Contacts of the helix formed by residues 53 - 80 (chain D) in PDB entry 2P4K
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 ASP 53 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA* 2.9 15.7 + - - +
51D LYS* 3.1 14.9 - - + +
52D GLY* 1.3 74.7 - - - +
54D VAL* 1.3 62.2 + - - +
55D THR* 3.3 10.7 + - - +
56D ALA* 3.0 34.9 + - + +
57D GLN* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HIS* 3.6 31.9 - - + +
38C LEU* 4.1 12.1 - - + -
42C GLU* 3.6 13.9 - - - +
64C LEU* 4.8 5.2 - - + -
68C GLY* 3.6 31.4 - - - +
71C HIS* 5.5 2.5 - - + -
72C ILE* 3.7 20.4 - - + -
52D GLY 3.1 3.6 + - - +
53D ASP* 1.3 69.6 - - - +
55D THR* 1.3 65.8 + - - +
57D GLN* 3.2 8.2 + - - +
58D ILE* 2.9 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 3.6 26.3 - - - +
145C PRO* 5.6 0.2 - - - +
147C GLN* 4.0 31.8 + - + +
148C GLY* 3.8 26.1 + - - +
53D ASP* 3.3 8.2 + - - +
54D VAL* 1.3 77.9 - - - +
56D ALA* 1.3 58.8 + - - +
58D ILE* 3.2 4.1 + - - +
59D ALA* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA* 4.0 12.8 - - + -
53D ASP* 3.0 33.4 + - - +
55D THR* 1.3 75.4 - - - +
57D GLN* 1.3 65.7 + - - +
59D ALA* 3.3 6.7 + - - +
60D LEU* 3.1 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 3.1 23.3 - - - +
45C TYR* 5.5 0.8 - - - -
64C LEU* 3.9 23.6 - - + +
45D TYR* 2.8 60.7 + - + +
48D ALA* 3.9 18.4 - - + +
49D LEU* 3.7 19.0 - - - +
52D GLY 4.5 0.2 - - - -
53D ASP 3.1 23.4 + - - +
54D VAL* 3.5 13.9 - - - +
56D ALA* 1.3 78.3 - - - +
58D ILE* 1.3 62.9 + - - +
60D LEU* 3.3 7.8 + - - -
61D GLN* 3.4 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.7 17.3 - - + +
65C LYS* 3.9 29.2 - - + +
68C GLY 4.1 0.2 - - - -
69C GLY 3.7 21.5 - - - +
72C ILE* 4.3 1.8 - - + -
145C PRO* 3.6 33.2 - - + -
148C GLY* 4.1 13.4 - - - +
149C THR* 4.1 12.3 - - + -
54D VAL* 2.9 29.7 + - + +
55D THR 3.9 3.4 - - - +
57D GLN* 1.3 77.4 - - - +
59D ALA* 1.3 62.8 + - - +
61D GLN* 3.1 24.7 + - - +
62D PRO* 3.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLN 5.3 0.9 - - - +
148C GLY* 3.3 23.6 - - - +
55D THR* 2.9 18.7 + - + +
56D ALA* 3.8 7.6 - - - +
58D ILE* 1.3 76.9 - - - +
60D LEU* 1.3 61.5 + - + +
62D PRO* 3.3 12.7 - - - +
63D ALA* 5.2 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D THR* 4.0 18.0 - - + +
44D LYS* 3.8 24.9 - - + +
45D TYR* 3.7 45.1 - - + +
48D ALA* 4.6 3.4 - - + -
56D ALA* 3.1 27.0 + - + +
57D GLN* 3.7 5.2 - - - +
58D ILE 3.1 0.4 - - - -
59D ALA* 1.3 77.6 - - + +
61D GLN* 1.3 65.2 + - - +
62D PRO* 3.4 0.9 - - - -
63D ALA* 3.3 10.7 + - + +
64D LEU* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 6.3 0.4 - - - -
61C GLN* 3.1 64.6 + - + +
64C LEU* 3.8 23.6 - - - +
65C LYS* 3.7 27.4 + - - +
45D TYR* 5.0 7.2 + - + -
57D GLN 3.5 9.9 - - - +
58D ILE* 3.1 21.1 + - - +
60D LEU* 1.3 77.6 - - - +
62D PRO* 1.3 68.7 - - + +
64D LEU* 3.1 1.5 + - - -
65D LYS* 2.8 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.8 16.8 - - - +
58D ILE 3.8 4.9 - - - +
59D ALA* 3.3 18.4 - - - +
60D LEU 3.5 0.9 - - - -
61D GLN* 1.3 93.0 - - + +
