Contacts of the helix formed by residues 42 - 52 (chain R) in PDB entry 1MVW
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 THR 42 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788P THR* 2.8 36.5 - - + +
789P ALA* 4.1 5.2 - - - -
792P ALA* 2.7 34.5 - - + +
41R PRO* 1.3 75.4 - - - +
43R ASN* 1.3 59.6 + - - +
44R ALA* 3.9 1.4 + - - +
45R GLU* 3.0 41.2 + - - +
46R ILE* 3.1 11.3 + - - +
81R GLN* 4.5 6.5 - - - +
116R GLU* 3.7 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 43 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795P ARG* 1.7 69.2 + - - +
31R GLY* 5.5 2.8 - - - -
32R ASP* 5.5 3.0 + - - -
35R ARG* 3.6 18.6 - - - +
42R THR* 1.3 71.1 - - - +
44R ALA* 1.3 56.5 + - - +
46R ILE* 3.3 16.9 + - - +
47R ASN* 2.9 29.0 + - - +
116R GLU* 3.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788P THR* 5.2 7.0 - - + -
42R THR* 3.2 3.6 - - - +
43R ASN* 1.3 76.7 - - - +
45R GLU* 1.3 59.0 + - - +
47R ASN* 3.5 8.3 - - - +
48R LYS* 2.8 37.1 + - + +
116R GLU* 3.0 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R ASN 5.0 0.2 - - - +
41R PRO* 3.5 22.1 - - + +
42R THR* 3.0 36.6 + - - +
44R ALA* 1.3 78.6 - - - +
46R ILE* 1.3 60.2 + - - +
48R LYS* 3.9 4.6 - - - +
49R ILE* 2.8 51.0 + - + +
75R ALA* 5.0 0.7 - - - -
78R ASN* 2.9 37.2 + - - +
81R GLN* 5.2 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R VAL* 5.0 6.1 - - + -
31R GLY* 3.7 40.8 - - - +
34R ALA* 5.7 0.4 - - + -
35R ARG* 4.7 1.8 - - - +
41R PRO* 3.4 42.8 - - + +
42R THR 3.1 10.1 + - - +
43R ASN* 3.6 21.8 - - - +
45R GLU* 1.3 77.0 - - - +
47R ASN* 1.3 53.4 + - - +
49R ILE* 4.2 6.7 - - + +
50R LEU* 2.5 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R ASN 2.9 16.5 + - - +
44R ALA* 3.5 10.0 - - - +
46R ILE* 1.3 77.8 - - - +
48R LYS* 1.3 78.0 + - - +
50R LEU* 3.4 9.1 - - - +
51R GLY* 3.1 19.1 + - - -
57R GLU* 3.6 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R ALA* 2.8 21.9 + - + +
45R GLU* 3.9 6.7 - - - +
46R ILE 3.5 0.2 - - - -
47R ASN* 1.3 86.4 - - - +
49R ILE* 1.3 54.5 - - + +
51R GLY* 3.1 3.0 + - - -
52R ASN* 1.9 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R PRO* 6.1 1.1 - - + -
45R GLU* 2.8 41.2 + - + +
46R ILE* 4.2 7.4 - - + +
48R LYS* 1.3 77.8 - - + +
50R LEU* 1.3 55.5 - - + +
52R ASN* 2.3 14.3 - - + +
53R PRO* 1.6 48.4 - - + +
71R MET* 5.5 15.5 - - + +
74R ALA* 5.6 13.9 - - + -
75R ALA* 5.6 9.0 - - + -
78R ASN* 5.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R ALA* 4.9 15.5 - - + +
30R VAL* 5.5 6.5 - - + -
46R ILE* 2.5 42.0 - - + +
47R ASN* 3.4 6.1 - - - +
49R ILE* 1.3 79.5 - - + +
51R GLY* 1.3 56.6 + - - +
53R PRO* 2.6 23.9 - - - +
55R LYS* 2.9 37.9 + - + +
57R GLU* 0.9 51.8 - - + +
63R ILE* 6.4 1.1 - - + -
71R MET* 4.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R ASN 3.1 6.5 + - - -
48R LYS* 3.1 6.4 + - - -
50R LEU* 1.3 77.4 - - - +
52R ASN* 1.3 59.4 - - - +
54R SER* 2.7 24.8 + - - -
55R LYS 3.6 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R LYS* 1.9 67.1 + - - +
49R ILE* 2.3 14.9 - - + +
51R GLY* 1.3 72.4 - - - +
53R PRO* 1.3 63.8 - - + +
54R SER* 3.3 3.1 + - - -
----------------------------------------------------------
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