Contacts of the helix formed by residues 46 - 67 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J ASN 4.7 1.1 - - - +
43J TRP* 3.8 49.8 - - + +
45J TRP* 1.3 76.5 - - - +
47J TRP* 1.3 94.3 + - + +
48J GLY 3.1 2.9 - - - -
49J VAL* 3.0 18.7 + - + +
50J VAL* 3.1 21.5 + - + +
251J LYS* 5.4 1.6 - - + +
252J ASP* 4.5 6.7 - - - +
255J ALA* 3.7 31.2 - - + -
259J VAL* 4.7 6.7 - - + -
505J ANJ 4.1 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J TRP 3.7 5.8 + - - -
44J MET* 3.5 54.5 - - + +
45J TRP 3.3 0.6 - - - -
46J ILE* 1.3 93.9 - - + +
48J GLY* 1.3 63.6 + - - +
50J VAL* 3.1 30.1 + - + +
51J LEU* 2.8 27.1 + - - +
103J LEU* 5.9 2.0 - - + -
106J ILE* 5.4 4.5 - - + -
107J ALA* 4.2 16.1 - - - +
110J LEU* 3.4 45.4 - - + +
111J HIS* 4.2 25.8 - - + +
259J VAL* 5.2 11.0 - - + -
501J HEM 5.2 0.2 - - - +
504J LOP 5.7 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J ILE 3.1 0.6 + - - -
47J TRP* 1.3 75.6 - - - +
49J VAL* 1.3 56.5 + - - +
51J LEU* 3.1 7.8 + - - +
52J ALA* 2.9 22.7 + - - +
111J HIS* 3.8 5.7 + - - -
501J HEM 3.1 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J TRP 4.9 0.2 + - - -
46J ILE* 3.0 9.4 + - + +
48J GLY* 1.3 70.6 - - - +
50J VAL* 1.3 71.0 + - + +
51J LEU 2.9 1.6 - - - -
52J ALA* 2.8 19.3 + - + +
53J PHE* 2.9 13.1 + - + +
252J ASP* 3.9 25.8 - - + +
256J LEU* 3.3 31.0 - - + -
501J HEM 3.9 1.4 - - - +
505J ANJ 3.3 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J ILE* 3.1 29.0 + - + +
47J TRP* 3.1 37.9 + - + +
49J VAL* 1.3 75.5 - - + +
51J LEU* 1.3 62.5 + - - +
53J PHE* 3.6 4.3 - - + +
54J CYS* 3.2 22.6 + - - -
103J LEU* 4.5 13.9 - - + -
107J ALA* 4.5 9.2 - - + -
256J LEU* 4.0 17.0 - - + +
259J VAL* 4.0 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J TRP 2.8 15.7 + - - +
48J GLY* 3.1 6.7 - - - +
50J VAL* 1.3 75.3 - - - +
52J ALA* 1.3 67.3 + - - +
54J CYS* 2.9 16.8 + - - +
55J LEU* 2.9 11.3 + - - +
104J PHE* 3.4 45.0 - - + +
107J ALA* 3.5 13.5 - - + -
108J VAL* 3.7 11.0 - - + +
111J HIS* 3.4 30.1 - - + +
501J HEM 3.2 46.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J GLY 2.9 9.8 + - - +
49J VAL* 2.8 19.7 + - + +
51J LEU* 1.3 69.8 - - - +
53J PHE* 1.3 63.9 + - - +
55J LEU* 2.9 19.3 + - - +
56J VAL* 3.1 17.8 + - + +
209J VAL* 6.0 0.2 - - - -
501J HEM 3.3 9.3 - - - +
505J ANJ 3.3 40.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J VAL* 2.9 9.4 + - + +
50J VAL* 3.6 11.2 - - + +
52J ALA* 1.3 76.4 - - - +
54J CYS* 1.3 57.0 + - - +
56J VAL* 3.1 9.5 + - + +
57J LEU* 2.7 68.2 + - + +
103J LEU* 4.9 7.2 - - + -
256J LEU* 4.1 31.4 - - + -
260J LEU* 3.3 46.9 - - + -
263J PHE* 5.2 0.7 - + - -
264J PHE* 5.6 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 54 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J VAL* 3.2 18.4 + - - -
51J LEU* 2.9 10.4 + - - +
53J PHE* 1.3 79.8 - - - +
55J LEU* 1.3 58.2 + - - +
57J LEU* 3.5 8.0 - - - +
58J GLN* 2.8 37.8 + - + +
100J GLY* 4.1 4.0 - - - +
103J LEU* 3.4 40.6 - - - -
104J PHE* 3.5 39.0 - - + -
107J ALA* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J LEU 2.9 8.8 + - - +
52J ALA* 2.9 13.7 + - - +
54J CYS* 1.3 76.6 - - - +
56J VAL* 1.3 65.6 + - + +
58J GLN* 3.3 1.6 + - - +
59J ILE* 2.9 45.8 + - + +
104J PHE* 4.2 22.3 - - + -
202J PRO* 4.5 4.9 - - + +
205J ILE* 4.1 15.0 - - + -
206J ALA* 3.7 34.1 - - + +
209J VAL* 3.9 19.7 - - + -
501J HEM 5.2 3.1 - - + -
502J HEM 4.5 10.8 - - + -
505J ANJ 4.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J ALA 3.1 14.4 + - - +
53J PHE* 3.6 8.3 - - + +
55J LEU* 1.3 75.0 - - + +
57J LEU* 1.3 70.7 + - - +
59J ILE* 2.8 19.6 + - + -