63D ALA* 1.3 56.2 + - - +
65D LYS* 4.0 8.4 - - + +
66D PHE* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 4.0 15.2 - - - +
41D THR* 3.8 20.8 + - + +
59D ALA 5.2 0.4 + - - +
60D LEU* 3.3 12.1 + - + +
61D GLN 3.3 0.4 - - - -
62D PRO* 1.3 77.3 - - - +
64D LEU* 1.3 61.8 + - - +
67D ASN* 2.9 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 3.7 21.3 - - - +
54C VAL* 4.7 4.3 - - + -
57C GLN* 3.8 21.8 - - + +
58C ILE* 3.7 24.5 - - + -
61C GLN* 3.8 12.8 - - - +
38D LEU* 3.4 31.2 - - + -
41D THR* 3.9 17.8 - - + +
42D GLU* 4.1 10.1 - - + +
45D TYR* 5.5 5.4 - - + -
60D LEU* 3.1 16.6 + - + +
61D GLN* 3.8 3.6 - - - +
63D ALA* 1.3 76.3 - - - +
65D LYS* 1.3 58.0 + - - +
68D GLY* 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 3.9 28.0 - - + +
61C GLN* 3.6 21.2 - - - +
61D GLN 2.8 16.6 + - - +
62D PRO* 4.0 7.0 - - - +
64D LEU* 1.3 78.7 - - - +
66D PHE* 1.3 54.5 + - - +
69D GLY* 2.7 31.2 + - - -
143D GLN 4.0 2.3 - - - +
144D ASP* 2.9 43.7 + - - +
145D PRO* 4.4 6.3 - - + -
149D THR* 4.5 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.7 50.9 - - + +
120A GLY 4.0 4.0 - - - -
34D ASN* 4.2 10.1 + - - -
62D PRO 3.0 19.4 + - - +
63D ALA 4.0 0.9 - - - +
65D LYS* 1.3 79.6 - - - +
67D ASN* 1.3 77.6 + - - +
70D GLY* 2.9 22.2 + - - -
142D ASN* 4.6 6.1 - - + -
143D GLN* 3.2 34.2 - - + +
144D ASP* 5.9 0.4 - - - -
161D TRP* 3.5 39.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 4.7 2.6 - - - +
33D ALA 4.4 0.2 - - - -
34D ASN* 3.2 49.7 + - - +
37D ASN* 3.4 33.2 + - - +
38D LEU* 3.9 11.9 - - - +
63D ALA* 2.9 34.0 + - - +
66D PHE* 1.3 90.8 - - - +
68D GLY* 1.3 61.9 + - - +
71D HIS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.6 24.5 - - - +
38D LEU* 3.8 18.8 - - - +
64D LEU 2.8 20.2 + - - -
67D ASN* 1.3 70.1 - - - +
69D GLY* 1.3 65.9 + - - +
71D HIS* 3.1 3.8 + - - +
72D ILE* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 3.7 2.6 - - - +
65D LYS 2.7 26.1 + - - -
68D GLY* 1.3 73.4 - - - +
70D GLY* 1.3 55.7 + - - +
72D ILE* 3.2 0.6 + - - +
73D ASN* 2.8 34.4 + - - +
143D GLN 3.2 16.8 - - - -
145D PRO* 3.9 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ASN* 3.4 20.6 - - - -
66D PHE 2.9 16.9 + - - -
67D ASN 3.8 0.4 - - - -
68D GLY 3.3 0.4 - - - -
69D GLY* 1.3 76.1 - - - +
71D HIS* 1.3 58.0 + - - +
73D ASN* 4.4 0.2 - - - -
74D HIS* 2.9 35.5 + - - +
143D GLN* 3.5 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 5.2 3.8 - - + -
2D HIS* 3.9 24.3 + + + +
3D SER 3.5 24.1 + - - -
5D PRO* 4.1 3.1 - - + -
31D HIS* 2.9 32.6 + - + +
34D ASN* 4.0 4.0 - - + +
35D VAL* 3.6 10.5 - - + +
38D LEU* 3.8 26.0 - - + -
67D ASN 2.9 17.5 + - - +
68D GLY 3.1 4.9 + - - +
70D GLY* 1.3 77.9 - - - +
72D ILE* 1.3 62.5 + - + +
75D SER* 2.8 47.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.5 33.9 - - + -
55C THR* 3.5 31.4 - - - +
58C ILE* 4.2 0.9 - - + -
68D GLY 3.0 13.4 + - - +
69D GLY 3.7 4.7 - - - +
71D HIS* 1.3 79.3 - - + +
73D ASN* 1.3 74.2 + - - +
75D SER* 3.8 3.0 - - - -
76D ILE* 3.2 40.0 + - + +
