Contacts of the helix formed by residues 30 - 45 (chain C) in PDB entry 1MJO
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 LEU 30 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS 4.4 0.2 - - - +
45A VAL* 3.8 42.4 - - - +
46A ASN* 5.3 1.6 - - - -
47A ASN* 3.6 27.4 - - - +
28C ILE 3.3 0.4 + - - -
29C PRO* 1.3 71.9 - - - +
31C LYS* 1.3 55.8 + - - +
33C LEU* 3.6 11.5 - - + +
34C LYS* 3.0 29.1 + - - +
19D GLU 3.7 15.3 - - - +
20D GLN* 2.8 23.5 + - + +
21D VAL* 4.4 1.3 - - - +
22D LYS* 3.8 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PRO* 3.1 5.5 - - + +
30C LEU* 1.3 78.8 - - - +
32C VAL* 1.3 64.8 + - + +
34C LYS* 3.7 6.0 + - - +
35C ILE* 3.5 29.8 + - + +
8D ILE* 5.6 8.5 - - + -
9D SER 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 3.6 22.0 - - + -
29C PRO* 2.9 16.8 + - + +
31C LYS* 1.3 76.8 - - + +
33C LEU* 1.3 66.0 + - - +
34C LYS 3.1 1.6 - - - -
35C ILE* 3.2 9.0 + - - +
36C LEU* 2.9 21.3 + - - +
8D ILE* 5.2 2.5 - - + -
9D SER 4.0 11.9 - - - +
10D PRO* 4.2 13.9 - - + +
58D CYS* 4.7 12.1 - - - +
61D PHE* 4.3 19.7 - - + -
62D LEU* 4.0 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 4.5 12.1 - - + -
45A VAL* 4.2 12.1 - - + -
28C ILE* 3.7 24.4 - - + +
29C PRO 2.9 12.3 + - - +
30C LEU* 3.3 20.8 + - + +
32C VAL* 1.3 79.4 - - - +
34C LYS* 1.3 55.0 + - - +
36C LEU* 4.3 8.3 - - + -
37C THR* 2.6 49.1 + - - +
53C ASN* 4.2 14.1 - - - +
22D LYS* 4.1 33.9 - - + -
24D ILE* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.9 6.5 - - + +
42A ARG* 6.3 0.4 - - - +
45A VAL* 3.8 29.3 - - + +
30C LEU 3.0 16.1 + - - +
31C LYS* 3.8 8.1 - - - +
32C VAL 3.1 0.2 - - - -
33C LEU* 1.3 75.8 - - - +
35C ILE* 1.3 66.7 + - + +
37C THR* 4.0 2.0 - - - -
38C ASP* 2.9 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS* 3.5 21.7 + - + +
32C VAL* 3.2 6.4 + - - +
34C LYS* 1.3 81.1 - - + +
36C LEU* 1.3 61.6 + - - +
38C ASP* 3.8 5.8 - - - +
39C GLU* 3.1 22.9 + - - +
8D ILE* 4.2 24.7 - - + -
61D PHE* 3.6 14.1 - - + -
62D LEU* 4.1 20.4 - - + -
65D PHE* 3.6 39.3 - - + -
66D THR* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 4.0 21.5 - - + -
32C VAL 2.9 15.4 + - - +
33C LEU* 3.7 8.1 - - + +
35C ILE* 1.3 77.5 - - - +
37C THR* 1.3 63.2 + - - +
39C GLU* 3.1 6.8 + - - +
40C ARG 3.1 16.5 + - - -
53C ASN* 3.7 35.1 - - + +
56C LEU* 3.6 28.7 - - + +
57C LEU* 4.0 21.5 - - + -
24D ILE* 4.5 3.1 - - + -
61D PHE* 3.4 38.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 5.6 0.2 - - - +
41A THR* 3.5 33.2 - - + +
44A LYS* 5.9 4.3 - - + +
45A VAL* 5.0 1.3 - - + +
33C LEU* 2.6 35.6 + - - +
34C LYS* 4.0 2.2 - - - -
36C LEU* 1.3 72.4 - - - +
38C ASP* 1.3 58.2 + - - +
40C ARG* 3.0 32.0 + - - +
41C THR* 2.9 28.8 + - - +
