Contacts of the helix formed by residues 41 - 56 (chain A) in PDB entry 4KBQ
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 LYS 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.1 28.6 + - + +
39A GLY* 3.7 15.7 - - - +
40A ARG* 1.3 78.0 - - - +
42A TYR* 1.3 56.6 + - - +
43A PRO* 4.7 0.7 - - - -
44A GLU* 3.2 36.9 + - + +
45A ALA* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.5 52.1 + + - -
40A ARG* 3.2 43.4 + - + +
41A LYS* 1.3 68.8 - - - +
43A PRO* 1.3 78.1 - - + +
45A ALA* 3.2 5.6 + - - +
46A ALA* 2.9 23.4 + - - +
69A CYS* 4.1 9.7 - - + +
72A LYS* 3.7 43.5 + - + +
73A MET* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.7 0.7 - - - -
42A TYR* 1.3 94.6 - - + +
44A GLU* 1.3 75.9 + - + +
46A ALA* 3.2 5.6 + - + +
47A ALA* 3.2 21.1 + - - +
73A MET* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.7 25.9 - - + +
41A LYS* 3.2 48.9 + - + +
43A PRO* 1.3 88.2 - - + +
45A ALA* 1.3 62.0 + - - +
47A ALA* 3.4 15.4 + - - +
48A CYS* 3.4 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 3.3 22.8 - - - +
36A LEU* 3.6 15.2 - - + +
37A PHE* 3.7 11.4 - - - +
41A LYS 3.1 18.5 + - - +
42A TYR* 3.2 5.6 + - - +
44A GLU* 1.3 75.6 - - - +
46A ALA* 1.3 63.1 + - - +
48A CYS* 3.3 5.9 + - - +
49A TYR* 3.0 29.9 + - + -
69A CYS* 4.1 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR 2.9 12.5 + - - +
43A PRO* 3.5 11.4 - - + +
45A ALA* 1.3 73.3 - - - +
47A ALA* 1.3 66.9 + - - +
49A TYR* 3.1 12.8 + - - +
50A GLY* 3.0 18.9 + - - -
66A ARG* 3.7 25.6 - - + -
69A CYS* 4.0 12.1 - - + -
70A TYR* 4.8 13.5 - - + +
73A MET* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO 3.2 11.7 + - - +
44A GLU* 3.6 12.6 - - - +
45A ALA 3.3 0.4 - - - -
46A ALA* 1.3 75.1 - - - +
48A CYS* 1.3 63.7 + - - +
50A GLY* 3.3 2.8 + - - +
51A ARG* 3.1 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.7 17.4 - - - +
32A GLN* 3.5 43.3 - - - -
33A GLY* 3.5 18.8 - - - -
36A LEU* 3.8 12.6 - - - -
44A GLU 3.4 4.0 + - - +
45A ALA 3.3 11.1 + - - +
46A ALA 3.2 0.2 - - - -
47A ALA* 1.3 76.5 - - - +
49A TYR* 1.3 58.9 + - - +
51A ARG* 3.3 16.6 + - - +
52A ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS* 3.8 24.7 - - + -
33A GLY 3.4 7.4 + - - -
34A ASN* 2.3 44.4 + - - -
37A PHE* 4.1 0.2 - - - +
45A ALA* 3.0 28.7 + - + -
46A ALA* 3.1 7.9 + - - +
48A CYS* 1.3 77.3 - - - +
50A GLY* 1.3 57.6 + - - +
52A ALA* 3.4 4.9 + - + +
53A ILE* 2.9 34.4 + - - +
62A TYR* 4.0 11.9 - - + +
65A ASN* 3.5 28.9 - - + -
66A ARG* 3.8 22.9 - - + -
69A CYS* 3.7 26.5 - - - -
645C VAL* 3.3 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.0 11.9 + - - -
47A ALA* 3.3 4.4 + - - -
48A CYS 3.2 0.2 - - - -
49A TYR* 1.3 77.4 - - - +
51A ARG* 1.3 56.1 + - - +
53A ILE* 2.9 7.5 + - - +
54A THR* 2.8 30.5 + - - -
66A ARG* 3.6 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 5.1 10.5 - - - +
29A LEU* 3.9 40.8 - - + +
32A GLN* 4.6 9.3 + - - +
47A ALA* 3.1 21.9 + - - +
48A CYS* 3.6 14.1 - - - +
50A GLY* 1.3 75.5 - - - +
52A ALA* 1.3 63.1 + - - +
54A THR* 3.3 10.9 + - - +
55A ARG* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.6 26.2 - - - +
29A LEU* 3.9 13.1 - - + +
30A LYS* 4.3 6.3 - - - +
48A CYS 3.0 13.9 + - - +
49A TYR* 3.5 11.7 - - + +
51A ARG* 1.3 77.4 - - - +
53A ILE* 1.3 60.7 + - - +
55A ARG* 3.4 1.5 + - - +
56A ASN 3.1 18.2 + - - -
62A TYR* 3.4 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR 2.9 19.1 + - - +
50A GLY* 2.9 11.0 + - - +
52A ALA* 1.3 76.8 - - - +
54A THR* 1.3 59.5 + - - +
56A ASN 3.0 6.0 - - - +
57A PRO* 2.9 37.9 - - + +
62A TYR* 3.6 28.7 - - + +
63A TYR* 3.3 53.6 - - + +
66A ARG* 3.6 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY 2.8 14.3 + - - -
51A ARG* 3.4 12.8 - - - +
53A ILE* 1.3 79.6 - - - +
55A ARG* 1.3 64.4 + - + +
57A PRO* 4.1 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO 3.5 16.7 + - - -
25A SER* 3.5 22.4 - - - +
26A ALA* 3.1 38.7 - - + +
29A LEU* 5.7 3.1 - - + -
51A ARG 3.2 11.4 + - - +
52A ALA 3.4 3.6 + - - +
53A ILE 3.3 0.4 - - - -
54A THR* 1.3 82.1 - - + +
56A ASN* 1.3 64.1 + - - +
57A PRO* 4.1 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 4.1 16.1 - - + +
52A ALA 3.1 11.4 + - - +
53A ILE* 3.0 5.2 - - - +
55A ARG* 1.3 83.5 - - - +
57A PRO* 1.3 64.5 - - - +
58A LEU* 3.1 22.3 + - - +
59A VAL* 3.5 30.3 - - + +
62A TYR* 3.8 7.6 - - - -
608C THR* 3.7 17.0 - - - +
612C GLN* 4.2 7.4 + - - +
----------------------------------------------------------
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