Contacts of the helix formed by residues 22 - 46 (chain A) in PDB entry 2KAD
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 SER 22 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 1.4 66.7 + - - +
24A ASP* 3.2 2.0 - - - -
25A PRO* 3.9 30.3 - - - +
26A LEU* 3.1 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 1.4 75.3 - - - +
24A ASP* 1.4 59.4 + - - +
26A LEU* 4.4 7.9 - - - +
27A VAL* 3.7 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.2 1.9 - - - -
23A SER* 1.4 76.0 - - - +
25A PRO* 1.3 76.3 - - + +
26A LEU 3.4 0.5 + - - -
27A VAL* 3.4 13.5 + - - +
28A VAL* 3.7 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.7 30.1 - - - +
24A ASP* 1.3 99.9 - - + +
26A LEU* 1.3 58.2 + - + +
28A VAL* 3.5 9.5 + - + +
29A ALA* 3.0 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.1 32.7 + - - +
23A SER* 4.6 7.2 - - - +
25A PRO* 1.3 75.3 - - + +
27A VAL* 1.4 64.2 + - + +
29A ALA* 3.2 10.2 + - + +
30A ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER 3.7 15.6 + - - +
24A ASP* 3.4 9.7 + - - +
25A PRO 3.4 0.8 - - - -
26A LEU* 1.4 76.4 - - + +
28A VAL* 1.4 63.7 + - + +
30A ALA* 3.5 7.2 + - - +
31A SER* 3.0 30.7 + - - +
28C VAL* 5.3 20.4 - - + -
31C SER* 5.8 9.2 - - - -
32C ILE* 5.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.7 12.4 + - - +
25A PRO* 3.5 11.1 + - + +
27A VAL* 1.4 77.4 - - + +
29A ALA* 1.4 63.7 + - - +
31A SER* 3.2 9.1 + - - +
32A ILE* 3.1 41.6 + - + +
27D VAL* 5.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO 3.0 13.8 + - - +
26A LEU* 3.2 17.0 + - + +
28A VAL* 1.4 75.7 - - - +
30A ALA* 1.3 60.6 + - - +
32A ILE* 3.5 13.8 + - - +
33A ILE* 3.3 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU 3.1 15.9 + - - +
27A VAL* 3.8 7.4 - - - +
29A ALA* 1.3 72.3 - - - +
31A SER* 1.3 59.6 + - - +
33A ILE* 3.4 6.9 + - - +
34A GLY 3.3 9.4 + - - -
32C ILE* 6.3 0.2 - - - -
35C ILE* 1.7 72.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 308 4.5 32.7 + - - +
27A VAL* 3.0 20.2 + - - +
28A VAL* 3.2 13.3 + - - +
30A ALA* 1.3 73.3 - - - +
32A ILE* 1.4 63.7 + - - +
34A GLY* 3.3 3.3 + - - -
35A ILE* 3.2 26.7 + - - +
31C SER* 6.0 0.9 - - - -
35C ILE* 3.2 4.9 - - - +
27D VAL* 5.8 8.3 - - - -
31D SER* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.1 35.1 + - + +
29A ALA* 3.7 11.2 - - - +
31A SER* 1.4 72.3 - - - +
33A ILE* 1.3 67.4 + - + +
35A ILE* 3.4 8.7 + - - +
36A LEU* 3.1 37.2 + - + +
27D VAL* 5.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 3.3 15.6 + - - +
30A ALA* 3.7 11.2 - - - +
31A SER 3.3 0.6 - - - -
32A ILE* 1.3 80.3 - - + +
34A GLY* 1.4 55.5 + - - +
36A LEU* 3.3 14.9 + - + +
37A HIS* 3.0 26.9 + - - +
35C ILE* 5.1 2.5 - - + -
38C LEU* 4.3 17.0 - - + -
39C ILE* 4.7 24.7 - - + +
42C ILE* 4.9 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 308 4.6 5.6 - - - -
30A ALA 3.3 11.8 + - - -
31A SER 3.3 4.9 + - - -
33A ILE* 1.4 75.5 - - - +
35A ILE* 1.3 59.5 + - - +
37A HIS 3.6 0.3 + - - -
38A LEU* 2.9 36.8 + - - +
38C LEU* 3.0 34.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 308 4.7 7.0 - - + -
