Contacts of the helix formed by residues 19 - 29 (chain D) in PDB entry 1EFU
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 MET 19 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA 4.1 7.9 - - - +
108C THR 4.0 4.5 - - - +
109C ASP 2.9 22.0 + - - +
140C VAL* 5.7 0.2 - - + -
145C LEU* 4.1 22.2 - - + -
148C LEU* 3.6 42.8 - - + -
149C VAL* 3.8 20.2 - - + +
152C GLU* 3.5 11.2 - - - +
8D VAL* 3.7 18.9 - - - +
9D LYS* 5.4 1.6 - - + -
12D ARG* 3.3 42.3 - - - +
17D ALA 3.8 1.4 + - - -
18D GLY* 1.3 70.4 - - - +
20D MET* 1.3 59.1 + - + +
22D CYS* 3.3 5.5 + - - +
23D LYS* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA 4.7 1.1 - - - +
108C THR* 3.0 45.0 + - + +
139C MET 3.6 20.0 - - - +
140C VAL* 3.9 17.3 - - + -
141C ASP* 3.3 36.1 - - - +
145C LEU* 3.8 20.0 - - - -
19D MET* 1.3 75.3 - - + +
21D ASP* 1.3 62.5 + - - +
23D LYS* 3.5 2.1 - - + +
24D LYS* 2.9 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C THR 4.5 0.6 + - - -
109C ASP* 4.7 9.1 - - - +
17D ALA* 4.6 7.6 - - + +
18D GLY* 2.9 23.8 + - - +
20D MET* 1.3 78.3 - - - +
22D CYS* 1.3 58.2 + - - +
24D LYS* 4.0 4.9 - - - +
25D ALA* 3.1 28.9 + - - +
40D MET* 4.0 7.1 - - - +
47D LYS* 3.0 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.1 14.1 - - + +
11D LEU* 3.4 23.6 - - + +
12D ARG* 3.5 33.2 - - + -
15D THR* 3.5 13.9 - - - -
17D ALA* 3.6 16.6 - - - -
18D GLY 2.8 14.3 + - - -
19D MET 3.5 8.5 - - - +
21D ASP* 1.3 75.3 - - - +
23D LYS* 1.3 66.3 + - - +
25D ALA 3.2 1.6 + - - -
26D LEU* 3.0 22.5 + - - +
40D MET* 4.0 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASP* 3.0 40.3 + - - +
142C ASP* 4.3 6.7 + - - +
145C LEU* 4.0 16.5 - - + +
3D ILE* 3.8 22.1 + - + +
8D VAL* 3.8 29.1 - - + +
19D MET 3.0 14.3 + - - +
20D MET* 3.5 12.8 - - + +
22D CYS* 1.3 76.5 - - - +
24D LYS* 1.3 84.4 + - - +
26D LEU* 3.3 3.3 + - - +
27D THR* 3.1 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASP* 3.0 24.8 + - - +
20D MET* 2.9 34.7 + - + +
21D ASP* 4.2 4.5 - - - +
23D LYS* 1.3 96.8 - - - +
25D ALA* 1.3 65.2 + - - +
27D THR* 3.2 32.7 + - + +
28D GLU* 3.2 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 4.4 0.2 - - + -
21D ASP 3.1 19.7 + - - +
22D CYS 3.2 4.7 + - - +
24D LYS* 1.3 76.6 - - - +
26D LEU* 1.3 58.5 + - - +
28D GLU* 3.3 7.8 + - - +
29D ALA* 2.9 28.2 + - - +
36D ALA* 4.1 15.4 - - + +
39D ASN* 4.7 5.9 - - + +
40D MET* 3.5 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ILE* 3.4 32.7 - - + +
7D LEU* 3.8 25.1 - - + +
8D VAL* 3.6 33.0 - - + +
11D LEU* 3.5 20.2 - - + -
22D CYS 3.0 9.7 + - - +
23D LYS 3.5 7.0 - - - +
24D LYS 3.2 0.2 - - - -
25D ALA* 1.3 74.2 - - - +
27D THR* 1.3 55.9 + - - +
29D ALA* 4.3 2.9 - - - +
30D ASN* 2.7 29.6 + - - -
31D GLY 2.9 26.1 + - - +
33D ILE* 4.0 21.1 - - + -
36D ALA* 4.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ILE* 4.2 10.4 - - - +
23D LYS* 3.1 21.7 + - - +
24D LYS* 3.2 34.4 + - + +
26D LEU* 1.3 76.9 - - - +
28D GLU* 1.3 63.7 + - + +
30D ASN* 3.3 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LYS 3.2 10.1 + - - +
25D ALA* 3.6 9.0 - - - +
27D THR* 1.3 79.2 - - + +
29D ALA* 1.3 58.2 + - - +
30D ASN* 2.9 13.2 + - - +
35D LEU* 5.0 2.5 - - - +
39D ASN* 4.6 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA 2.9 17.9 + - - +
26D LEU* 4.0 3.8 - - - +
28D GLU* 1.3 74.2 - - - +
30D ASN* 1.3 67.9 + - - +
32D ASP* 3.1 42.0 + - - +
35D LEU* 3.8 23.3 - - + +
36D ALA* 3.5 18.6 - - + +
39D ASN* 4.6 2.2 + - - +
----------------------------------------------------------
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