.1 + - - +
97A HIS* 3.7 6.1 - - - -
502A HEM 3.5 30.1 - - - +
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Residues in contact with ILE 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* 2.9 38.9 + - + +
60A VAL* 3.7 6.5 - - - +
62A GLY* 1.3 69.2 - - - -
64A VAL* 1.3 65.8 + - + +
66A ALA* 3.2 7.9 - - - +
67A MET* 3.1 18.4 - - + +
199A TYR* 3.8 14.4 - - + +
203A PHE* 4.9 2.2 - - + -
502A HEM 3.6 8.8 - - + +
196D SER* 2.8 35.0 + - - +
197D LEU* 4.8 1.3 - - + -
200D LEU* 3.3 43.7 - - + -
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Residues in contact with VAL 64 (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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60A VAL* 3.1 15.5 - - + +
61A THR* 3.4 8.3 - - - +
63A ILE* 1.3 75.5 - - + +
65A LEU* 1.3 69.7 + - + +
67A MET* 2.7 30.8 + - - +
68A HIS* 3.4 8.2 - - + -
93A LEU* 3.4 30.5 - - + -
34C LEU* 4.0 25.6 - - + +
37C GLN* 3.6 29.8 - - + +
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Residues in contact with LEU 65 (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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61A THR 2.9 17.6 + - - +
62A GLY* 2.9 8.2 + - - +
64A VAL* 1.3 78.4 - - + +
66A ALA* 1.3 53.4 + - - +
68A HIS* 2.7 29.8 + - + +
69A TYR* 3.1 11.5 + - - +
83A ILE* 3.7 39.6 - - + +
93A LEU* 4.1 17.9 - - + +
94A ARG* 4.2 18.2 - - + +
97A HIS* 3.6 36.6 - - + -
502A HEM 4.1 28.3 - - + +
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Residues in contact with ALA 66 (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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62A GLY 2.7 15.0 + - - +
63A ILE* 3.2 16.8 - - - +
64A VAL 3.1 0.2 - - - -
65A LEU* 1.3 72.1 - - - +
67A MET* 1.3 55.2 + - - +
68A HIS 3.1 0.6 + - - -
69A TYR* 3.8 7.5 + - - +
195A PHE* 4.5 15.7 - - + -
199A TYR* 4.6 2.2 - - + -
502A HEM 3.8 32.5 - - + +
192D ASN* 3.0 18.0 + - - +
195D PHE* 5.2 2.1 - - - -
196D SER* 3.3 19.6 + - - +
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Residues in contact with MET 67 (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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63A ILE* 3.1 20.2 - - + +
64A VAL* 2.7 13.4 + - - +
66A ALA* 1.3 72.9 - - - +
68A HIS* 1.3 73.9 + - + +
37C GLN* 3.7 25.6 - - - -
38C MET* 4.2 16.2 - - - -
189D ALA* 4.6 2.4 - - - +
192D ASN* 3.0 33.3 + - - +
193D ARG* 3.8 24.4 + - + +
196D SER* 3.7 9.2 - - - +
197D LEU* 3.4 47.3 - - + -
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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