145D PRO* 4.0 25.1 - - + -
146D LEU 5.7 0.9 - - - +
147D GLN* 6.3 0.9 - - + +
154D PRO* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLY 2.8 18.5 + - - +
72D ILE* 1.3 77.2 - - - +
74D HIS* 1.3 63.2 + - - +
76D ILE* 3.3 3.1 + - - +
77D PHE* 3.0 23.2 + - - +
123D TRP* 3.4 34.7 - - + +
125D TRP* 3.8 23.1 - - + -
143D GLN* 3.0 45.1 + - - +
144D ASP 4.0 3.6 + - - -
145D PRO* 3.4 22.7 - - - +
146D LEU 4.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D HIS* 3.1 20.1 + + - -
30D HIS* 4.7 3.4 - - + -
31D HIS* 3.4 33.6 - + + +
34D ASN* 3.1 21.0 + - - -
70D GLY 2.9 24.3 + - - +
73D ASN* 1.3 77.8 - - - +
75D SER* 1.3 64.2 + - - +
77D PHE* 3.2 6.3 + + - +
78D TRP* 3.1 38.2 + + - +
123D TRP* 4.0 7.5 - + - -
143D GLN* 3.5 19.7 - - - -
159D ASP* 3.9 4.3 - - - -
163D HIS* 4.5 2.5 - + - -
199D MN 2.2 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO* 3.8 10.1 - - - +
31D HIS* 3.4 17.3 - - - -
71D HIS* 2.8 38.1 + - - -
72D ILE* 3.8 4.5 - - - -
74D HIS* 1.3 79.6 - - - +
76D ILE* 1.3 64.2 + - - +
78D TRP* 3.6 9.7 + - - +
79D THR* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ILE* 3.2 32.5 + - + +
73D ASN 3.7 4.5 - - - +
75D SER* 1.3 76.8 - - - +
77D PHE* 1.3 65.0 + - - +
79D THR* 2.7 20.3 + - - -
80D ASN* 3.0 24.5 + - - +
125D TRP* 3.9 22.4 - - + -
154D PRO* 3.7 30.5 - - + -
155D LEU 5.0 0.9 - - - +
192D ARG* 3.8 38.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 5.0 5.2 - - + -
23D MET* 6.0 1.1 - - - -
26D HIS* 3.9 25.6 - + - -
73D ASN 3.0 17.7 + - - +
74D HIS* 3.5 5.6 - + - +
76D ILE* 1.3 78.1 - - - +
78D TRP* 1.3 86.7 + + - +
80D ASN* 3.0 17.5 + - + +
81D LEU* 3.4 41.3 - - + +
123D TRP* 3.8 20.6 - + + -
125D TRP* 5.5 0.2 - - - -
157D GLY* 3.2 26.9 - - - -
159D ASP* 3.7 14.1 - - + -
164D ALA* 5.4 0.2 - - + -
176D TYR* 3.8 20.4 - - - -
180D ILE* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO* 4.2 13.0 - - + -
6D ASP 5.6 1.1 - - - +
7D LEU* 3.3 33.4 - - + -
8D PRO* 3.7 9.0 - - + +
9D TYR* 2.8 25.8 + - - +
23D MET* 4.1 24.2 - - + -
26D HIS* 3.5 43.5 - + + -
27D HIS* 3.8 26.6 - + + -
31D HIS* 2.9 25.5 + - - -
74D HIS* 3.1 33.3 + + + +
75D SER* 4.1 9.0 - - - +
76D ILE 3.2 0.4 - - - -
77D PHE* 1.3 97.5 - + - +
79D THR* 1.3 62.9 - - + +
81D LEU* 3.3 12.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 4.5 12.3 - - + -
75D SER 3.4 14.1 - - - +
76D ILE 2.7 17.1 + - - -
78D TRP* 1.3 80.0 - - + +
80D ASN* 1.3 57.3 + - - +
81D LEU 3.2 1.8 - - - -
185D ASN* 3.4 10.9 + - - -
188D ASN* 3.1 38.1 + - - +
192D ARG* 2.8 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 3.0 24.8 + - - +
77D PHE* 3.0 13.0 + - - +
79D THR* 1.3 77.6 - - - +
81D LEU* 1.3 59.9 + - + +
155D LEU 3.1 18.4 + - - -
156D LEU* 3.3 17.9 - - + -
157D GLY* 2.8 31.2 + - - +
184D ILE* 3.5 10.4 - - - +
185D ASN* 2.7 29.0 + - - -
188D ASN* 3.0 22.2 + - - -
189D VAL* 4.1 4.0 - - + +
192D ARG* 3.7 5.1 - - - +
----------------------------------------------------------
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