53C ASN* 3.5 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 4.3 13.5 - - - +
41A THR* 3.8 18.0 + - - +
34C LYS* 2.9 53.8 + - - +
35C ILE* 3.8 6.0 - - - +
37C THR* 1.3 76.6 - - - +
39C GLU* 1.3 57.6 + - - +
41C THR* 3.3 8.1 + - - -
42C ARG* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE 3.1 14.3 + - - +
36C LEU 3.1 9.1 + - - +
38C ASP* 1.3 73.8 - - - +
40C ARG* 1.3 66.6 + - - +
42C ARG* 3.0 40.1 + - - +
43C ARG* 3.1 27.1 + - - +
56C LEU* 3.7 25.6 - - + -
61D PHE* 4.6 3.4 - - + -
65D PHE* 3.5 30.3 - - + -
200D SAM 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.7 29.0 - - - +
36C LEU 3.1 4.6 + - - -
37C THR* 3.0 33.3 + - - +
39C GLU* 1.3 73.9 - - - +
41C THR* 1.3 67.1 + - - +
43C ARG* 3.1 8.0 + - - +
44C LYS* 2.9 24.3 + - + +
51C ALA* 3.5 23.2 - - + +
52C THR* 3.7 5.6 - - - +
53C ASN* 3.3 45.8 + - - +
56C LEU* 3.5 12.9 - - + +
10F G 3.0 33.9 + - - -
11F A 5.0 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 4.8 8.3 - - + +
37A THR* 3.2 33.6 - - + +
38A ASP* 3.6 23.2 + - - +
41A THR* 4.1 8.7 + - - -
37C THR* 2.9 16.9 + - - +
38C ASP* 3.5 11.3 - - - +
40C ARG* 1.3 80.0 + - - +
42C ARG* 1.3 56.2 + - - +
44C LYS* 3.2 7.5 + - + +
45C VAL* 2.9 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP 2.9 14.0 + - - +
39C GLU* 3.0 43.3 + - - +
40C ARG 3.2 0.2 - - - -
41C THR* 1.3 78.8 - - - +
43C ARG* 1.3 65.7 + - - +
45C VAL* 3.7 6.0 + - + -
46C ASN* 2.8 43.8 + - - +
48C LEU* 4.3 12.4 - - - +
73C ASP* 2.9 42.8 + - - -
76C LEU* 5.3 1.0 - - - +
200D SAM 3.6 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLU* 3.1 16.5 + - - +
40C ARG* 3.1 9.5 + - - +
42C ARG* 1.3 81.8 - - - +
44C LYS* 1.3 64.9 + - - +
46C ASN 3.2 5.9 + - - -
47C ASN 3.2 0.2 + - - -
48C LEU* 3.0 52.7 + - + +
49C ARG 3.8 6.1 - - - -
50C HIS* 2.9 33.2 + - - +
51C ALA* 3.7 13.0 - - + +
56C LEU* 3.4 26.6 - - - +
59C GLU* 2.8 42.2 + - - -
71C PRO* 3.9 2.8 - - - +
76C LEU* 3.4 21.0 - - + +
200D SAM 3.1 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.5 5.7 - - - +
33A LEU* 4.9 9.6 - - + -
37A THR* 6.2 2.5 - - + -
22B LYS* 3.0 42.4 - - - +
40C ARG* 2.9 14.5 + - + +
41C THR* 3.2 13.2 + - + +
43C ARG* 1.3 78.7 - - - +
45C VAL* 1.3 62.7 + - + +
46C ASN 3.2 4.3 + - - -
47C ASN* 3.3 12.8 + - - +
48C LEU 5.1 1.3 - - - -
51C ALA* 3.6 25.0 - - + +
11G A 3.1 41.9 + - - +
12G C 4.6 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.6 43.7 - - + +
33A LEU* 4.4 14.4 - - + +
34A LYS* 3.9 45.1 - - + +
37A THR* 5.3 1.3 - - - +
41C THR* 2.9 30.6 + - + +
42C ARG* 3.8 5.4 - - - +
44C LYS* 1.3 76.3 - - + +
46C ASN* 1.3 73.5 + - - +
47C ASN 3.5 1.6 - - - -
----------------------------------------------------------
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