Contacts of the helix formed by residues 32 - 42 (chain M) in PDB entry 6CM9
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 HIS 32 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M SER* 3.0 29.4 + - - -
29M GLU* 3.4 20.7 + - - +
30M VAL 3.1 1.0 - - - -
31M GLU* 1.3 84.3 - - + +
33M PHE* 1.3 63.2 + - - +
34M MET 3.7 0.2 - - - -
35M PRO* 4.1 5.3 - - - +
36M ILE* 3.3 25.7 + - - +
52M HIS* 3.3 44.8 + + + -
57M PHE* 4.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LEU* 3.5 24.0 - - + -
29M GLU 3.8 1.0 + - - -
30M VAL* 3.1 18.9 + - + +
32M HIS* 1.3 77.4 - - - +
34M MET* 1.3 70.3 + - + +
36M ILE* 2.9 22.2 + - - +
37M LEU* 2.9 37.1 + - + +
50M LEU* 3.6 11.2 - - + -
57M PHE* 3.5 39.7 - + + -
59M TRP* 3.5 36.1 - + - -
66M TYR* 4.5 10.1 - + - -
68M VAL* 3.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 34 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LEU* 5.1 2.5 - - + -
10M ASP 3.6 13.9 - - - +
11M LEU 4.3 3.4 - - - +
12M LYS 3.8 15.3 - - - +
13M GLY* 3.5 34.5 - - - +
30M VAL 4.3 3.1 + - - +
31M GLU 4.6 0.4 + - - +
33M PHE* 1.3 90.6 - - + +
35M PRO* 1.3 65.1 - - + +
37M LEU* 4.4 14.8 - - - +
38M MET* 2.9 65.6 + - + +
66M TYR* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 35 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M GLU 3.5 21.5 - - - +
32M HIS* 4.1 4.9 - - - +
33M PHE 3.8 2.0 - - - -
34M MET* 1.3 91.9 - - + +
36M ILE* 1.3 57.9 + - + +
38M MET* 3.8 5.5 - - + +
39M GLU* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M HIS 3.3 17.4 + - - +
33M PHE* 2.9 9.4 + - - +
35M PRO* 1.3 76.4 - - + +
37M LEU* 1.3 61.6 + - - +
39M GLU* 3.3 12.5 + - - +
40M LYS* 2.9 39.0 + - + +
50M LEU* 3.8 34.5 - - + -
51M ALA 4.0 13.7 - - - +
52M HIS* 3.5 39.9 - - + +
57M PHE* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M PHE* 2.9 45.2 + - + +
34M MET* 3.9 16.8 - - - +
36M ILE* 1.3 78.6 - - - +
38M MET* 1.3 67.6 + - + +
40M LYS* 3.8 3.2 - - - +
41M GLU* 2.9 40.1 + - + +
46M LEU* 4.6 8.0 - - + +
50M LEU* 4.1 11.0 - - + +
59M TRP* 3.6 32.8 - - + +
66M TYR* 4.0 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 38 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M LEU 5.2 7.2 - - - +
34M MET* 2.9 47.4 + - + +
35M PRO* 3.9 6.3 - - + +
37M LEU* 1.3 86.2 - - + +
39M GLU* 1.3 58.5 + - - +
41M GLU* 4.6 8.7 - - - +
42M GLU* 3.1 48.2 + - - +
66M TYR* 5.8 2.0 - - - +
33S ARG* 5.4 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M PRO 2.9 19.4 + - - +
36M ILE* 3.7 13.6 - - - +
37M LEU 3.2 0.2 - - - -
38M MET* 1.3 78.2 - - - +
40M LYS* 1.3 69.5 + - + +
41M GLU 3.5 0.5 + - - -
42M GLU* 3.5 11.9 + - - +
43M GLU* 3.4 27.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
36M ILE* 2.9 27.6 + - + +
37M LEU* 4.2 2.5 - - - +
39M GLU* 1.3 83.9 - - + +
41M GLU* 1.3 60.0 + - - +
43M GLU* 3.9 18.3 + - - +
44M GLY 3.5 1.2 + - - -
45M MET* 3.1 48.5 + - + +
46M LEU* 3.3 10.3 + - + -
49M ILE 5.9 0.2 + - - -
50M LEU* 3.9 28.9 - - + +
51M ALA* 4.8 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M LEU* 2.9 25.8 + - + +
38M MET* 4.3 9.6 - - - +
40M LYS* 1.3 75.7 - - - +
42M GLU* 1.3 66.4 + - - +
43M GLU 3.1 9.1 + - - -
44M GLY* 3.4 11.0 + - - +
46M LEU* 4.3 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M MET* 3.1 32.7 + - - +
39M GLU* 3.5 7.1 + - - +
41M GLU* 1.3 83.9 - - - +
43M GLU* 1.3 58.7 + - - +
44M GLY 3.8 0.2 - - - -
33S ARG* 2.9 46.8 + - - +
37S GLN* 5.1 8.5 + - - +
----------------------------------------------------------
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