Contacts of the helix formed by residues 79 - 92 (chain C) in PDB entry 1MN8
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 79 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 3.6 36.3 - - + -
42C GLU* 3.0 34.1 + - - +
43C TRP* 2.8 33.2 + - + +
46C PHE* 3.4 10.4 - - - -
68C VAL* 3.6 15.7 - - + +
76C HIS* 2.9 29.2 + - - +
78C ASP* 1.3 84.2 + - - +
80C VAL* 1.3 64.0 + - - +
81C PRO* 3.4 1.8 - - - -
82C TYR* 3.2 6.0 + - - +
83C ILE* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 5.3 5.2 - - + -
68C VAL* 3.9 13.9 - - + +
69C PHE* 3.7 38.1 - - + -
76C HIS 3.7 0.4 + - - -
77C PRO* 3.4 28.7 - - + +
79C GLN* 1.3 76.9 - - - +
81C PRO* 1.3 71.8 - - + +
82C TYR 3.0 0.3 + - - -
83C ILE* 3.4 2.8 + - - +
84C VAL* 3.0 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.6 30.2 - - + +
29C ASP 3.3 28.5 - - - +
30C VAL* 3.6 4.6 - - + +
77C PRO 3.9 4.5 - - - +
78C ASP* 3.7 11.7 - - - +
79C GLN 3.6 2.7 - - - -
80C VAL* 1.3 96.1 - - + +
82C TYR* 1.3 59.9 + - + +
84C VAL* 3.6 0.4 + - + -
85C THR* 2.8 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASP 4.4 2.1 + - - -
30C VAL* 3.7 23.4 - - + -
31C LYS* 3.0 28.6 + - - +
34C ARG* 3.3 26.4 - - + +
35C TRP* 3.5 45.0 - + + -
38C PHE* 3.5 23.3 - + + -
43C TRP* 3.8 19.3 - - + -
78C ASP 3.6 19.5 - - - -
79C GLN 3.5 5.8 - - - +
80C VAL 3.1 0.6 - - - -
81C PRO* 1.3 87.2 - - + +
83C ILE* 1.3 65.9 + - - +
85C THR* 3.2 4.2 + - - -
86C TRP* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 3.6 23.9 - - + -
50C TRP* 4.8 2.7 - - + -
61C ILE* 3.7 26.2 - - + +
64C VAL* 3.7 21.8 - - + -
65C LYS* 3.8 30.3 - - + +
68C VAL* 3.9 22.0 - - + -
69C PHE* 4.0 14.4 - - + -
79C GLN 3.1 13.4 + - - +
80C VAL 3.7 8.5 - - - +
82C TYR* 1.3 74.3 - - - +
84C VAL* 1.3 68.7 + - - +
86C TRP* 4.4 5.6 - - + -
87C GLU* 2.9 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN* 3.8 32.1 - - + +
28C VAL* 4.2 15.7 - - + -
65C LYS* 4.5 10.1 - - - +
69C PHE* 3.9 26.7 - - + -
80C VAL* 3.0 26.6 + - + +
81C PRO* 3.8 4.0 - - + +
83C ILE* 1.3 77.4 - - - +
85C THR* 1.3 57.1 + - - +
87C GLU* 3.6 10.0 - - - +
88C ALA* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C VAL* 3.8 29.2 - - + +
22C ILE* 4.4 6.7 - - + -
23C ALA* 3.3 28.8 - - + +
26C GLN* 5.5 0.4 - - - -
28C VAL* 3.5 6.6 - - - +
30C VAL* 3.9 2.0 - - + +
35C TRP* 3.7 21.5 - - + -
81C PRO 2.8 18.6 + - - -
82C TYR 3.2 3.3 + - - -
84C VAL* 1.3 75.0 - - - +
86C TRP* 1.3 66.3 + - - +
88C ALA* 3.2 6.6 + - - +
89C LEU* 3.0 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PRO* 4.2 4.3 - - + -
9C LEU* 4.2 14.1 - - + -
12C THR* 4.2 6.3 - - + -
35C TRP* 3.2 49.3 + + - +
39C CYS* 3.8 22.3 - - + +
43C TRP* 3.6 25.4 - + - -
50C TRP* 3.9 9.2 - + + -
54C GLY* 3.9 15.9 - - - -
55C THR 3.3 33.9 - - - -
56C PHE* 3.8 27.5 - + - -
61C ILE* 3.7 14.6 - - + +
82C TYR* 3.0 27.7 + - - +
83C ILE* 3.9 14.1 - - + +
85C THR* 1.3 75.0 - - - +
87C GLU* 1.3 62.3 + - - +
89C LEU* 3.2 9.5 + - + +
90C ALA 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ILE* 3.7 23.3 - - + +
62C THR* 5.1 6.4 + - - -
65C LYS* 2.7 44.6 + - + +
83C ILE 2.9 17.7 + - - +
84C VAL* 3.6 9.6 - - - +
85C THR 3.2 0.2 - - - -
86C TRP* 1.3 76.6 - - - +
88C ALA* 1.3 62.4 + - - +
90C ALA* 3.2 2.5 + - - +
91C PHE* 3.0 57.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.9 20.6 - - + -
26C GLN* 4.0 27.4 - - + +
84C VAL 3.0 18.2 + - - +
85C THR* 3.2 5.8 + - - +
87C GLU* 1.3 77.0 - - - +
89C LEU* 1.3 55.3 + - - +
91C PHE* 3.9 5.0 - - - +
92C ASP* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C THR* 4.0 26.9 - - + -
19C VAL* 4.5 9.0 - - + -
22C ILE* 3.6 34.3 - - + -
35C TRP* 4.1 17.7 - - + -
56C PHE* 4.3 17.7 - - + -
85C THR* 3.0 20.5 + - + +
86C TRP* 3.2 10.1 + - + +
88C ALA* 1.3 77.2 - - - +
90C ALA* 1.3 61.0 + - - +
92C ASP 4.5 2.7 - - - -
93C PRO* 3.1 29.1 - - - +
94C PRO* 3.6 21.4 - - + +
96C TRP* 4.1 8.1 - - + -
97C VAL* 4.9 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 3.4 33.6 - - - +
58C ARG* 3.1 28.2 + - - +
61C ILE* 3.4 23.8 - - + -
86C TRP 3.0 6.9 + - - +
87C GLU* 3.7 4.0 - - - +
89C LEU* 1.3 77.4 - - - +
91C PHE* 1.3 63.2 + - + +
92C ASP 3.7 0.2 + - - -
93C PRO* 3.7 13.1 - - - +
97C VAL* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ARG* 3.9 43.7 + - + +
62C THR* 6.0 1.3 - - - -
87C GLU* 3.0 54.5 + - + +
88C ALA* 4.0 4.7 - - - +
90C ALA* 1.3 77.9 - - + +
92C ASP* 1.3 61.8 + - + +
93C PRO* 3.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 5.6 2.4 - - - +
88C ALA 3.0 14.3 + - - +
89C LEU* 3.5 3.9 - - - +
91C PHE* 1.3 79.6 - - + +
93C PRO* 1.3 71.9 - - - +
94C PRO* 3.3 6.4 - - - +
----------------------------------------------------------
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