Contacts of the helix formed by residues 29 - 42 (chain C) in PDB entry 1MF8
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 VAL 29 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 3.1 14.3 + - + +
28C LYS* 1.3 79.7 - - + +
30C PRO* 1.3 65.4 - - - +
32C THR* 4.1 2.7 - - - +
33C ALA* 3.1 21.0 + - - +
86C GLU* 3.0 27.4 - - + +
87C ASN* 2.6 45.5 - - - +
90C LEU* 5.2 0.4 - - + -
127C VAL* 4.4 4.9 - - + -
128C VAL 3.7 11.4 - - - +
129C PHE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA* 3.0 35.2 - - + +
27C ASP 4.8 0.4 - - - -
28C LYS 3.4 8.5 - - - +
29C VAL* 1.3 82.8 - - - +
31C LYS* 1.3 60.4 + - + +
33C ALA* 3.4 1.6 - - - +
34C GLU* 2.9 28.9 + - - +
86C GLU* 3.9 7.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
30C PRO* 1.3 71.2 - - + +
32C THR* 1.3 65.4 + - - +
34C GLU* 3.0 10.3 + - - -
35C ASN* 3.0 3.1 + - - +
79C TYR* 2.9 64.8 + - + +
83C PHE* 4.5 8.5 - - + +
84C GLU* 3.3 28.3 + - - +
86C GLU* 2.6 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.1 4.0 - - - -
31C LYS* 1.3 71.8 - - - +
33C ALA* 1.3 63.7 + - - +
35C ASN* 3.2 6.6 + - - +
36C PHE* 3.1 19.9 + - - +
83C PHE* 3.9 23.8 - - + -
86C GLU* 2.5 40.7 + - - +
100C MET* 3.7 23.6 - - + -
108C ASN* 5.7 1.6 + - - -
127C VAL* 3.8 10.1 - - + +
129C PHE* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 5.4 2.0 - - + -
24C LEU* 3.3 26.5 - - + +
25C PHE 4.1 4.0 - - - +
26C ALA* 3.6 29.2 - - + +
29C VAL 3.1 17.4 + - - +
30C PRO 3.4 5.2 - - - +
32C THR* 1.3 78.6 - - - +
34C GLU* 1.3 64.8 + - - +
36C PHE* 3.1 3.1 + - - +
37C ARG* 2.9 17.7 + - - +
129C PHE* 4.4 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PRO 2.9 13.8 + - - +
31C LYS* 3.0 9.8 + - - +
33C ALA* 1.3 74.5 - - - +
35C ASN* 1.3 57.7 + - - +
37C ARG* 2.5 74.3 + - - +
38C ALA* 2.7 22.2 + - - +
43C GLU* 4.5 0.5 - - - +
44C LYS* 4.8 3.3 + - - -
78C ILE* 4.2 8.2 - - + +
79C TYR* 3.3 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS 3.0 3.9 + - - +
32C THR 3.2 11.2 + - - +
34C GLU* 1.3 79.3 - - - +
36C PHE* 1.3 52.3 + - - +
38C ALA* 3.7 0.5 + - - +
39C LEU* 2.2 58.8 + - - +
48C TYR* 4.6 0.8 + - - -
77C SER* 3.1 24.6 - - - -
78C ILE* 3.2 23.6 + - - +
79C TYR* 3.4 15.8 + - + -
83C PHE* 3.7 21.1 - - + -
100C MET* 4.1 12.3 - - - +
109C GLY 3.5 15.8 + - - -
110C SER* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 4.5 4.7 - - + -
8C PHE* 3.3 31.9 - + - -
22C PHE* 4.4 11.4 - + - -
24C LEU* 3.5 22.2 - - + -
32C THR 3.1 5.9 + - - +
33C ALA 3.1 8.9 + - - +
35C ASN* 1.3 75.2 - - - +
37C ARG* 1.3 60.2 + - - +
39C LEU* 3.4 6.1 + - - -
40C SER* 2.5 44.5 + - - -
48C TYR* 3.3 27.2 - + - -
98C LEU* 3.9 20.4 - - + -
100C MET* 5.6 1.3 - - - -
112C PHE* 3.8 25.4 - + + -
129C PHE* 3.5 31.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 4.0 21.8 - - + -
6C VAL* 4.3 3.8 - - + -
24C LEU* 3.8 11.6 - - + +
33C ALA 2.9 11.6 + - - +
34C GLU* 2.5 56.1 + - - +
36C PHE* 1.3 71.1 - - - +
38C ALA* 1.3 58.4 + - - +
40C SER* 2.9 22.8 + - - -
41C THR* 3.0 21.5 + - - +
43C GLU* 3.0 40.3 + - - -
163C GLN* 2.5 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 2.7 27.9 + - - +
37C ARG* 1.3 74.0 - - - +
39C LEU* 1.3 57.0 + - - +
40C SER 3.2 0.2 - - - -
41C THR* 2.9 20.0 + - - -
42C GLY* 3.0 14.9 + - - -
43C GLU* 3.6 10.2 + - + +
44C LYS* 4.1 20.3 + - + +
46C PHE 4.7 1.4 - - - +
78C ILE* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASN* 2.2 55.0 - - - +
36C PHE* 3.6 2.0 - - - -
37C ARG 3.1 0.4 - - - -
38C ALA* 1.3 73.4 - - - +
40C SER* 1.3 63.7 + - - +
42C GLY* 4.0 2.3 + - - -
46C PHE* 4.3 10.3 - - + +
47C GLY* 3.3 14.3 - - - -
48C TYR* 2.7 73.8 + - + +
49C LYS 4.6 0.3 + - - -
67C PHE* 5.2 2.7 - - + -
76C LYS 4.5 9.2 - - - +
78C ILE* 3.2 33.9 - - + +
110C SER* 4.7 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 3.2 37.9 - - - +
8C PHE* 4.2 2.3 - - - -
36C PHE* 2.5 31.1 + - - -
37C ARG 2.9 8.9 + - - -
39C LEU* 1.3 81.1 - - - +
41C THR* 1.3 61.6 + - - +
42C GLY* 4.8 0.2 - - - -
48C TYR* 3.8 9.8 - - - -
49C LYS* 5.6 0.2 - - - +
161C CYS* 3.0 37.4 - - - +
162C GLY* 4.2 4.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
37C ARG* 3.0 20.9 + - - +
38C ALA* 2.9 20.8 + - - -
40C SER* 1.3 80.8 - - - +
42C GLY* 1.3 55.5 + - - +
43C GLU* 2.9 38.4 + - - +
161C CYS 4.7 2.8 - - - +
162C GLY* 4.5 5.4 - - - -
163C GLN* 3.9 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA 3.0 11.2 + - - -
39C LEU 4.0 5.1 - - - -
40C SER 3.5 2.2 - - - -
41C THR* 1.3 77.3 - - - +
43C GLU* 1.3 48.9 + - - +
44C LYS 3.0 5.2 - - - -
45C GLY* 2.5 38.3 + - - -
46C PHE 4.3 14.8 - - - -
47C GLY* 4.6 2.2 - - - -
----------------------------------------------------------
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