Contacts of the helix formed by residues 37 - 51 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E THR* 5.4 1.1 - - - -
35E SER* 5.6 5.1 + - - -
36E ALA* 1.3 75.5 - - - +
38E HIS* 1.3 70.4 + - - +
39E SER* 3.2 7.9 - - - +
40E GLN* 3.0 17.0 + - - +
41E ILE* 3.3 10.8 + - - +
17N T 4.0 34.4 + - + +
18N T 3.7 53.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E THR* 4.0 28.1 - - + +
36E ALA 4.0 0.6 + - - -
37E LYS* 1.3 76.7 - - + +
39E SER* 1.3 67.4 + - - +
40E GLN 3.1 1.6 + - - -
41E ILE* 3.1 12.9 + - - +
42E TYR* 3.2 35.6 + + + +
8M T 3.6 25.9 + + + -
9M G 2.7 48.1 + + - -
18N T 5.8 4.0 - - + -
19N A 4.5 10.7 + - - -
20N C 4.6 5.8 - - - -
21N A 4.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LYS* 4.1 1.9 - - - +
38E HIS* 1.3 84.3 + - - +
40E GLN* 1.3 57.4 + - - +
43E PRO* 3.3 20.7 - - - +
10M T 3.1 32.5 - - - +
11M A 4.1 7.3 + - - -
17N T 3.6 18.5 + - - +
18N T 2.6 35.6 + - - +
19N A 3.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LEU* 3.5 23.9 - - + +
36E ALA* 4.7 8.2 - - - +
37E LYS 3.0 13.0 + - - +
39E SER* 1.3 80.1 + - - +
41E ILE* 1.3 63.7 + - + +
42E TYR 3.7 0.4 - - - -
43E PRO* 3.7 5.1 - - - +
44E GLU* 3.3 22.3 + - - +
15N A 3.8 15.8 - - - +
16N T 3.1 51.8 + - + +
17N T 3.6 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LEU* 4.5 6.1 - - + -
8E ILE* 3.9 11.0 - - + -
19E GLY* 4.4 7.9 - - - +
22E ILE* 3.9 20.0 - - + -
23E THR* 3.9 18.8 - - - +
26E PHE* 3.6 25.8 - - + -
36E ALA* 3.4 35.2 - - + +
37E LYS 3.3 9.6 - - - +
38E HIS* 3.1 6.8 + - - +
40E GLN* 1.3 77.3 - - - +
42E TYR* 1.3 62.8 + - + +
44E GLU* 3.0 7.7 + - - +
45E LEU* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E GLY* 3.8 13.7 - - - -
20E TYR* 3.3 17.4 + - - +
23E THR* 4.8 3.4 - - - -
38E HIS* 3.2 32.3 + - + +
41E ILE* 1.3 80.6 - - + +
43E PRO* 1.4 67.9 - - + +
45E LEU* 3.5 16.8 + - + +
46E LYS* 3.5 18.2 + - - +
70E TYR* 5.5 1.1 + - - -
7M A 4.0 0.3 - - - +
8M T 2.6 86.2 + + + +
9M G 3.9 47.1 - + + +
10M T 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E SER 3.3 29.4 - - - +
40E GLN* 3.7 5.4 - - - +
41E ILE 3.6 2.5 - - - -
42E TYR* 1.4 94.6 - - + +
44E GLU* 1.3 60.5 + - - +
46E LYS* 3.4 8.0 + - + +
47E LYS* 3.2 21.2 + - - +
10M T 4.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ARG* 2.5 35.8 + - - -
4E LEU* 4.0 21.0 - - + +
5E LYS* 3.7 19.3 - - - +
8E ILE* 3.9 18.4 - - + -
40E GLN* 3.3 16.8 + - - +
41E ILE 3.0 6.3 + - - +
43E PRO* 1.3 78.4 - - - +
45E LEU* 1.3 56.5 + - - +
47E LYS* 3.3 12.5 + - - +
48E LEU* 2.8 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 3.9 13.0 - - + -
19E GLY* 3.8 22.9 - - - -
22E ILE* 3.9 17.9 - - + -
41E ILE* 2.9 29.2 + - + +
42E TYR* 3.8 18.2 - - + +
43E PRO 3.3 0.2 - - - -
44E GLU* 1.3 77.2 - - - +
46E LYS* 1.3 52.4 + - - +
48E LEU* 3.3 4.7 + - - +
49E THR* 2.7 37.2 + - - -
54E ILE* 3.7 20.5 - - + +
70E TYR* 3.6 49.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR 3.5 9.1 + - - +
43E PRO* 3.4 10.4 + - + +
44E GLU 3.3 0.2 - - - -
45E LEU* 1.3 75.1 - - - +
47E LYS* 1.3 66.5 + - - +
49E THR* 3.1 8.8 + - - -
50E ASP* 3.1 33.1 + - - +
70E TYR* 4.8 2.4 + - - -
9M G 6.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ARG* 3.7 35.2 - - - +
43E PRO 3.2 10.9 + - - +
44E GLU* 3.4 17.0 + - - +
46E LYS* 1.3 78.5 - - - +
48E LEU* 1.3 56.3 + - - +
50E ASP* 3.3 10.7 + - + +
51E GLU* 3.0 40.8 + - + +
14N T 5.6 3.8 + - - -
15N A 5.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E LYS* 3.6 35.4 - - + +
8E ILE* 4.0 31.0 - - + -
9E LEU* 4.5 9.6 - - + -
44E GLU* 2.8 39.0 + - + +
45E LEU* 3.6 0.7 - - - +
46E LYS 3.2 0.4 - - - -
47E LYS* 1.3 75.0 - - - +
49E THR* 1.3 62.0 + - - +
51E GLU* 3.6 11.9 + - - +
52E GLY 3.3 2.8 + - - -
53E PHE* 3.2 45.3 + - + -
54E ILE* 3.5 25.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LEU 2.7 22.1 + - - -
46E LYS* 3.1 10.3 + - - -
48E LEU* 1.3 75.8 - - - +
50E ASP* 1.3 66.4 + - - +
52E GLY* 3.3 12.6 + - - -
54E ILE* 3.6 19.9 - - - +
55E THR* 4.9 2.7 - - - -
56E PHE* 4.1 27.1 - - + -
70E TYR* 3.7 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LYS* 3.1 19.9 + - - +
47E LYS* 3.3 10.9 + - + +
49E THR* 1.3 80.2 - - - +
51E GLU* 1.3 60.2 + - + +
52E GLY* 3.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ARG* 2.8 39.4 + - - -
5E LYS* 5.6 0.2 + - - -
47E LYS* 3.0 28.9 + - + +
48E LEU* 3.6 15.6 + - - +
49E THR 3.3 0.2 - - - -
50E ASP* 1.3 76.5 - - + +
52E GLY* 1.3 60.9 + - - +
53E PHE* 3.3 36.9 + - + -
75E SER* 4.7 1.7 + - - -
----------------------------------------------------------
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