Contacts of the helix formed by residues 34 - 43 (chain M) in PDB entry 5A2Q
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 GLY 34 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12842 A 3.7 7.1 + - - -
12852 G 3.3 13.6 + - - -
13122 G 3.4 26.2 - - - +
33M ARG* 1.3 76.1 - - - +
35M ILE* 1.3 61.1 + - - -
36M ARG 3.5 2.0 - - - -
37M GLU 4.3 0.7 - - - -
38M ALA* 3.0 26.9 + - - +
106M CYS* 5.0 0.2 - - - -
108M CYS* 3.6 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12852 G 3.1 23.5 + - - -
12862 G 5.1 4.0 - - - +
13122 G 4.1 3.6 - - - +
34M GLY* 1.3 71.7 - - - -
36M ARG* 1.3 61.4 + - + +
38M ALA* 3.6 0.3 - - - +
39M ALA* 2.9 32.7 + - + +
61M TYR* 3.3 35.7 - - + +
64M LEU* 3.8 18.8 - - + -
65M VAL* 5.5 4.5 - - + -
108M CYS* 3.7 15.9 - - - -
100f LEU* 5.4 0.9 - - + -
102f VAL* 3.9 26.9 - - + -
103f LEU* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 36 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12862 G 2.8 35.1 + - - +
13092 C 4.6 0.6 - - - -
13102 U 2.2 51.7 + - - -
13112 C 3.2 30.3 + - - +
13122 G 3.1 18.4 + - - +
35M ILE* 1.3 75.9 - - - +
37M GLU* 1.3 62.9 + - - +
38M ALA 3.1 4.5 - - - -
39M ALA* 4.6 1.8 - - - -
40M LYS* 2.9 70.3 + - + +
102f VAL* 3.6 36.4 - - + +
105f TYR* 4.8 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13112 C 4.7 7.4 + - - +
13122 G 2.9 76.7 + - + +
32M ALA* 3.3 26.0 - - + +
33M ARG 4.1 11.2 - - - +
34M GLY 3.8 1.0 + - - -
35M ILE 3.5 0.2 - - - -
36M ARG* 1.3 78.9 - - - +
38M ALA* 1.3 58.2 + - - +
40M LYS* 5.1 3.5 - - - +
41M ALA* 3.6 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M ALA* 4.0 10.3 - - - +
34M GLY 3.0 20.5 + - - +
35M ILE 3.6 3.8 - - - +
36M ARG 3.1 0.2 - - - -
37M GLU* 1.3 77.7 - - - +
39M ALA* 1.3 66.0 + - - +
41M ALA 3.6 1.4 + - - -
42M LEU* 2.9 26.5 + - - +
50M CYS* 5.5 0.9 - - - -
108M CYS* 4.0 17.3 - - + -
110M VAL* 3.4 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ILE* 2.9 27.7 + - + +
36M ARG* 4.3 3.6 - - - +
38M ALA* 1.3 74.0 - - - +
40M LYS* 1.3 60.2 + - + +
42M LEU* 3.5 6.8 - - - +
43M ASP* 2.9 38.4 + - - +
64M LEU* 6.2 2.0 - - + -
68M LEU* 3.9 25.6 - - + -
102f VAL* 5.5 4.5 - - + -
106f TYR* 5.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13102 U 3.3 39.8 + - - -
13112 C 3.6 7.9 + - - +
36M ARG* 2.9 58.5 + - + +
37M GLU* 5.1 3.4 - - - +
39M ALA* 1.3 79.1 - - + +
41M ALA* 1.3 59.5 + - - +
43M ASP* 3.0 25.3 + - - +
44M LYS* 3.2 10.7 + - - +
102f VAL* 6.3 0.2 - - + -
105f TYR* 5.7 4.7 - - - -
106f TYR* 5.1 3.6 - - + +
129f GLY* 3.1 30.9 - - - +
130f VAL* 4.1 10.7 - - + +
131f PHE* 4.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M ALA* 5.1 2.2 - - + -
37M GLU* 3.6 24.3 + - + +
38M ALA 3.6 1.6 + - - +
39M ALA 3.5 0.4 - - - -
40M LYS* 1.3 77.7 - - - +
42M LEU* 1.3 58.0 + - - +
43M ASP 3.4 0.2 - - - -
44M LYS* 3.3 28.4 - - + +
46M GLN* 4.3 1.0 + - - +
47M ALA* 4.0 14.6 + - - +
110M VAL* 5.0 1.3 - - + -
112M LYS* 3.5 34.8 - - - +
129f GLY* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ALA 2.9 19.8 + - - +
39M ALA* 3.5 6.5 - - - +
41M ALA* 1.3 73.6 - - - +
43M ASP* 1.3 63.0 + - - +
44M LYS 3.1 6.3 + - - -
45M ARG* 3.5 11.8 + - - -
47M ALA* 3.6 39.6 - - + +
49M LEU 4.2 2.9 - - - +
50M CYS* 3.6 22.9 - - + -
65M VAL* 5.4 2.7 - - + -
68M LEU* 5.8 4.3 - - + -
69M CYS* 4.6 5.8 - - - -
72M HIS* 5.0 2.1 - - - +
74M ILE* 3.5 41.6 - - + +
110M VAL* 3.5 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M ALA 2.9 24.7 + - - +
40M LYS* 3.0 10.0 + - - +
42M LEU* 1.3 75.2 - - - +
44M LYS* 1.3 55.9 + - - +
45M ARG* 3.1 11.8 + - - +
68M LEU* 3.2 32.1 - - - +
72M HIS* 3.4 32.3 + - + +
74M ILE* 5.1 1.6 - - - +
106f TYR* 2.7 28.7 + - - +
116f ARG* 5.5 7.7 + - - +
128f ALA* 4.1 12.7 - - - +
131f PHE* 6.0 1.3 - - + -
----------------------------------------------------------
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