Contacts of the helix formed by residues 30 - 44 (chain A) in PDB entry 2KT0
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 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 1.3 74.9 - - - +
31A SER* 1.3 67.8 + - - +
32A THR* 3.0 16.5 + - - -
33A GLN* 3.1 33.6 + - - +
34A LEU* 3.0 23.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
14A LYS* 2.9 45.3 + - - +
29A PHE 4.1 0.8 + - - -
30A SER* 1.3 75.5 + - - +
32A THR* 1.3 57.6 + - - +
34A LEU* 3.7 16.7 - - - +
35A CYS* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 3.0 9.3 + - - -
31A SER* 1.3 78.4 - - - +
33A GLN* 1.3 75.3 + - + +
35A CYS* 3.7 4.7 - - - +
36A VAL* 3.2 33.8 + - + +
59A LEU* 6.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL 5.4 1.0 + - - -
29A PHE* 4.4 17.5 - - + +
30A SER* 3.1 41.0 + - - +
32A THR* 1.3 81.4 - - - +
34A LEU* 1.3 60.2 + - - +
36A VAL* 3.1 7.8 + - - +
37A LEU* 2.8 44.8 + - + +
59A LEU* 3.5 37.0 - - + +
61A LEU* 5.8 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 6.0 6.1 - - + -
29A PHE* 4.1 27.4 - - + +
30A SER 3.0 22.1 + - - +
31A SER* 3.7 17.3 - - - +
33A GLN* 1.3 77.3 - - - +
35A CYS* 1.3 56.0 + - - +
37A LEU* 3.6 16.5 - - + +
38A ASN* 2.9 32.3 + - - +
69A TRP* 5.4 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN 4.5 5.8 - - - -
11A VAL* 4.4 9.0 - - - -
12A ALA* 3.5 38.3 - - - +
13A LYS 4.1 16.2 - - - +
14A LYS* 5.7 3.6 - - + -
31A SER 2.8 19.1 + - - +
32A THR* 3.7 5.6 - - - +
34A LEU* 1.3 76.2 - - - +
36A VAL* 1.3 59.0 + - + +
38A ASN* 3.4 4.7 + - - +
39A ASP* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 5.3 16.2 - - + -
32A THR* 3.2 21.7 + - + +
33A GLN* 3.1 9.1 + - - +
35A CYS* 1.3 74.7 - - + +
37A LEU* 1.3 61.8 + - + +
39A ASP* 4.4 4.0 - - - -
40A ARG* 2.9 50.5 + - + +
55A LEU* 4.7 19.1 - - + -
59A LEU* 5.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 5.6 6.3 - - + -
33A GLN* 2.8 38.4 + - + +
34A LEU* 3.6 14.8 - - + +
36A VAL* 1.3 76.8 - - + +
38A ASN* 1.3 57.1 + - - +
40A ARG* 3.9 4.3 - - - +
41A PHE* 2.9 41.0 + - + -
47A LEU* 5.0 4.3 - - + -
55A LEU* 3.5 36.3 - - + -
59A LEU* 6.0 1.3 - - + -
69A TRP* 3.6 46.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 6.2 0.8 - - - +
13A LYS* 4.2 22.4 + - - +
15A GLU* 3.6 34.6 + - + +
34A LEU 2.9 17.1 + - - +
35A CYS* 3.9 4.3 - - - +
37A LEU* 1.3 73.7 - - - +
39A ASP* 1.3 67.0 + - - +
41A PHE* 3.4 8.4 + - - +
42A GLN* 3.0 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 5.3 0.2 - - - +
9A ASN* 3.2 25.9 + - + +
12A ALA* 4.7 10.2 - - + +
35A CYS* 2.9 20.8 + - - +
36A VAL* 3.7 5.6 - - - +
38A ASN* 1.3 76.3 - - - +
40A ARG* 1.3 85.6 + - - +
42A GLN* 2.9 7.1 + - - +
43A ARG* 2.6 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 6.6 0.2 - - - -
4A PRO* 3.3 36.6 + - + +
6A SER 3.7 3.2 + - - -
7A ALA 2.7 28.9 + - - -
8A GLU* 3.6 24.3 - - - +
9A ASN* 4.0 1.8 - - - +
36A VAL* 2.9 35.7 + - + +
37A LEU* 3.9 4.3 - - - +
39A ASP* 1.3 105.2 + - - +
41A PHE* 1.3 59.4 + - + +
43A ARG* 4.4 9.4 - - - +
44A GLN* 2.8 55.3 + - - +
46A TYR 5.3 0.6 + - - +
47A LEU* 5.1 14.8 - - + -
55A LEU* 6.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.9 30.9 + - + +
38A ASN* 3.7 9.0 - - - +
39A ASP 3.2 0.2 - - - -
40A ARG* 1.3 76.8 - - - +
42A GLN* 1.3 66.7 + - - +
44A GLN 2.9 15.5 - - - +
45A LYS 3.8 7.3 - - - +
46A TYR* 3.9 25.6 - + + -
47A LEU* 3.7 47.6 - - + -
69A TRP* 3.8 28.3 - + - -
70A PHE* 3.8 21.3 - + - -
73A GLN* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 6.0 5.3 - - - +
38A ASN* 3.0 34.2 + - - +
39A ASP* 2.9 7.0 + - - +
41A PHE* 1.3 87.3 - - - +
43A ARG* 1.3 71.6 + - - +
44A GLN 3.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 6.1 2.5 - - - +
9A ASN* 3.6 26.6 + - - +
12A ALA* 4.9 4.9 - - - +
39A ASP* 2.6 54.7 + - - +
40A ARG* 4.2 8.7 - - - +
42A GLN* 1.3 81.5 - - - +
44A GLN* 1.3 64.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
2A LYS* 3.5 43.6 + - + +
4A PRO* 3.9 9.0 - - - +
40A ARG* 2.8 40.3 + - - +
41A PHE 2.9 20.4 - - - +
42A GLN 3.8 2.6 - - - +
43A ARG* 1.3 84.5 - - + +
45A LYS* 1.3 63.2 + - - +
46A TYR 4.3 8.5 - - - +
47A LEU* 5.5 0.3 - - - +
51A GLN* 3.2 37.7 + - - +
----------------------------------------------------------
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