Contacts of the helix formed by residues 43 - 64 (chain U) in PDB entry 1JJ2
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 43 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570 C 3.4 42.9 + - + +
900 A 4.0 25.4 - - + +
910 G 4.0 13.7 - - - +
41U GLU* 3.7 16.8 - - + +
42U ASN* 1.3 86.4 - - - +
44U GLY* 1.3 63.1 + - - +
45U ARG 3.1 1.5 + - - -
46U ILE* 3.1 29.1 - - + +
47U LYS* 3.5 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910 G 3.4 9.8 + - - -
920 G 3.6 37.6 + - - -
42U ASN 2.5 8.8 + - - -
43U PRO* 1.3 74.8 - - - +
45U ARG* 1.3 56.3 + - - -
47U LYS* 3.9 9.3 - - - +
48U GLU* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920 G 6.1 4.0 - - - +
1U THR* 6.4 0.9 - - + -
2U VAL* 5.0 20.3 - - + +
26U GLU* 4.0 25.4 + - - +
42U ASN* 2.7 28.3 + - + +
44U GLY* 1.3 71.2 - - - +
46U ILE* 1.3 52.5 + - - +
47U LYS 2.8 4.9 - - - -
48U GLU* 2.7 11.9 + - + +
49U LEU* 2.6 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570 C 3.7 27.8 - - - +
27U LEU* 3.8 16.1 - - + +
30U ALA* 4.4 19.3 - - + +
31U ARG* 4.4 18.8 - - + +
34U GLN* 4.0 28.9 - - + +
42U ASN 4.3 1.4 + - - -
43U PRO* 3.1 27.1 - - + +
45U ARG* 1.3 75.0 - - - +
47U LYS* 1.3 55.8 + - - +
49U LEU* 4.0 10.5 - - - -
50U ARG* 3.4 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570 C 3.8 28.0 - - - +
710 G 5.7 2.7 + - - -
830 C 3.7 29.7 + - - -
910 G 5.7 2.2 - - - +
920 G 5.9 1.3 - - - +
43U PRO 3.6 14.1 - - - +
44U GLY* 3.9 8.5 - - - +
45U ARG 2.8 0.4 - - - -
46U ILE* 1.3 80.3 - - - +
48U GLU* 1.3 72.7 + - - +
49U LEU 3.3 0.2 - - - -
50U ARG* 3.3 17.1 + - - +
51U LYS* 3.3 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920 G 4.4 3.9 + - - +
930 C 4.2 20.9 - - - +
1U THR* 3.4 44.1 + - + -
44U GLY 2.9 21.7 + - - +
45U ARG* 2.7 20.7 + - + +
47U LYS* 1.3 82.8 - - - +
49U LEU* 1.3 55.0 + - - +
51U LYS* 3.1 15.6 + - - +
52U ALA* 2.8 38.1 + - - +
55U ARG* 4.3 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U LEU* 3.4 35.7 - - + +
26U GLU* 3.7 40.8 - - + +
27U LEU* 3.5 46.9 - - + +
30U ALA* 4.6 5.2 - - + -
45U ARG* 2.6 23.5 + - + +
46U ILE* 4.0 7.2 - - - +
48U GLU* 1.3 74.4 - - - +
50U ARG* 1.3 59.4 + - - +
52U ALA* 3.8 4.4 - - - +
53U ILE* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550 U 3.3 16.1 + - - -
560 G 3.2 35.8 + - - -
570 C 4.5 9.4 + - - -
680 U 4.4 1.6 - - - +
690 A 3.3 70.9 + - - +
700 A 3.5 14.7 + - - -
27U LEU* 4.4 15.5 - - + -
31U ARG* 4.8 11.4 - - - +
46U ILE* 3.4 19.7 - - - +
47U LYS* 3.3 10.8 + - - +
48U GLU 3.1 0.4 - - - -
49U LEU* 1.3 75.4 - - - +
51U LYS* 1.3 61.0 + - + +
53U ILE* 3.3 10.3 + - - +
54U ALA* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690 A 4.4 2.5 - - - +
710 G 3.3 42.6 + - - +
720 C 3.5 28.0 + - - +
47U LYS* 3.3 36.1 + - - +
48U GLU* 3.1 20.5 + - - +
50U ARG* 1.3 76.6 - - + +
52U ALA* 1.3 61.3 + - - +
54U ALA* 3.0 8.6 + - - +
55U ARG* 2.9 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U LEU* 4.4 16.4 - - + -
8U ILE* 4.7 0.3 - - - +
23U LEU* 3.7 24.0 - - + -
48U GLU 2.8 21.9 + - - +
49U LEU* 3.8 4.9 - - - +
51U LYS* 1.3 72.6 - - - +
53U ILE* 1.3 63.8 + - - +
55U ARG* 3.2 21.2 + - - +
56U ILE* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 4.5 11.2 - - - -
20U LEU* 3.7 22.2 - - + -
23U LEU* 3.6 21.8 - - + -
24U LYS* 3.9 31.4 - - + +
27U LEU* 3.8 27.4 - - + -
49U LEU 2.9 24.7 + - - +
50U ARG* 3.5 7.0 - - - +
51U LYS 3.2 0.2 - - - -
