Contacts of the helix formed by residues 37 - 51 (chain D) in PDB entry 5X11
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 37 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D THR* 5.0 2.0 - - - -
27D LYS* 5.7 11.2 - - - +
35D SER* 5.9 5.5 - - - -
36D ALA* 1.3 76.3 - - - +
38D HIS* 1.3 68.2 + - - +
39D SER* 3.1 15.3 - - - +
40D GLN* 3.0 18.9 + - + +
41D ILE* 3.1 17.2 + - - +
3J A 4.1 36.3 + - + +
4J A 4.0 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TYR* 6.4 0.7 - - + -
23D THR* 3.7 32.9 - - + +
37D LYS* 1.3 75.6 - - - +
39D SER* 1.3 68.6 + - - +
41D ILE* 3.7 3.4 - - - -
42D TYR* 3.2 46.7 + + + +
22I T 3.7 22.6 + - + +
23I G 2.7 50.2 + - - -
24I A 4.1 1.2 + - - -
5J T 4.6 15.9 - - + -
6J C 4.8 4.5 - - - -
7J A 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LYS* 3.1 8.8 - - - +
38D HIS* 1.3 84.9 + - - +
40D GLN* 1.3 58.1 + - - +
42D TYR* 5.4 0.2 - - - -
43D PRO* 3.3 20.8 - - - +
23I G 5.4 0.7 - - - -
24I A 3.0 35.0 + - - +
25I T 4.8 5.2 - - - +
3J A 3.7 15.2 + - - -
4J A 3.2 28.4 + - - -
5J T 3.7 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.9 26.4 - - + +
35D SER 5.0 0.9 - - - +
36D ALA* 4.3 13.5 - - + +
37D LYS* 3.0 13.2 + - + +
39D SER* 1.3 82.8 + - - +
41D ILE* 1.3 63.6 + - - +
42D TYR 3.5 0.4 - - - -
43D PRO* 3.6 4.0 - - - +
44D GLU* 3.3 22.3 + - - +
1J G 3.3 33.7 + - - -
2J T 3.3 44.5 + - + +
3J A 4.3 7.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 4.4 6.7 - - + -
8D ILE* 4.3 5.2 - - + -
19D GLY* 4.2 10.5 - - - +
22D ILE* 3.7 22.2 - - + -
23D THR* 3.5 19.3 - - - +
26D PHE* 3.5 31.9 - - + -
36D ALA* 3.8 20.0 - - + +
37D LYS 3.1 16.0 + - - +
38D HIS* 3.3 5.8 + - - +
40D GLN* 1.3 75.9 - - - +
42D TYR* 1.3 61.1 + - + +
44D GLU* 3.1 6.5 + - - +
45D LEU* 2.8 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLY* 3.7 23.7 - - - -
20D TYR* 3.5 10.7 + - - -
23D THR* 5.2 0.4 - - - -
38D HIS* 3.2 41.5 + + + +
39D SER* 5.8 0.2 - - - -
41D ILE* 1.3 76.7 - - + +
43D PRO* 1.3 69.7 - - + +
45D LEU* 3.2 15.9 + - + +
46D LYS* 3.2 18.9 + - - +
70D TYR* 5.4 0.8 + + - -
21I A 4.0 2.1 - - - +
22I T 2.6 70.1 + + + +
23I G 3.3 55.2 + + + +
24I A 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D SER* 3.3 26.2 - - - +
40D GLN* 3.6 7.9 - - - +
42D TYR* 1.3 92.8 - - + +
44D GLU* 1.3 59.1 + - - +
46D LYS* 3.2 10.1 + - + +
47D LYS* 3.0 23.1 + - - +
24I A 4.5 25.8 - - + +
25I T 5.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ARG* 4.7 8.5 - - - +
4D LEU* 3.7 21.4 - - + +
5D LYS* 3.3 30.4 - - - +
8D ILE* 3.7 20.4 - - + -
40D GLN 3.3 16.4 + - - +
41D ILE 3.1 5.4 + - - +
43D PRO* 1.3 75.8 - - - +
45D LEU* 1.3 67.2 + - - +
47D LYS* 3.8 19.6 - - - +
48D LEU* 3.0 41.7 + - + +
51D GLU* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 3.8 29.8 - - + -
12D LEU* 5.2 0.2 - - + -
19D GLY* 3.5 32.1 - - - +
22D ILE* 4.1 7.6 - - + -
41D ILE* 2.8 28.3 + - + +
42D TYR* 3.2 17.0 + - + +
44D GLU* 1.3 77.5 - - - +
46D LYS* 1.3 54.7 + - - +
48D LEU* 3.6 0.4 + - - -
49D THR* 2.7 34.8 + - - -
54D ILE* 3.7 20.1 - - + +
70D TYR* 3.5 37.0 - - + +
23I G 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR 3.2 10.2 + - - +
43D PRO* 3.2 12.6 + - + +
44D GLU 3.2 0.4 - - - -
45D LEU* 1.3 76.9 - - - +
47D LYS* 1.3 58.5 + - - +
49D THR* 3.2 8.6 + - + -
50D ASP* 2.9 47.4 + - - +
70D TYR* 4.7 3.1 + - - -
24I A 5.8 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PRO 3.0 15.3 + - - +
44D GLU* 3.2 21.7 + - - +
46D LYS* 1.3 78.8 - - - +
48D LEU* 1.3 56.6 + - - +
50D ASP* 3.3 10.3 + - + +
51D GLU* 2.9 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LYS* 3.3 44.6 - - + +
8D ILE* 3.8 31.2 - - + -
9D LEU* 4.1 9.6 - - + -
44D GLU* 3.0 32.3 + - + +
47D LYS* 1.3 77.3 - - - +
49D THR* 1.3 59.9 + - - +
51D GLU* 3.6 15.8 + - - +
52D GLY 3.3 2.9 + - - -
53D PHE* 3.0 45.7 + - + -
54D ILE* 3.4 19.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LEU 2.7 19.0 + - - -
46D LYS* 3.4 12.7 - - - -
47D LYS 3.2 0.2 - - - -
48D LEU* 1.3 77.3 - - - +
50D ASP* 1.3 64.7 + - - +
52D GLY* 3.3 12.8 + - - -
54D ILE* 3.5 21.0 - - - +
55D THR* 4.8 4.0 - - - +
56D PHE* 3.9 25.4 - - + -
70D TYR* 3.3 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LYS* 2.9 41.9 + - - +
47D LYS* 3.5 11.9 - - + +
49D THR* 1.3 78.3 - - - +
51D GLU* 1.3 62.6 + - + +
52D GLY 3.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LYS* 5.1 4.1 + - - +
44D GLU* 5.2 0.7 - - - +
47D LYS* 2.9 55.6 + - + +
48D LEU* 3.6 19.5 + - - +
49D THR 3.3 0.4 - - - -
50D ASP* 1.3 77.2 - - + +
52D GLY* 1.3 59.9 + - - +
53D PHE* 3.4 32.5 + - + -
75D SER* 4.9 1.2 + - - -
----------------------------------------------------------
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