31A SER* 3.2 14.9 + - - +
32A ILE* 3.7 9.9 - - - +
33A ILE 3.3 0.2 - - - -
34A GLY* 1.3 74.2 - - - +
36A LEU* 1.4 60.5 + - + +
38A LEU* 3.3 9.7 + - + +
39A ILE* 3.0 52.0 + - + +
30D ALA* 1.7 75.4 - - + +
31D SER* 3.2 4.9 - - - +
33D ILE* 4.8 4.0 - - + +
34D GLY* 4.2 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.1 32.0 + - + +
33A ILE* 3.3 14.8 + - + +
35A ILE* 1.4 75.7 - - + +
37A HIS* 1.4 61.7 + - - +
39A ILE* 3.5 18.4 + - + +
40A ALA* 3.2 22.5 + - - +
42C ILE* 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE 3.0 11.2 + - - +
36A LEU* 1.4 76.2 - - - +
38A LEU* 1.4 58.2 + - - +
40A ALA* 3.5 1.8 + - - -
41A TRP* 3.3 20.3 + - + +
37C HIS* 5.0 5.4 - + - -
38C LEU* 2.7 46.6 - - + +
41C TRP* 2.0 101.4 + + + -
42C ILE* 4.4 8.6 - - + +
37D HIS* 5.7 4.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 308 4.8 9.9 - - + -
34A GLY* 2.9 30.5 + - - +
35A ILE* 3.3 12.5 + - + +
37A HIS* 1.4 71.9 - - - +
39A ILE* 1.4 58.6 + - - +
41A TRP* 3.3 3.3 + - - +
42A ILE* 3.0 34.7 + - - +
38C LEU* 4.9 7.2 - - + -
33D ILE* 4.2 12.8 - - + -
34D GLY* 3.0 33.9 - - - +
37D HIS* 2.6 50.4 + - + +
38D LEU* 4.8 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.0 43.1 + - + +
36A LEU* 3.6 18.2 - - + +
38A LEU* 1.4 75.9 - - - +
40A ALA* 1.4 62.2 + - - +
42A ILE* 3.4 8.3 + - - +
43A LEU* 3.0 26.2 + - + +
33D ILE* 4.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 3.2 10.8 + - - +
37A HIS 3.7 8.7 - - - +
38A LEU 3.4 0.2 - - - -
39A ILE* 1.4 79.1 - - - +
41A TRP* 1.3 61.2 + - - +
43A LEU* 3.3 11.9 + - - +
44A ASP* 3.0 31.3 + - - +
41C TRP* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A HIS* 3.3 10.8 + - + +
38A LEU 3.5 3.6 - - - +
40A ALA* 1.3 77.1 - - - +
42A ILE* 1.4 89.6 + - + +
44A ASP* 3.2 12.7 + - + +
45A ARG* 3.0 72.9 + - + +
41C TRP* 4.7 16.5 - + + -
45C ARG* 5.7 4.5 - - - +
37D HIS* 2.0 73.4 + + + -
40D ALA* 3.9 18.2 - - + -
41D TRP* 4.9 14.6 - + + -
44D ASP* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 3.0 22.6 + - - +
39A ILE* 3.7 7.0 - - - +
41A TRP* 1.4 101.8 - - + +
43A LEU* 1.4 61.2 + - - +
45A ARG* 3.3 7.1 + - + +
46A LEU* 3.1 27.0 + - + +
33D ILE* 4.9 10.8 - - + +
36D LEU* 5.6 2.9 - - + -
37D HIS* 4.4 13.7 - - + +
40D ALA* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.0 16.8 + - + +
40A ALA* 3.3 12.8 + - - +
42A ILE* 1.4 75.2 - - - +
44A ASP* 1.3 62.6 + - - +
46A LEU* 3.3 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 3.0 27.1 + - - +
41A TRP* 3.2 12.5 + - + +
43A LEU* 1.3 78.1 - - - +
45A ARG* 1.3 61.3 + - + +
46A LEU* 3.5 5.2 + - - +
41C TRP* 5.3 1.4 - - - -
45C ARG* 4.4 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 3.0 65.3 + - + +
42A ILE* 3.3 11.4 + - + +
44A ASP* 1.3 76.1 - - + +
46A LEU* 1.3 60.8 + - - +
41D TRP* 5.8 4.6 - - - -
44D ASP* 4.3 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.1 20.6 + - + +
43A LEU* 3.3 31.1 - - + +
44A ASP 3.6 5.1 - - - +
45A ARG* 1.3 79.6 - - - +
----------------------------------------------------------
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