Contacts of the helix formed by residues 58 - 76 (chain C) in PDB entry 1JPL
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 GLN 58 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PRO* 3.7 13.1 - - - +
56C SER* 3.1 12.4 + - - +
57C PRO* 1.3 77.5 - - - +
59C GLU* 1.3 73.6 + - - +
60C TRP* 3.1 32.0 + - - +
61C GLU* 3.0 30.7 + - + +
62C ALA* 3.1 12.5 + - - +
1D MSE 2.9 32.8 - - - +
2D ALA* 3.8 6.6 - - - +
6D GLY 3.7 21.1 - - - +
7D GLU* 3.6 19.7 - - - +
10D GLU* 4.2 7.2 - - + -
49D LEU* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER 5.5 0.2 - - - -
57C PRO 3.5 7.0 + - - -
58C GLN* 1.3 73.6 + - - +
60C TRP* 1.3 58.9 + - - +
62C ALA* 3.2 7.3 + - - +
63C LEU* 2.8 49.8 + - + +
107C SER* 2.8 38.8 + - - +
109C LYS* 4.4 14.0 + - - +
110C VAL* 4.1 4.7 - - + +
2D ALA* 4.1 30.4 - - + +
203D MSE 5.2 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PRO* 3.2 28.2 + - + -
21C ASN* 2.9 21.9 + - - +
22C ARG 4.2 3.8 - - - -
23C GLN* 4.1 17.9 - - - -
24C GLU* 3.3 28.7 - - - -
58C GLN* 3.1 14.4 + - - +
59C GLU* 1.3 77.6 + - - +
61C GLU* 1.3 62.4 + - - +
63C LEU* 4.0 23.8 - - + -
64C GLN* 3.0 62.4 + - + +
109C LYS* 5.9 3.1 - - - -
2D ALA 5.6 0.6 + - - +
7D GLU* 3.7 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.5 25.0 - - - +
19C PRO* 3.9 11.2 - - + -
53C LYS* 3.4 36.4 + - + +
56C SER* 2.4 31.7 + - - +
58C GLN* 3.0 16.4 + - + +
60C TRP* 1.3 75.8 - - - +
62C ALA* 1.3 59.3 + - - +
64C GLN* 3.5 2.9 + - - +
65C ALA* 2.9 27.0 + - - +
10D GLU* 2.8 39.2 - - - +
14D ASN* 3.7 7.6 + - - +
52D HIS* 5.6 0.9 - - - -
53D LYS* 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LYS 3.6 14.3 + - - +
54C ILE* 3.7 23.9 - - - +
56C SER* 4.2 8.1 - - - +
58C GLN 3.1 8.3 + - - +
59C GLU* 3.6 7.6 - - - +
61C GLU* 1.3 78.7 - - - +
63C LEU* 1.3 65.5 + - - +
65C ALA* 2.9 4.6 + - - +
66C LEU* 2.9 27.3 + - - +
110C VAL* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 2.8 45.2 + - + +
60C TRP* 4.1 24.0 - - + -
62C ALA* 1.3 73.1 - - - +
64C GLN* 1.3 63.3 + - - +
66C LEU* 3.1 14.4 + - + +
67C THR* 3.0 23.3 + - - -
109C LYS* 3.7 52.7 - - + +
110C VAL* 4.0 18.6 - - + -
113C LYS* 4.7 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA 3.6 12.1 + - - +
17C THR* 3.6 21.8 - - + +
18C ASN 3.1 11.4 - - - +
21C ASN* 2.9 33.1 + - - +
23C GLN 4.1 5.1 + - - -
24C GLU* 4.5 13.1 - - + +
25C ASP 4.8 0.6 - - - +
29C ILE* 5.8 0.8 - - + +
60C TRP* 3.0 64.0 + - + +
61C GLU 3.7 4.0 - - - +
62C ALA 3.2 0.4 - - - -
63C LEU* 1.3 77.6 - - - +
65C ALA* 1.3 64.0 + - - +
67C THR* 3.0 9.6 + - - -
68C VAL* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.6 10.9 - - + +
50C LEU* 3.6 8.4 - - + +
53C LYS* 3.4 33.4 - - + -
54C ILE* 3.7 17.4 - - + +
61C GLU 2.9 13.0 + - - +
62C ALA 3.2 8.7 - - - +
64C GLN* 1.3 77.0 - - - +
66C LEU* 1.3 56.3 + - - +
68C VAL* 3.2 5.1 + - - +
69C LEU* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE* 3.8 32.3 - - + -
62C ALA 2.9 17.0 + - - +
63C LEU* 3.4 13.2 - - - +
64C GLN 3.1 0.2 - - - -
65C ALA* 1.3 73.0 - - - +
67C THR* 1.3 65.7 + - - +
69C LEU* 3.4 9.1 + - + +
70C GLU* 3.1 24.9 + - - +
93C LEU* 5.1 2.2 - - + -
110C VAL* 3.9 27.8 - - + +
113C LYS* 3.6 38.8 - - + -
114C VAL* 4.1 12.3 - - + -
