Contacts of the helix formed by residues 37 - 45 (chain R) in PDB entry 4M8B
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 TYR 37 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1R SER* 4.8 8.5 - - - +
34R ARG* 3.4 44.4 + - - -
35R ARG 4.1 4.5 - - - -
36R PRO* 1.3 76.5 - - - +
38R ASP* 1.3 69.6 + - - +
39R ALA* 3.2 5.2 - - + +
40R GLU* 2.8 38.3 + - + +
41R LYS* 3.0 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B G 4.3 15.5 + - - -
36R PRO 5.2 0.2 - - - +
37R TYR* 1.3 75.6 - - - +
39R ALA* 1.3 60.7 + - - +
41R LYS* 3.4 33.5 + - - +
42R VAL* 3.9 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1R SER* 4.8 15.4 + - - +
37R TYR* 3.2 3.6 - - + +
38R ASP* 1.3 77.0 - - - +
40R GLU* 1.3 63.6 + - - +
41R LYS 3.6 0.2 + - - -
42R VAL* 3.8 18.3 + - - +
43R GLU* 4.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1R SER* 3.3 46.8 - - - +
3R PRO* 3.9 16.1 - - - +
34R ARG* 2.6 39.4 + - - -
36R PRO* 3.2 10.3 - - + +
37R TYR* 2.8 38.0 + - + +
39R ALA* 1.3 77.8 - - + +
41R LYS* 1.3 63.1 + - - +
43R GLU* 3.3 15.4 + - - +
44R LEU* 3.3 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B C 3.0 35.6 + - - -
17B G 5.5 3.0 + - - -
35R ARG* 4.9 2.0 - - - -
36R PRO* 3.8 25.4 - - + -
37R TYR 3.0 16.2 + - - +
38R ASP* 3.5 25.7 + - - +
39R ALA 3.3 0.6 - - - -
40R GLU* 1.3 77.8 - - - +
42R VAL* 1.3 63.4 + - + +
44R LEU* 3.2 26.5 + - + +
45R VAL* 4.2 0.3 + - - +
64R THR* 3.5 31.1 + - - +
65R ASP* 3.5 24.3 - - - +
66R GLY* 4.2 7.2 - - - +
67R PHE* 3.9 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ASP 3.9 15.3 - - - +
39R ALA* 4.0 12.8 - - - +
40R GLU 3.3 0.6 - - - -
41R LYS* 1.3 77.8 - - + +
43R GLU* 1.3 67.1 + - + +
44R LEU 3.6 0.3 + - - -
45R VAL* 4.0 15.1 + - - +
46R ASN* 5.0 2.4 - - - +
67R PHE* 4.2 18.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1R SER 5.3 11.2 - - - +
39R ALA 4.2 12.8 - - - +
40R GLU* 3.3 9.8 + - - +
41R LYS 3.2 0.8 - - - -
42R VAL* 1.3 81.5 - - + +
44R LEU* 1.3 64.8 + - + +
45R VAL 3.1 3.8 + - - -
46R ASN* 3.3 30.7 + - - +
49R ASN* 3.6 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R PRO 5.2 9.0 - - - +
4R GLY* 6.1 0.7 - - - -
32R ILE* 6.1 0.7 - - + -
36R PRO* 3.8 22.0 - - + -
40R GLU* 3.3 15.5 - - + +
41R LYS* 3.2 26.9 + - + +
43R GLU* 1.3 80.2 - - - +
45R VAL* 1.3 61.8 + - + +
46R ASN 3.0 2.3 + - - -
49R ASN* 2.9 21.9 + - - +
51R PHE* 3.4 40.3 - - + -
63R TRP* 3.5 25.6 - - + -
64R THR 4.7 0.7 - - - +
65R ASP* 4.4 12.8 - - + -
143R TYR* 3.8 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R VAL 4.1 7.2 - - - +
43R GLU 3.1 2.2 - - - -
44R LEU* 1.3 76.0 - - + +
46R ASN* 1.3 65.1 + - - +
47R PRO* 3.6 1.9 - - - +
65R ASP* 4.2 7.2 - - + +
67R PHE* 3.6 47.1 - - + -
69R TRP* 4.3 1.6 - - + -
116R LEU* 3.7 35.2 - - + +
143R TYR* 3.2 39.5 - - + +
----------------------------------------------------------
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