Contacts of the helix formed by residues 54 - 69 (chain C) in PDB entry 1MBU
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 54 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLN* 3.3 5.4 - - - +
52C SER 3.8 1.2 + - - -
53C TYR* 1.3 75.4 - - - +
55C VAL* 1.3 66.4 + - - +
56C GLU* 3.2 11.6 + - - +
57C ARG* 2.9 25.8 + - - +
58C ALA* 2.9 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 5.0 6.9 - - + +
48C GLN* 3.1 29.6 - - - +
54C ASP* 1.3 73.7 - - - +
56C GLU* 1.3 60.3 + - - +
58C ALA* 3.8 2.4 - - - +
59C THR* 2.7 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 3.2 10.8 + - - +
55C VAL* 1.3 82.6 - - - +
57C ARG* 1.3 64.0 + - - +
59C THR* 3.2 6.1 + - - -
60C GLN* 3.2 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TYR* 3.4 32.7 - - + -
54C ASP* 2.9 21.1 + - - +
56C GLU* 1.3 71.1 - - - +
58C ALA* 1.3 66.0 + - - +
60C GLN* 2.6 57.0 + - - +
61C LEU* 3.1 49.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
44C ILE* 4.0 13.2 - - + -
47C LEU* 3.4 35.1 - - + +
48C GLN* 3.9 18.4 - - + -
53C TYR* 3.9 9.2 - - + +
54C ASP 2.9 18.1 + - - +
55C VAL 3.8 3.4 - - - +
57C ARG* 1.3 76.6 - - - +
59C THR* 1.3 56.9 + - - +
61C LEU* 3.2 2.6 + - - -
62C MET* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 3.9 22.1 - - + +
55C VAL* 2.7 32.5 + - - +
56C GLU* 3.4 6.7 - - - -
58C ALA* 1.3 74.5 - - - +
60C GLN* 1.3 64.5 + - - +
62C MET* 3.3 13.1 + - + +
63C LEU* 3.1 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU* 3.2 30.2 + - + +
57C ARG* 2.6 61.5 + - - +
59C THR* 1.3 76.3 - - - +
61C LEU* 1.3 58.8 + - - +
63C LEU* 3.2 13.8 + - + +
64C ALA* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.7 16.6 - - + -
53C TYR* 3.5 48.9 - - + +
57C ARG* 3.1 41.4 + - - +
58C ALA 3.6 6.7 - - - +
60C GLN* 1.3 74.9 - - - +
62C MET* 1.3 59.7 + - - +
64C ALA* 3.3 8.3 + - + +
65C VAL* 3.0 34.7 + - + +
71C ALA* 4.3 15.1 - - + +
72C ILE 3.8 21.8 - - - +
73C CYS* 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 3.4 60.1 - - + +
43C VAL* 3.9 27.6 - - + -
44C ILE* 3.9 22.0 - - + -
47C LEU* 4.0 0.4 - - - +
58C ALA 2.9 15.2 + - - +
59C THR* 3.6 10.1 - - + +
60C GLN 3.3 0.2 - - - -
61C LEU* 1.3 75.8 - - - +
63C LEU* 1.3 94.5 + - + +
65C VAL* 3.2 4.6 + - - +
66C HIS* 3.0 24.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
40C MET* 5.1 4.9 - - - -
59C THR* 3.1 29.5 + - + +
60C GLN* 3.5 11.2 - - + +
61C LEU 3.2 0.2 - - - -
62C MET* 1.3 96.5 - - + +
64C ALA* 1.3 61.0 + - - +
66C HIS* 3.2 7.6 - - + +
67C TYR* 2.9 57.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLN 3.0 13.4 + - - +
61C LEU* 3.3 14.3 + - + +
63C LEU* 1.3 78.3 - - - +
65C VAL* 1.3 56.1 + - - +
67C TYR* 4.9 2.2 - - - -
68C GLN* 2.8 56.7 + - - +
70C LYS 4.4 1.6 - - - -
71C ALA* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.9 27.4 - - + +
33C VAL 3.9 7.0 - - - +
34C ASN* 3.4 37.1 - - + +
43C VAL* 4.8 14.8 - - + -
47C LEU* 5.8 0.4 - - + -
61C LEU* 3.0 22.0 + - + +
62C MET* 3.2 9.8 + - - +
64C ALA* 1.3 76.3 - - - +
66C HIS* 1.3 58.0 + - - +
69C GLY* 2.9 30.7 + - - -
70C LYS* 4.0 7.9 - - - +
71C ALA* 3.7 16.4 - - + -
99C LEU* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 3.8 26.1 + - - -
40C MET* 4.3 34.3 - - + +
62C MET* 3.0 16.7 + - - +
63C LEU* 3.2 15.9 - - + +
65C VAL* 1.3 79.0 - - - +
67C TYR* 1.3 81.7 + + + +
69C GLY* 4.1 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 2.9 53.8 + - + +
64C ALA* 4.4 1.6 - - - +
66C HIS* 1.3 89.9 - + + +
68C GLN* 1.3 66.9 + - + +
69C GLY 3.3 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 2.8 35.9 + - - +
67C TYR* 1.3 76.9 - - + +
69C GLY* 1.3 57.5 + - - +
70C LYS* 3.1 29.4 + - + +
71C ALA* 4.5 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 3.9 5.2 - - - +
34C ASN* 3.0 29.3 + - - +
65C VAL 2.9 17.7 + - - -
66C HIS 4.1 2.8 + - - -
67C TYR 3.3 3.0 + - - -
68C GLN* 1.3 78.8 - - - +
70C LYS* 1.3 68.7 + - - +
----------------------------------------------------------
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