52U ALA* 1.3 77.2 - - - +
54U ALA* 1.3 62.0 + - - +
56U ILE* 3.5 2.1 + - - +
57U LYS* 3.1 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 3.4 42.9 + - - +
690 A 4.2 1.3 - - - +
710 G 5.7 0.9 - - - +
720 C 3.7 16.8 - - - +
50U ARG 3.0 13.7 + - - +
51U LYS* 3.0 11.4 + - - +
53U ILE* 1.3 78.2 - - - +
55U ARG* 1.3 52.6 + - - +
57U LYS* 3.2 2.9 + - - +
58U THR* 2.7 37.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720 C 3.3 28.1 + - - +
730 C 3.1 27.0 + - - -
1U THR 4.1 17.9 - - - +
3U LEU 3.9 19.6 + - - -
5U VAL* 4.1 16.2 - - + +
8U ILE* 3.6 17.7 - - + -
48U GLU* 4.3 6.7 + - - -
51U LYS* 2.9 39.4 + - - +
52U ALA* 3.2 29.3 + - - +
54U ALA* 1.3 75.9 - - - +
56U ILE* 1.3 58.1 + - - +
58U THR* 3.0 3.1 + - - -
59U ILE* 2.8 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U LEU* 4.3 3.6 - - + -
8U ILE* 4.1 26.4 - - + +
11U MET* 5.4 0.9 - - + -
16U ARG* 3.8 32.5 - - + +
19U GLU* 3.6 24.0 - - + -
20U LEU* 4.0 16.8 - - + +
23U LEU* 3.4 32.1 - - + -
52U ALA 3.1 10.8 + - - +
53U ILE 3.8 4.3 - - - +
55U ARG* 1.3 76.3 - - - +
57U LYS* 1.3 56.7 + - - +
59U ILE* 3.2 2.6 + - - +
60U GLN* 2.8 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 3.4 75.7 + - + +
1R SER* 6.0 2.2 - - - +
20U LEU* 4.0 19.5 - - + +
24U LYS* 4.3 15.7 - - - +
53U ILE* 3.1 31.4 + - - +
54U ALA 3.7 2.7 - - - +
56U ILE* 1.3 74.9 - - - +
58U THR* 1.3 62.5 + - - +
60U GLN* 3.5 19.4 - - - +
61U GLY* 3.2 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 3.5 17.8 + - - +
720 C 2.6 38.6 + - - +
730 C 3.5 26.5 - - - +
1050 G 4.3 4.7 - - - +
1060 A 4.9 9.6 + - - +
54U ALA 2.7 16.2 + - - -
55U ARG 3.3 4.0 - - - -
57U LYS* 1.3 77.7 - - - +
59U ILE* 1.3 59.0 + - + +
61U GLY* 3.2 3.8 + - - -
62U GLU* 3.0 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 C 4.6 10.3 - - - -
5U VAL* 4.2 11.9 - - + -
8U ILE* 3.5 25.1 - - + -
9U ARG* 3.6 51.1 - - + +
16U ARG* 3.9 13.7 - - - +
55U ARG* 2.8 23.0 + - - +
56U ILE 3.7 3.4 - - - +
58U THR* 1.3 72.5 - - - +
60U GLN* 1.3 66.4 + - - +
61U GLY 3.0 2.0 - - - -
62U GLU* 2.9 10.4 + - - +
63U GLU* 2.8 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U ARG* 4.1 17.0 - - + +
17U GLU* 3.7 25.7 - - - +
20U LEU* 3.2 30.1 - - - +
56U ILE* 2.8 33.4 + - + +
57U LYS* 3.5 27.7 - - - +
59U ILE* 1.3 72.4 - - - +
61U GLY* 1.3 58.0 + - - +
64U GLY 3.1 4.7 + - - -
65U ASP* 2.6 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 5.9 0.7 - - - -
1060 A 5.7 3.8 - - - -
57U LYS 3.2 10.5 + - - -
58U THR 3.2 4.0 + - - -
59U ILE 3.0 1.0 - - - -
60U GLN* 1.3 79.1 - - - +
62U GLU* 1.3 64.6 + - - +
64U GLY* 3.4 11.0 + - - -
65U ASP* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 C 2.9 31.2 + - - +
1050 G 5.1 1.6 + - - +
1060 A 6.4 1.8 - - - -
9U ARG* 2.7 29.8 + - - -
58U THR* 3.0 26.5 + - + +
59U ILE* 2.9 12.9 + - - +
61U GLY* 1.3 76.7 - - - +
63U GLU* 1.3 68.1 + - - +
64U GLY* 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U ARG* 3.9 21.3 - - - +
13U PRO* 6.0 0.4 - - + -
16U ARG* 3.3 42.4 + - - +
59U ILE* 2.8 30.4 + - + +
62U GLU* 1.3 79.7 - - - +
64U GLY* 1.3 60.1 + - - +
65U ASP 4.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60U GLN 3.1 4.3 + - - -
61U GLY 3.4 7.0 + - - -
62U GLU 3.3 3.6 - - - -
63U GLU* 1.3 80.0 - - - +
65U ASP* 1.3 79.2 + - - +
----------------------------------------------------------
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