Contacts of the helix formed by residues 46 - 67 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P ASN 4.8 0.7 - - - +
43P TRP* 3.5 49.1 - - + +
45P TRP* 1.3 77.2 - - - +
47P TRP* 1.3 95.2 + - + +
48P GLY 3.2 3.1 - - - -
49P VAL* 3.0 18.8 + - + +
50P VAL* 3.1 21.3 + - + +
251P LYS* 4.9 2.7 - - - +
252P ASP* 5.2 5.8 - - - +
255P ALA* 3.8 30.3 - - + -
259P VAL* 4.7 6.3 - - + -
505P ANJ 4.2 15.5 - - - -
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Residues in contact with TRP 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P TRP 3.7 5.2 + - - -
44P MET* 3.5 51.6 - - + +
45P TRP 3.3 0.8 - - - -
46P ILE* 1.3 94.2 - - + +
48P GLY* 1.3 63.7 + - - +
50P VAL* 3.1 31.6 + - + +
51P LEU* 2.8 27.3 + - - +
103P LEU* 5.9 2.2 - - + -
106P ILE* 5.6 2.5 - - + -
107P ALA* 4.2 15.4 - - + +
110P LEU* 3.4 46.1 - - + +
111P HIS* 4.1 24.7 - - + +
259P VAL* 5.1 9.9 - - + -
501P HEM 5.2 0.2 - - - +
504P LOP 4.4 31.4 - - + -
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Residues in contact with GLY 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P TRP* 1.3 76.4 - - - +
49P VAL* 1.3 56.5 + - - +
51P LEU* 3.1 7.5 + - - +
52P ALA* 3.0 22.9 + - - +
111P HIS* 3.8 8.4 + - - -
501P HEM 3.0 58.5 + - - +
505P ANJ 4.1 0.2 - - - +
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Residues in contact with VAL 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ILE* 3.0 10.8 + - + +
48P GLY* 1.3 71.2 - - - +
50P VAL* 1.3 71.7 + - + +
51P LEU 2.9 1.6 - - - -
52P ALA* 2.8 17.6 + - + +
53P PHE* 2.9 12.5 + - + +
252P ASP* 3.1 41.3 - - + +
256P LEU* 3.3 31.2 - - + -
501P HEM 4.1 2.2 + - - +
505P ANJ 3.3 37.6 + - + +
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Residues in contact with VAL 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ILE* 3.1 29.0 + - + +
47P TRP* 3.4 36.8 - - + +
49P VAL* 1.3 75.5 - - + +
51P LEU* 1.3 62.7 + - - +
53P PHE* 3.6 4.3 - - + +
54P CYS* 3.2 22.5 + - - -
103P LEU* 4.5 13.9 - - + -
107P ALA* 4.5 9.9 - - + -
256P LEU* 4.0 16.2 - - + +
259P VAL* 4.0 32.8 - - + -
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Residues in contact with LEU 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P TRP 2.8 15.1 + - - +
48P GLY* 3.1 6.5 - - - +
50P VAL* 1.3 75.5 - - - +
52P ALA* 1.3 67.6 + - - +
54P CYS* 2.8 17.3 + - - +
55P LEU* 2.9 11.3 + - - +
104P PHE* 3.4 45.0 - - + +
107P ALA* 3.5 12.8 - - + -
108P VAL* 3.7 13.5 - - + +
111P HIS* 3.4 37.0 - - + +
501P HEM 3.3 37.5 - - + +
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Residues in contact with ALA 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P GLY 3.0 8.5 + - - +
49P VAL* 2.8 15.7 + - + +
51P LEU* 1.3 73.3 - - - +
53P PHE* 1.3 65.1 + - - +
55P LEU* 2.8 19.5 + - - +
56P VAL* 3.1 17.2 + - + +
501P HEM 3.5 9.3 - - - +
505P ANJ 3.1 42.7 - - + +
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Residues in contact with PHE 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P VAL* 2.9 6.6 + - + +
50P VAL* 3.6 11.7 - - + +
52P ALA* 1.3 77.5 - - - +
