Contacts of the helix formed by residues 38 - 64 (chain C) in PDB entry 3J41
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 PRO 38 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ALA* 4.2 5.2 - - + -
36C PRO* 3.4 28.9 - - + +
37C GLY* 1.3 92.5 - - - +
39C LEU* 1.3 63.7 + - + +
42C LEU* 4.2 0.2 - - - +
177C TYR* 3.6 5.0 - - - +
33D ARG* 5.7 2.2 - - - +
39D LEU* 3.3 38.3 - - + +
43D GLN* 2.3 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PRO* 3.3 44.9 - - + +
39B LEU* 3.3 35.4 - - + +
42B LEU* 5.0 5.8 - - + +
33C ARG* 5.2 4.7 - - - +
35C ALA* 5.4 5.2 - - + -
38C PRO* 1.3 81.2 - - + +
40C HIS* 1.3 75.9 + - + +
41C VAL 3.3 0.2 - - - -
42C LEU* 3.7 10.6 - - + +
43C GLN* 3.0 26.2 + - - +
39D LEU* 3.3 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER* 3.8 16.4 - - - -
33C ARG* 2.7 44.4 + - + +
34C TRP* 2.8 24.1 + - - +
35C ALA* 3.3 28.0 - - + -
37C GLY* 4.3 14.1 - - - -
39C LEU* 1.3 84.6 - - + +
41C VAL* 1.3 60.9 + - + +
43C GLN 3.3 0.2 + - - -
44C VAL* 2.9 42.6 + - + +
176C MET* 3.8 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLY* 2.7 39.9 + - - +
40C HIS* 1.3 77.0 - - + +
42C LEU* 1.3 56.3 + - - +
45C ALA* 2.7 38.5 + - - +
172C HIS 3.8 8.7 - - - +
173C LEU* 3.8 35.9 - - + +
176C MET* 3.9 23.6 - - + +
177C TYR* 3.6 17.7 - - + -
43D GLN* 3.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.6 17.5 - - + -
38C PRO 4.2 1.3 - - - +
39C LEU* 3.5 12.1 + - + +
40C HIS 3.4 0.4 - - - -
41C VAL* 1.3 78.3 - - - +
43C GLN* 1.3 57.2 + - - +
45C ALA* 3.7 1.0 - - - +
46C LEU* 3.0 58.6 + - + +
169C THR* 6.2 0.4 - - + -
173C LEU* 4.0 13.7 - - + -
39D LEU* 4.9 5.8 - - + +
42D LEU* 3.6 38.8 - - + -
43D GLN* 3.3 28.6 - - + +
46D LEU* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY 3.4 4.6 + - - -
38B PRO* 2.3 34.0 + - - +
41B VAL* 3.4 7.9 - - - +
42B LEU* 3.3 31.9 - - + +
173B LEU* 3.9 24.0 - - + +
177B TYR* 3.3 21.7 + - - -
30C ALA* 4.9 4.7 - - + +
33C ARG* 3.4 19.1 + - - +
39C LEU 3.0 16.7 + - - +
40C HIS 3.5 3.4 - - - +
42C LEU* 1.3 76.6 - - - +
44C VAL* 1.3 60.2 + - - +
46C LEU* 3.5 3.5 + - - +
47C ALA* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 5.1 0.2 - - - +
30C ALA 3.6 23.6 - - - +
31C SER* 3.2 28.5 - - - +
33C ARG* 4.0 2.7 - - - +
40C HIS* 2.9 34.5 + - + +
43C GLN* 1.3 73.5 - - - +
45C ALA* 1.3 66.1 + - - +
47C ALA* 3.7 5.7 - - - +
48C PHE* 3.1 40.2 + - + -
172C HIS* 4.3 1.3 - - + -
176C MET* 3.3 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL 2.7 23.5 + - - +
42C LEU 3.7 0.9 - - - +
44C VAL* 1.3 74.4 - - - +
46C LEU* 1.3 57.5 + - - +
48C PHE* 4.1 1.4 - - - +
49C GLY 3.0 15.2 + - - -
169C THR* 2.8 45.9 + - + +
172C HIS* 3.5 20.6 - - + +
173C LEU* 3.6 20.9 - - + +
176C MET* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.7 24.5 - - + -
46B LEU* 5.1 9.2 - - + -
173B LEU* 4.0 12.3 - - + -
42C LEU* 3.0 41.9 + - + +
43C GLN* 3.8 4.0 - - - +
45C ALA* 1.3 75.3 - - - +
47C ALA* 1.3 56.7 + - - +
50C LEU* 2.7 50.8 + - + +
166C PHE* 4.2 21.1 - - + -
