Contacts of the helix formed by residues 39 - 50 (chain A) in PDB entry 3KHE
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 39 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.9 25.8 - - + +
35A THR 3.2 15.2 + - - +
36A LEU* 3.1 18.0 + - - +
37A GLU 3.1 0.2 - - - -
38A GLU* 1.3 80.1 - - + +
40A LYS* 1.3 64.3 + - - +
41A GLU 3.3 2.7 - - - -
42A LEU* 3.1 15.9 + - + +
43A THR* 2.9 21.4 + - - -
106A TYR* 3.3 18.4 + - - +
110A VAL* 4.0 22.9 - - + -
114A MET* 4.7 6.7 - - - -
122B ARG* 5.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 3.0 7.0 + - - +
37A GLU* 2.6 50.8 + - - +
38A GLU 3.4 1.0 - - - -
39A THR* 1.3 77.2 - - - +
41A GLU* 1.3 85.1 + - + +
43A THR* 3.3 6.0 + - - -
44A GLN* 3.2 20.1 + - - +
177B GLU* 3.5 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA* 6.3 1.8 - - + -
37A GLU 4.3 0.5 - - - +
38A GLU 3.6 18.5 - - - +
39A THR 4.2 0.3 - - - -
40A LYS* 1.3 99.5 + - + +
42A LEU* 1.3 67.5 + - + +
44A GLN* 3.3 8.6 + - - +
45A ILE* 3.1 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 4.8 2.7 - - + -
38A GLU 5.8 0.2 - - - +
39A THR* 3.1 16.5 + - + +
41A GLU* 1.3 76.9 - - + +
43A THR* 1.3 60.5 + - - +
45A ILE* 3.2 16.1 + - + +
46A PHE* 2.8 26.5 + - - +
106A TYR* 4.8 1.3 - - - -
109A PHE* 3.4 21.6 - - + -
110A VAL* 4.0 26.5 - - + +
113A CYS* 3.6 29.6 - - + +
114A MET* 3.7 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 5.0 1.0 + - - +
39A THR* 2.9 13.5 + - - -
40A LYS* 3.5 11.8 - - - -
41A GLU 3.3 0.2 - - - -
42A LEU* 1.3 76.0 - - - +
44A GLN* 1.3 57.9 + - - +
46A PHE* 3.4 1.6 + - - +
47A ARG* 2.9 35.7 + - - +
106A TYR* 2.6 36.1 + - + -
126B LEU* 3.8 20.2 - - + -
176B PHE* 3.7 31.9 - - + -
177B GLU* 4.5 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS 3.2 12.8 + - - +
41A GLU* 3.8 9.2 - - - +
42A LEU 3.3 0.4 - - - -
43A THR* 1.3 77.5 - - - +
45A ILE* 1.3 61.7 + - + +
47A ARG* 3.4 27.7 + - - +
48A GLN* 3.1 40.3 + - + +
137B SER 5.6 4.0 + - - -
138B GLY* 5.7 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA* 3.5 43.3 - - + +
5A LEU* 4.0 28.4 - - + +
8A ALA* 4.2 15.0 - - + -
41A GLU* 3.1 21.5 + - + +
42A LEU* 3.2 15.5 + - + +
44A GLN* 1.3 73.5 - - + +
46A PHE* 1.3 64.8 - - - +
48A GLN* 3.0 19.3 + - - +
49A LEU* 3.1 14.5 + - + +
109A PHE* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 2.8 17.0 + - - +
43A THR 3.6 4.3 - - - +
45A ILE* 1.3 77.5 - - - +
47A ARG* 1.3 57.1 + - - +
49A LEU* 3.1 7.4 + - - +
50A ASP* 2.8 51.1 + - + +
55A GLY* 3.7 17.7 - - - -
56A GLN* 3.7 7.4 - - - -
57A LEU* 3.7 22.4 - - + -
104A ILE 3.9 4.5 - - - -
105A GLU 4.0 1.3 - - - -
106A TYR* 3.5 39.0 - + + -
109A PHE* 3.6 38.1 - + + -
126B LEU* 3.6 24.9 - - + -
130B GLN* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 2.9 25.2 + - - +
44A GLN* 3.7 36.9 - - - +
45A ILE 3.3 0.2 - - - -
46A PHE* 1.3 76.7 - - - +
48A GLN* 1.3 78.1 + - - +
50A ASP* 3.4 4.1 + - - +
196A MG 2.8 23.3 - - - -
126B LEU* 3.6 31.2 - - + -
129B PHE* 4.3 20.7 - - - -
130B GLN* 3.6 24.1 - - + +
133B ASP* 3.9 4.4 + - - -
136B GLY* 3.6 15.0 + - - -
137B SER 4.4 0.4 - - - -
138B GLY* 3.4 37.4 + - - +
176B PHE* 5.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 5.6 8.3 - - + -
44A GLN* 3.1 29.2 + - + +
45A ILE* 3.0 12.0 + - + +
47A ARG* 1.3 99.9 + - - +
49A LEU* 1.3 63.9 + - + +
51A ASN* 4.9 3.3 + - - +
136B GLY 5.2 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.7 30.5 - - + -
9A LEU* 4.4 14.8 - - + -
12A MET* 4.8 1.6 - - + -
45A ILE* 3.1 12.9 + - + +
46A PHE* 3.1 5.4 + - - +
48A GLN* 1.3 79.1 - - - +
50A ASP* 1.3 58.0 + - - +
51A ASN* 2.8 11.3 + - - +
57A LEU* 3.5 35.7 - - + -
61A GLU* 3.7 27.3 - - - +
62A LEU* 4.9 3.4 - - + -
65A GLY* 3.9 25.6 - - - -
109A PHE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 2.8 32.9 + - + +
47A ARG 3.4 2.7 + - - -
49A LEU* 1.3 68.5 - - - +
51A ASN* 1.3 63.4 + - - +
52A ASN* 3.1 8.1 - - - +
53A GLY* 3.0 10.6 + - - -
54A ASP* 3.0 1.3 + - - +
55A GLY 2.9 18.7 + - - -
56A GLN 3.8 7.4 - - - -
57A LEU* 3.7 6.7 - - + -
61A GLU* 4.2 0.9 - - - -
195A CA 2.3 31.9 - - - -
196A MG 2.5 25.6 - - - -
130B GLN* 2.9 30.1 + - - +
----------------------------------------------------------
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