54P CYS* 1.3 57.5 + - - +
56P VAL* 3.2 10.1 + - + +
57P LEU* 2.7 68.7 + - + +
103P LEU* 4.9 7.2 - - + -
256P LEU* 4.1 31.4 - - + -
260P LEU* 3.3 44.4 - - + -
263P PHE* 5.2 0.7 - + - -
264P PHE* 5.6 4.0 - + - -
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Residues in contact with CYS 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P VAL* 3.2 18.6 + - - -
51P LEU* 2.8 14.7 + - - +
53P PHE* 1.3 78.9 - - - +
55P LEU* 1.3 63.6 + - - +
57P LEU* 3.6 5.7 - - - +
58P GLN* 2.8 32.1 + - + +
100P GLY* 4.2 4.0 - - - +
103P LEU* 3.4 40.6 - - - -
104P PHE* 3.5 39.0 - - + -
107P ALA* 5.2 0.7 - - - -
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Residues in contact with LEU 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P LEU 2.9 8.6 + - - +
52P ALA* 2.8 19.9 + - - +
54P CYS* 1.3 71.6 - - - +
56P VAL* 1.3 64.8 + - + +
58P GLN* 3.3 1.5 + - - +
59P ILE* 2.9 45.1 + - + +
104P PHE* 4.2 22.6 - - + -
202P PRO* 4.5 5.6 - - + +
205P ILE* 4.1 14.4 - - + -
206P ALA* 3.7 23.1 - - + +
209P VAL* 3.9 15.0 - - + -
501P HEM 5.3 2.5 - - + -
502P HEM 4.6 10.5 - - + -
505P ANJ 3.5 29.6 - - + -
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Residues in contact with VAL 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P ALA* 3.1 14.3 + - + +
53P PHE* 3.6 7.9 - - + +
55P LEU* 1.3 72.6 - - + +
57P LEU* 1.3 69.3 + - - +
59P ILE* 2.9 19.3 + - + +
60P VAL* 2.9 31.9 + - + +
505P ANJ 4.6 24.5 - - + -
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Residues in contact with LEU 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P PHE* 2.7 47.0 + - + +
54P CYS* 3.6 6.1 - - - +
56P VAL* 1.3 75.7 - - - +
58P GLN* 1.3 62.0 + - - +
60P VAL* 3.3 7.9 + - + +
61P THR* 2.6 53.3 + - + +
96P LEU* 4.5 16.8 - - + +
100P GLY* 4.5 13.0 - - - -
103P LEU* 5.3 3.4 - - + -
263P PHE* 3.8 34.1 - - + -
264P PHE* 6.5 0.4 - - + -
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Residues in contact with GLN 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P CYS* 2.8 25.6 + - - +
55P LEU 3.6 2.7 - - - +
57P LEU* 1.3 77.4 - - - +
59P ILE* 1.3 57.6 + - - +
61P THR* 3.5 2.7 - - - -
62P GLY* 2.8 27.4 + - - -
96P LEU 3.9 0.3 - - - +
97P HIS* 2.9 66.2 + - - +
100P GLY* 3.1 20.5 - - - +
101P ALA 3.9 6.5 - - - +
104P PHE* 4.3 10.5 - - + -
502P HEM 3.2 47.8 - - + +
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Residues in contact with ILE 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P LEU* 2.9 40.3 + - + +
56P VAL* 2.9 16.3 + - + +
58P GLN* 1.3 71.6 - - + +
60P VAL* 1.3 62.9 + - + +
62P GLY* 3.6 0.2 - - - -
63P ILE* 2.8 53.7 + - + +
202P PRO* 4.3 20.0 - - + +
203P PHE* 4.6 18.4 - - + -
206P ALA* 4.9 6.7 - - + -
502P HEM 3.8 19.0 - - + +
505P ANJ 6.0 1.1 - - + -
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Residues in contact with VAL 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P VAL* 2.9 34.2 + - + +
57P LEU* 3.5 12.6 - - + +
59P ILE* 1.3 71.2 - - + +
61P THR* 1.3 86.1 + - + +
62P GLY 2.9 2.2 + - - -
63P ILE* 3.0 8.8 + - - +