169C THR* 3.9 17.9 - - + +
46D LEU* 5.0 9.4 - - + -
50D LEU* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.6 12.7 - - + +
173B LEU* 3.6 18.3 - - + +
26C PHE 4.8 2.5 - - - +
27C GLY* 5.2 1.8 - - - -
30C ALA* 3.6 30.1 - - + -
43C GLN 2.9 19.3 + - - +
44C VAL* 3.4 5.6 + - - +
46C LEU* 1.3 75.4 - - - +
48C PHE* 1.3 59.8 + - + +
51C ALA* 2.7 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 4.0 27.3 - + - -
24C VAL* 5.6 0.2 - - - -
27C GLY* 3.4 35.2 - - - -
28C LEU* 4.0 2.2 - - + -
31C SER* 3.4 22.2 - - - -
44C VAL* 3.1 32.0 + - + +
45C ALA 4.1 2.2 - - - +
47C ALA* 1.3 76.2 - - + +
49C GLY* 1.3 58.1 + - - +
51C ALA* 3.1 5.6 + - - +
52C LEU 2.9 26.2 + - - -
168C LEU* 3.5 13.2 - - + +
172C HIS* 3.4 34.8 - + + +
187C ARG* 3.8 46.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA 3.0 10.7 + - - -
48C PHE* 1.3 77.2 - - - +
50C LEU* 1.3 58.5 + - - +
53C ALA* 2.9 24.9 + - - +
165C GLY* 3.1 37.6 - - - -
168C LEU* 4.2 3.9 - - - +
169C THR* 3.2 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 5.6 1.6 - - + -
166B PHE* 3.7 55.6 - - + +
169B THR* 3.7 29.6 - - + -
170B LEU* 4.1 7.6 - - + -
173B LEU* 4.5 6.3 - - + -
46C LEU* 2.7 35.3 + - + +
47C ALA* 4.1 2.0 - - - +
49C GLY* 1.3 72.1 - - - +
51C ALA* 1.3 57.5 + - - +
53C ALA* 4.0 3.0 - - + +
54C THR* 2.6 38.4 + - - -
162C LEU* 4.3 14.1 - - + -
166C PHE* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.8 24.2 - - + +
22C PHE 5.3 0.2 - - - +
23C TYR* 4.6 16.4 - - + +
26C PHE* 4.6 11.2 - - + -
27C GLY 5.1 1.1 - - - +
47C ALA 2.7 19.4 + - - +
48C PHE* 3.4 8.1 - - - +
50C LEU* 1.3 77.9 - - - +
52C LEU* 1.3 57.7 + - - +
54C THR* 3.5 1.6 - - - -
55C LEU* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 4.1 17.7 - - + -
48C PHE 2.9 15.4 + - - +
49C GLY 3.6 4.3 - - - +
51C ALA* 1.3 74.9 - - - +
53C ALA* 1.3 56.5 + - - +
55C LEU* 3.0 6.1 + - + -
56C VAL* 2.7 54.0 + - + +
65C ALA 4.9 7.0 - - - +
66C HIS 5.2 3.1 - - - +
67C VAL* 5.1 11.4 - - + -
141C PHE* 3.3 36.3 - - + -
164C VAL* 3.6 21.5 - - + +
165C GLY* 4.2 0.9 - - - -
168C LEU* 3.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 6.1 2.2 - - + -
49C GLY 2.9 19.9 + - - +
50C LEU* 4.0 8.1 - - + +
52C LEU* 1.3 73.2 - - - +
54C THR* 1.3 61.5 + - - +
57C GLN* 3.2 30.1 + - + +
161C ALA* 3.1 33.7 + - - +
162C LEU* 3.8 22.7 - - + +
165C GLY* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 3.5 30.7 - - + +
144B CYS* 3.9 23.3 - - + -
163B ALA* 4.7 2.1 + - - -
166B PHE* 4.4 2.3 + - - +
167B SER* 3.6 26.8 + - - +
170B LEU* 4.6 4.2 - - + +
50C LEU 2.6 23.8 + - - -
51C ALA* 3.5 6.7 - - - -
53C ALA* 1.3 77.7 - - - +
55C LEU* 1.3 64.4 + - + +
57C GLN* 3.2 6.2 + - - +
58C ALA* 2.9 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 5.5 5.2 - - + -
143B LEU* 5.4 2.9 - - + -
170B LEU* 6.5 0.2 - - + -
19C ALA* 3.2 39.9 - - + +
22C PHE* 3.8 30.5 - - + -
23C TYR* 3.5 29.6 - - + +
26C PHE* 6.2 0.2 - - + -
51C ALA* 2.9 22.9 + - + +
52C LEU* 3.7 5.6 - - + +
54C THR* 1.3 79.3 - - + +
56C VAL* 1.3 60.4 + - + +
