Contacts of the helix formed by residues 44 - 57 (chain E) in PDB entry 4XUJ
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 GLY 44 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E PRO* 1.3 72.1 - - - +
45E THR* 1.3 58.9 + - - +
47E ALA* 3.7 13.0 - - - +
48E LEU* 3.4 34.8 + - - +
44F LYS* 3.8 20.2 - - - -
8I A 3.3 7.6 + - - -
9I A 3.0 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PRO* 5.6 6.9 - - - +
41E TYR* 3.8 20.4 - - + -
42E ARG* 3.2 13.8 + - - +
43E PRO 3.5 0.5 + - - -
44E GLY* 1.3 76.6 - - - +
46E VAL* 1.3 64.1 + - - +
47E ALA 3.2 0.9 - - - -
48E LEU* 3.7 6.1 + - - +
49E ARG* 3.2 25.3 + - - +
69J T 3.9 21.1 - - - +
70J G 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TYR* 4.0 17.5 - - + -
45E THR* 1.3 74.3 - - - +
47E ALA* 1.3 55.2 + - - +
49E ARG* 3.0 31.9 + - - +
50E GLU* 2.7 55.2 + - + +
9I A 2.9 24.5 + - + +
10I C 3.6 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLY* 3.7 19.1 - - - +
46E VAL* 1.3 77.3 - - - +
48E LEU* 1.3 56.9 + - - +
50E GLU* 3.1 7.1 + - - +
51E ILE* 2.9 32.0 + - - +
39F ARG* 3.5 25.0 - - - +
44F LYS* 3.7 29.2 - - + +
8I A 4.8 2.5 - - - +
9I A 3.3 8.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
111C ILE* 3.8 39.0 - - + -
115C LEU* 3.4 29.4 - - + +
116C LEU* 4.5 2.5 - - + -
117C PRO* 4.1 25.4 - - + -
44E GLY 3.4 19.3 + - - +
45E THR* 4.2 5.2 - - - +
46E VAL 3.4 0.2 - - - -
47E ALA* 1.3 75.7 - - - +
49E ARG* 1.3 65.3 + - - +
51E ILE* 3.8 14.1 - - + +
52E ARG* 3.1 46.9 + - - +
44F LYS* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TYR* 3.4 45.5 - - - -
45E THR* 3.2 17.3 + - - +
46E VAL* 3.0 33.7 + - - +
48E LEU* 1.3 77.1 - - - +
50E GLU* 1.3 63.3 + - - +
52E ARG* 3.2 13.3 + - - +
53E ARG* 3.0 25.0 + - + +
-66I A 3.4 34.6 + - - -
-65I T 3.3 27.4 + - - +
69J T 5.6 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E VAL* 2.7 37.4 + - + +
47E ALA 3.3 8.1 - - - +
49E ARG* 1.3 75.6 - - + +
51E ILE* 1.3 56.8 + - - +
53E ARG* 3.1 12.0 + - - +
54E TYR* 2.9 55.2 + - + +
35F ARG* 3.8 14.0 - - - -
36F ARG* 5.6 1.4 + - - +
39F ARG* 2.8 41.3 + - - +
9I A 4.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 3.7 18.2 - - + -
115C LEU* 5.0 2.2 - - + -
47E ALA 2.9 20.2 + - - +
48E LEU* 3.9 24.7 - - + +
49E ARG 3.3 0.2 - - - -
50E GLU* 1.3 74.6 - - - +
52E ARG* 1.3 62.9 + - - +
55E GLN* 3.1 45.7 + - - +
39F ARG* 3.3 36.3 - - - +
42F GLY* 3.8 13.5 - - - +
43F VAL 3.7 24.5 - - - +
44F LYS* 4.2 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 3.6 23.5 - - + +
116C LEU* 4.3 19.4 - - - +
117C PRO* 5.4 4.6 - - - +
48E LEU* 3.1 39.2 + - - +
49E ARG* 3.5 11.8 - - - +
51E ILE* 1.3 77.3 - - - +
53E ARG* 1.3 61.8 + - - +
55E GLN* 4.4 3.5 - - - +
56E LYS* 3.4 26.6 + - + +
-65I T 5.9 2.5 - - - -
69J T 5.3 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ARG* 3.0 15.1 + - + +
50E GLU* 3.1 14.5 + - - +
52E ARG* 1.3 77.0 - - - +
54E TYR* 1.3 97.1 + - + +
56E LYS* 3.1 25.0 - - - +
57E SER* 3.2 12.8 + - - +
59E GLU* 5.4 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E GLU* 2.9 53.0 + - + +
51E ILE 4.5 0.7 - - - +
53E ARG* 1.3 114.1 + - + +
55E GLN* 1.3 59.7 + - - +
56E LYS 3.1 1.6 - - - -
57E SER* 3.1 16.0 - - - +
59E GLU* 4.3 7.2 - - - -
61E LEU* 3.7 20.4 - - + -
36F ARG* 3.3 43.6 + - + +
39F ARG* 3.8 12.1 - - + -
40F ARG* 2.7 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 3.2 19.2 + - - -
107C VAL* 3.2 27.0 - - + +
108C LEU 4.1 4.6 + - - -
109C PRO* 3.4 18.4 - - + +
110C ASN* 2.8 49.9 + - - +
111C ILE* 4.0 4.0 - - - +
51E ILE* 3.1 29.8 + - - +
52E ARG* 4.5 3.3 - - - +
54E TYR* 1.3 75.4 - - - +
56E LYS* 1.3 57.4 + - - +
57E SER 4.2 1.5 - - - +
105E GLU* 6.0 1.0 - - - +
39F ARG 4.1 4.5 - - - +
40F ARG 3.4 26.4 + - - +
41F GLY 4.3 2.0 + - - -
42F GLY* 3.9 12.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 2.9 28.1 + - - +
109C PRO* 5.3 5.1 - - + +
52E ARG 3.4 16.9 + - - +
53E ARG* 3.1 14.1 - - - +
55E GLN* 1.3 79.4 - - - +
57E SER* 1.3 60.3 + - - +
58E THR* 4.5 0.2 - - - +
-64I C 3.8 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLY* 4.5 4.7 - - - -
53E ARG* 3.2 14.7 + - - +
54E TYR* 3.1 10.6 + - - +
55E GLN 4.2 2.9 - - - +
56E LYS* 1.3 81.8 - - - +
58E THR* 1.3 63.6 + - - +
59E GLU* 2.9 27.5 + - - -
40F ARG* 2.8 36.9 + - - -
----------------------------------------------------------
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