64P VAL* 3.0 26.4 + - + +
34R LEU* 4.0 30.7 - - + -
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Residues in contact with THR 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P LEU* 2.6 42.0 + - + +
58P GLN* 3.3 1.0 + - - -
60P VAL* 1.3 87.4 - - + +
62P GLY* 1.3 62.7 + - - +
64P VAL* 3.3 8.8 - - - +
65P LEU* 3.0 30.4 + - - +
93P LEU* 4.2 25.6 - - + +
96P LEU* 4.5 14.1 - - + -
97P HIS* 3.3 27.9 + - - +
34R LEU* 5.1 2.0 - - + -
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Residues in contact with GLY 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P GLN 2.8 21.8 + - - -
60P VAL 2.9 0.2 - - - -
61P THR* 1.3 74.8 + - - +
63P ILE* 1.3 66.1 + - - +
65P LEU* 2.9 7.2 + - - +
66P ALA 2.8 20.1 + - - -
97P HIS* 3.8 5.6 - - - -
502P HEM 3.1 32.6 - - - +
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Residues in contact with ILE 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M SER* 2.8 34.9 + - - +
197M LEU* 4.8 1.6 - - + -
200M LEU* 3.2 47.1 - - + -
59P ILE* 2.8 36.1 + - + +
60P VAL* 3.0 6.9 + - - +
62P GLY* 1.3 69.7 - - - +
64P VAL* 1.3 64.3 + - + +
66P ALA* 3.2 5.1 - - - +
67P MET* 3.1 17.9 - - + +
199P TYR* 3.8 11.7 - - + +
203P PHE* 4.9 1.8 - - + -
502P HEM 3.3 11.5 - - + +
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Residues in contact with VAL 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P VAL* 3.0 15.7 + - + +
61P THR* 3.3 9.4 - - - +
63P ILE* 1.3 77.7 - - + +
65P LEU* 1.3 57.7 + - + +
67P MET* 2.7 40.7 + - - +
68P HIS* 3.4 7.8 - - + -
93P LEU* 3.4 30.1 - - + -
34R LEU* 3.9 26.9 - - + +
37R GLN* 3.6 29.2 - - + +
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Residues in contact with LEU 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P THR 3.0 14.7 + - - +
62P GLY* 2.9 9.9 + - - +
64P VAL* 1.3 78.4 - - - +
66P ALA* 1.3 55.6 + - - +
68P HIS* 2.8 28.2 + - + +
69P TYR* 3.0 12.3 + - - +
83P ILE* 3.6 40.4 - - + +
93P LEU* 4.1 18.8 - - + +
94P ARG* 4.2 15.5 - - + +
97P HIS* 3.6 35.4 - - + -
502P HEM 3.9 31.2 - - + +
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Residues in contact with ALA 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M ASN* 3.0 17.8 + - - +
195M PHE* 5.3 1.7 - - - -
196M SER* 3.3 19.1 + - - +
62P GLY 2.8 11.2 + - - +
63P ILE* 3.2 17.3 - - - +
64P VAL 3.1 0.2 - - - -
65P LEU* 1.3 76.1 - - - +
67P MET* 1.3 55.5 + - - +
68P HIS 3.1 0.6 + - - -
69P TYR* 3.7 8.3 + - - +
195P PHE* 4.4 16.7 - - + -
199P TYR* 4.2 9.4 - - + -
502P HEM 4.1 24.1 - - + +
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Residues in contact with MET 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189M ALA* 4.4 3.5 - - - +
192M ASN* 3.0 29.8 + - - +
193M ARG* 3.7 30.1 + - + +
196M SER* 3.7 8.5 - - - +
197M LEU* 3.4 47.3 - - + -
63P ILE* 3.1 16.2 - - + +
64P VAL* 2.7 18.8 + - - +
66P ALA* 1.3 74.0 - - - +
68P HIS* 1.3 69.3 + - + +
37R GLN* 3.7 25.1 - - - -
38R MET* 4.2 15.7 - - - +
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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