58C ALA* 3.9 11.0 - - + -
59C VAL* 2.8 36.0 + - + +
65C ALA* 4.4 2.2 - - - -
67C VAL* 5.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG* 4.3 2.9 + - - -
154B ASN* 5.5 0.5 + - - -
52C LEU* 2.7 47.4 + - + +
55C LEU* 1.3 72.8 - - - +
57C GLN* 1.3 57.8 + - - +
60C GLY* 2.9 26.0 + - - -
65C ALA* 3.6 20.2 - - + +
149C TYR* 4.0 22.2 - - + +
160C VAL* 4.6 9.9 - - + +
161C ALA* 3.6 29.6 - - + +
164C VAL* 4.5 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B CYS* 4.4 3.8 - - - -
147B ALA* 3.6 1.9 - - - +
148B THR* 3.8 15.3 - - + +
153B ARG* 2.7 36.7 + - - -
154B ASN* 4.4 3.5 + - - -
156B ARG 4.8 1.4 - - - +
157B LEU* 2.9 55.0 + - - +
159B SER 4.7 0.8 + - - -
160B VAL* 5.3 0.6 - - - +
163B ALA* 3.8 27.8 - - + +
53C ALA* 3.2 18.0 + - + +
54C THR* 3.2 9.7 + - - +
56C VAL* 1.3 77.7 - - - +
58C ALA* 1.3 61.7 + - - +
59C VAL 3.6 0.3 + - - -
61C HIS* 3.8 0.2 - - - -
159C SER* 3.6 6.8 + - - +
161C ALA* 3.4 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN 5.7 0.2 - - - +
143B LEU* 3.7 34.9 - - + +
144B CYS* 4.6 4.0 - - + +
147B ALA* 3.4 16.3 - - - +
219B TYR* 4.0 6.9 - - - -
54C THR* 2.9 18.6 + - + +
55C LEU* 3.2 13.2 + - + +
57C GLN* 1.3 76.9 - - - +
59C VAL* 1.3 67.2 + - + +
61C HIS* 3.1 16.0 + - - -
62C ILE* 4.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 5.0 11.2 - - + -
219B TYR* 6.4 0.2 - - + -
15C ALA* 3.8 28.3 - - + +
18C PHE* 6.3 1.8 - - + -
19C ALA* 4.0 23.6 - - + +
55C LEU* 2.8 19.2 + - + +
58C ALA* 1.3 86.0 - - + +
60C GLY* 1.3 61.6 + - - +
61C HIS* 3.2 6.5 - - - -
62C ILE* 3.1 11.6 + - + -
63C SER* 3.0 35.4 + - - +
65C ALA* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG* 4.8 0.7 - - - -
154B ASN* 5.7 1.3 - - - -
56C VAL* 2.9 28.2 + - - -
59C VAL* 1.3 78.3 - - - +
61C HIS* 1.3 60.0 + - - +
64C GLY* 3.0 25.2 + - - -
65C ALA* 3.7 17.3 - - - -
149C TYR* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 4.1 0.4 - - - +
150B ASP* 4.6 1.1 - - - -
153B ARG* 3.5 49.3 + - + +
154B ASN* 3.4 21.3 - - - +
219B TYR* 3.1 28.8 + + - -
58C ALA 3.1 25.4 + - - -
60C GLY* 1.3 80.6 - - - +
62C ILE* 1.3 80.7 + - + +
64C GLY 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 4.5 13.2 - - + +
11C ARG* 4.1 17.7 - - + +
12C ALA* 3.5 28.6 - - - +
15C ALA* 4.2 5.2 - - + -
58C ALA 4.4 7.9 - - - +
59C VAL* 3.1 15.8 + - + +
61C HIS* 1.3 112.6 - - + +
63C SER* 1.3 58.0 + - - +
85C ARG* 5.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 3.5 24.2 - - - -
15C ALA* 3.6 9.4 - - - +
16C GLU* 2.6 25.8 + - - -
59C VAL* 3.0 8.8 + - - +
62C ILE* 1.3 76.8 - - - +
64C GLY* 1.3 61.9 + - - +
65C ALA* 3.2 6.6 + - - -
66C HIS* 3.7 4.9 - - - -
89C TYR* 2.9 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLY* 3.0 20.8 + - - -
61C HIS 4.9 0.2 - - - -
62C ILE 3.9 0.2 - - - -
63C SER* 1.3 78.5 - - - +
65C ALA* 1.3 63.5 + - - +
66C HIS* 3.5 10.6 + - - -
149C TYR* 2.7 40.7 + - - -
----------------------------------------------------------
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