Contacts of the helix formed by residues 42 - 55 (chain B) in PDB entry 1MHQ
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 42 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP* 5.9 0.2 - - - -
32B LYS* 3.8 26.9 + - - +
33B ALA* 4.3 1.1 + - - -
38B MET* 4.1 23.7 - - + +
40B GLU 3.6 1.4 + - - -
41B GLN* 1.3 72.9 - - - +
43B TRP* 1.3 57.9 + - - +
44B SER* 3.2 12.0 + - - -
45B ALA* 2.8 45.6 + - + +
46B ILE* 3.0 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU* 4.9 12.4 + - - +
41B GLN* 3.2 41.9 + - + +
42B ASP* 1.3 72.6 + - - +
44B SER* 1.3 62.1 + - - +
46B ILE* 3.0 24.4 + - + +
47B GLN* 2.9 37.4 + - + +
84B THR* 3.7 26.7 - - + -
88B MET* 4.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASP* 3.2 9.1 + - - -
43B TRP* 1.3 76.7 - - - +
45B ALA* 1.3 64.2 + - - +
47B GLN* 3.3 16.0 + - - +
48B ASN* 3.0 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP* 3.8 12.3 - - + +
32B LYS* 3.6 12.6 - - + -
33B ALA* 3.6 25.8 - - - +
42B ASP* 2.8 34.2 + - - +
44B SER* 1.3 77.8 - - - +
46B ILE* 1.3 64.1 + - - +
48B ASN* 3.2 10.7 + - - +
49B PHE* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.7 19.3 - - + -
41B GLN* 3.4 38.6 - - + +
42B ASP 3.0 8.6 + - - +
43B TRP* 3.0 39.0 + - + +
45B ALA* 1.3 77.0 - - - +
47B GLN* 1.3 63.4 + - + +
49B PHE* 3.0 13.9 + - - +
50B CYS* 3.0 16.3 + - - -
84B THR* 4.5 3.8 - - + +
85B VAL* 4.2 15.3 - - + -
88B MET* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP* 2.9 22.8 + - + +
44B SER* 3.3 14.6 + - - +
46B ILE* 1.3 77.6 - - + +
48B ASN* 1.3 65.0 + - - +
50B CYS* 3.4 3.8 + - - +
51B GLU* 2.9 26.9 + - - +
88B MET* 5.6 12.0 - - + -
92B HIS* 6.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP* 3.5 57.7 + - + +
44B SER* 3.0 30.3 + - - +
45B ALA 3.6 2.5 - - - +
46B ILE 3.2 0.2 - - - -
47B GLN* 1.3 77.0 - - - +
49B PHE* 1.3 52.6 + - - +
51B GLU* 3.2 8.1 - - - +
52B GLN* 2.7 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.5 39.0 - - + -
29B TRP* 3.8 12.3 - - + +
30B LEU* 3.4 40.4 - - + -
33B ALA* 5.1 0.7 - - + -
45B ALA 2.9 13.8 + - - +
46B ILE* 3.0 10.3 + - - +
48B ASN* 1.3 74.9 - - - +
50B CYS* 1.3 68.7 + - - +
52B GLN* 3.0 8.6 + - - +
53B VAL* 3.0 30.9 + - + +
63B ALA* 3.8 29.2 - - + -
66B LEU* 5.0 0.4 - - + -
67B LEU* 4.4 6.1 - - + -
85B VAL* 3.7 23.8 - - + -
89B CYS* 3.7 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.0 18.2 + - - +
47B GLN* 4.3 2.9 - - - +
49B PHE* 1.3 75.3 - - - +
51B GLU* 1.3 67.3 + - - +
53B VAL* 2.9 25.8 - - - +
54B ASN* 3.1 13.8 + - - -
85B VAL* 4.0 6.1 - - - -
88B MET* 3.9 11.4 - - + -
89B CYS* 2.1 57.7 - - - -
92B HIS* 4.7 10.8 - - + -
93B CYS* 3.3 11.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN 2.9 20.8 + - - +
48B ASN* 3.2 11.2 - - - +
50B CYS* 1.3 78.3 - - - +
52B GLN* 1.3 57.2 + - - +
54B ASN* 2.9 20.4 + - - +
55B THR* 2.8 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.6 33.6 + - - +
26B LEU* 4.2 15.0 + - + +
29B TRP* 3.7 22.4 - - + +
48B ASN 2.7 20.7 + - - +
49B PHE* 3.1 11.0 - - - +
51B GLU* 1.3 73.3 - - - +
53B VAL* 1.3 65.3 + - - +
55B THR* 2.8 41.2 + - - +
56B ASP* 3.3 20.3 - - - +
59B GLY* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.8 2.2 - - + -
49B PHE* 3.0 34.2 + - + +
50B CYS* 2.9 19.9 + - - +
52B GLN* 1.3 76.3 - - - +
54B ASN* 1.3 56.4 + - - +
56B ASP 3.6 2.9 - - - +
59B GLY* 4.1 10.3 - - - +
60B PRO* 3.3 42.2 - - + +
63B ALA* 4.1 11.2 - - + -
89B CYS* 4.1 5.6 - - - -
93B CYS* 3.7 22.0 - - + -
97B PHE* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B CYS 3.1 19.1 + - - -
51B GLU* 2.9 21.7 + - - +
53B VAL* 1.3 76.9 - - - +
55B THR* 1.3 61.1 + - - +
56B ASP 3.3 8.1 + - - +
92B HIS* 3.3 21.4 + - - +
93B CYS* 3.2 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU* 2.8 28.7 + - - +
52B GLN* 2.8 21.6 + - - +
54B ASN* 1.3 75.3 - - - +
56B ASP* 1.3 65.5 + - - +
----------------------------------------------------------
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