60J VAL* 2.9 30.6 + - + +
505J ANJ 4.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J PHE* 2.7 45.2 + - + +
54J CYS* 3.5 7.0 - - - +
56J VAL* 1.3 74.2 - - - +
58J GLN* 1.3 63.1 + - - +
60J VAL* 3.5 8.5 - - + +
61J THR* 2.7 52.8 + - + +
96J LEU* 4.5 16.2 - - + +
100J GLY* 4.5 13.2 - - - -
103J LEU* 5.3 2.9 - - + -
263J PHE* 3.8 33.7 - - + -
264J PHE* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J CYS 2.8 26.1 + - - +
55J LEU 3.6 2.2 - - - +
57J LEU* 1.3 76.6 - - - +
59J ILE* 1.3 59.0 + - - +
61J THR* 3.6 2.9 - - - -
62J GLY* 2.8 23.7 + - - -
96J LEU 4.0 0.3 - - - +
97J HIS* 2.9 69.4 + - - +
100J GLY* 3.0 21.4 - - - -
101J ALA* 3.9 7.1 - - - +
104J PHE* 4.3 10.8 - - + -
502J HEM 3.3 47.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J LEU* 2.9 39.9 + - + +
56J VAL* 2.8 16.3 + - + +
58J GLN* 1.3 70.6 - - + +
60J VAL* 1.3 60.9 + - + +
63J ILE* 2.8 54.2 + - + +
202J PRO* 4.3 17.9 - - + +
203J PHE* 4.6 18.2 - - + -
206J ALA* 4.9 7.2 - - + -
502J HEM 3.9 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J VAL* 2.9 33.8 + - + +
57J LEU* 3.5 12.6 - - + +
59J ILE* 1.3 71.0 - - + +
61J THR* 1.3 89.1 + - + +
62J GLY 2.9 2.5 + - - -
63J ILE* 3.1 8.8 + - - +
64J VAL* 3.0 26.3 + - + +
34L LEU* 3.9 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J LEU* 2.7 41.8 + - + +
58J GLN* 3.6 0.5 - - - -
60J VAL* 1.3 87.5 - - + +
62J GLY* 1.3 59.4 + - - +
64J VAL* 3.4 9.1 - - - +
65J LEU* 3.0 34.8 + - - +
93J LEU* 4.1 26.2 - - + -
96J LEU* 4.4 14.6 - - + -
97J HIS* 3.2 28.4 + - - +
34L LEU* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLN 2.8 21.8 + - - -
60J VAL 2.9 1.2 + - - -
61J THR* 1.3 75.3 + - - +
63J ILE* 1.3 64.3 + - - +
65J LEU* 2.9 6.9 + - - +
66J ALA* 2.8 22.7 + - - +
97J HIS* 3.8 6.3 - - - -
502J HEM 3.3 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G SER* 2.9 35.3 + - - +
197G LEU* 4.9 1.8 - - + -
200G LEU* 3.3 41.7 - - + -
59J ILE* 2.8 37.2 + - + +
60J VAL* 3.6 7.0 - - - +
62J GLY* 1.3 69.2 - - - +
64J VAL* 1.3 64.3 + - + +
66J ALA* 3.2 5.6 - - - +
67J MET* 3.1 18.6 - - + +
199J TYR* 3.8 13.5 - - + +
203J PHE* 4.9 2.7 - - + -
502J HEM 3.5 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J VAL* 3.0 16.5 + - + +
61J THR* 3.4 9.0 - - - +
63J ILE* 1.3 74.0 - - + +
65J LEU* 1.3 60.5 + - + +
67J MET* 2.7 41.7 + - - +
68J HIS* 3.4 7.9 - - + -
93J LEU* 3.4 31.2 - - + -
34L LEU* 4.0 26.0 - - + +
37L GLN* 3.5 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J THR 3.0 15.3 + - - +
62J GLY* 2.9 7.7 + - - +
64J VAL* 1.3 79.1 - - + +
66J ALA* 1.3 53.9 + - - +
68J HIS* 2.8 28.6 + - - +
69J TYR* 3.0 11.8 + - - +
83J ILE* 3.6 40.0 - - + +
93J LEU* 4.1 18.4 - - + +
94J ARG* 4.2 11.7 - - + +
97J HIS* 3.6 36.6 - - + -
502J HEM 4.1 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G ASN* 2.9 19.6 + - - +
195G PHE* 5.3 1.7 - - - -
196G SER* 3.5 16.4 + - - +
62J GLY 2.8 11.3 + - - +
63J ILE* 3.2 16.6 - - - +
64J VAL 3.1 0.2 - - - -
65J LEU* 1.3 75.9 - - - +
67J MET* 1.3 54.4 + - - +
68J HIS 3.2 1.0 + - - -
69J TYR* 3.7 8.4 + - - +
195J PHE* 4.4 17.1 - - + -
199J TYR* 4.3 14.6 - - + -
502J HEM 4.0 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G ALA* 4.5 4.0 - - - +
192G ASN* 3.0 35.2 + - - +
193G ARG* 3.8 22.4 + - + +
196G SER* 3.8 9.0 - - - +
197G LEU* 3.6 44.9 - - + -
63J ILE* 3.1 17.0 - - + +
64J VAL* 2.7 24.2 + - - +
66J ALA* 1.3 68.1 - - - +
68J HIS* 1.3 72.5 + - + +
37L GLN* 3.6 26.2 - - - -
38L MET* 4.1 19.1 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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