117C LEU* 4.0 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU* 4.1 24.6 + - + +
26C TRP* 3.6 33.1 - - + -
29C ILE* 4.2 7.4 - - + -
63C LEU 3.0 12.4 + - - -
64C GLN* 3.0 12.9 + - - -
66C LEU* 1.3 74.3 - - - +
68C VAL* 1.3 65.0 + - - +
70C GLU* 3.5 17.0 + - + +
71C ALA* 3.2 21.1 + - - +
113C LYS* 5.5 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.9 3.8 - - + -
16C ALA* 4.1 20.4 - - + +
17C THR* 4.0 17.5 - - + -
29C ILE* 4.1 23.6 - - + +
32C PHE* 3.5 35.4 - - + -
50C LEU* 3.6 14.6 - - + -
64C GLN 2.9 18.1 + - - +
65C ALA* 3.5 7.4 - - - +
67C THR* 1.3 76.3 - - - +
69C LEU* 1.3 67.2 + - - +
71C ALA* 3.1 2.9 + - - +
72C CYS* 3.0 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 3.9 27.8 - - + +
54C ILE* 3.8 21.3 - - + -
65C ALA 2.8 16.5 + - - +
66C LEU* 3.6 8.3 - - + +
67C THR 3.3 0.2 - - - -
68C VAL* 1.3 77.7 - - - +
70C GLU* 1.3 57.4 + - - +
72C CYS* 3.2 6.6 + - - +
73C MSE 3.1 24.4 + - + +
80C PHE* 4.1 15.0 - - + -
84C VAL* 4.3 6.5 - - + -
89C PHE* 3.9 23.8 - - + -
93C LEU* 4.9 3.8 - - + -
117C LEU* 4.2 12.1 - - + -
121C TRP* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 6.4 1.1 - - + -
66C LEU 3.1 15.1 + - - +
67C THR* 3.6 19.7 + - + +
68C VAL 3.2 0.2 - - - -
69C LEU* 1.3 74.9 - - - +
71C ALA* 1.3 65.4 + - - +
73C MSE 3.3 14.4 + - + +
74C LYS* 3.2 43.5 + - + +
113C LYS* 3.1 32.6 + - - -
117C LEU* 3.9 25.2 - - + +
121C TRP* 5.5 1.8 - - + +
151C PRO* 5.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 4.2 12.1 - - + -
29C ILE* 3.8 23.8 - - + -
30C ILE* 5.1 1.3 - - + -
33C CYS* 3.8 10.3 - - - -
67C THR 3.2 13.1 + - - +
68C VAL 3.1 9.7 + - - +
70C GLU* 1.3 76.6 - - - +
72C CYS* 1.3 60.6 + - - +
74C LYS* 3.0 8.2 + - - +
75C ASN* 2.8 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PHE* 3.9 14.1 - - - -
33C CYS* 3.8 13.5 - - - -
36C ILE* 3.6 29.4 - - - -
50C LEU* 4.3 2.2 - - - -
68C VAL* 3.0 17.5 + - - -
69C LEU 3.3 5.6 - - - +
71C ALA* 1.3 79.0 - - - +
73C MSE 1.3 56.6 + - - +
76C CYS* 2.8 41.6 + - - +
80C PHE* 3.3 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 3.1 19.1 + - - +
70C GLU* 3.5 11.9 - - + +
71C ALA 3.2 0.2 - - - -
72C CYS* 1.3 77.4 - - - +
74C LYS* 1.3 62.6 + - + +
77C GLY 4.6 2.1 + - - -
80C PHE* 3.8 10.8 - - - -
81C HIS* 2.8 37.3 + - + +
84C VAL* 3.8 34.3 - - + -
121C TRP* 3.7 48.7 - - + +
125C LEU* 3.3 35.0 - - + -
131C ILE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU* 3.2 32.2 + - + +
71C ALA* 3.0 11.7 + - - +
73C MSE 1.3 80.8 - - + +
75C ASN* 1.3 72.6 + - - +
76C CYS 3.9 0.2 - - - -
77C GLY 5.1 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 4.0 23.9 - - + +
33C CYS* 4.1 20.0 - - + +
34C ASP* 6.0 1.3 - - - +
37C ASN* 3.0 18.0 - - - +
71C ALA* 2.8 24.7 + - - +
74C LYS* 1.3 91.0 + - - +
76C CYS* 1.3 59.0 + - - +
77C GLY 3.5 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C CYS* 3.7 25.6 - - - -
36C ILE* 4.1 13.2 - - + -
37C ASN* 3.3 26.5 + - - +
43C PRO* 6.1 0.2 - - + -
72C CYS* 2.8 37.9 + - - +
75C ASN* 1.3 76.0 - - - +
77C GLY* 1.3 66.7 + - - +
79C ARG* 4.0 11.4 - - - +
80C PHE* 3.5 26.3 + - + +
----------------------------------------------------------
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