Contacts of the helix formed by residues 13 - 24 (chain B) in PDB entry 2EZT
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 ALA 13 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE 3.5 1.0 + - - -
12B LEU* 1.3 71.8 - - - +
14B GLY* 1.3 57.1 + - - +
16B ALA* 3.3 3.6 + - - +
17B VAL* 3.0 32.9 + - - +
143B ALA* 3.6 29.4 - - + +
146B LEU* 4.4 6.5 - - + -
147B PRO* 4.4 1.3 - - + +
172B LEU 3.5 22.7 - - - +
173B PRO* 3.7 3.7 + - + -
175B GLN 2.9 14.1 + - - +
177B ILE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 1.3 77.3 - - - +
15B ALA* 1.3 60.4 + - - +
17B VAL* 3.2 9.8 + - - +
18B ILE* 3.2 19.6 + - - +
39B SER 4.9 0.2 - - - -
40B ILE* 4.6 3.3 - - - +
43B ALA* 3.4 21.2 - - - +
173B PRO* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.9 18.2 - - + -
12B LEU* 2.9 24.0 + - + +
14B GLY* 1.3 73.9 - - - +
16B ALA* 1.3 61.1 + - - +
18B ILE* 3.4 6.6 + - - +
19B LYS* 3.1 28.3 + - + +
43B ALA* 3.7 12.4 - - + +
47B GLU* 5.6 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.1 8.2 - - + +
12B LEU 3.1 10.3 + - - +
13B ALA 3.5 9.0 - - - +
15B ALA* 1.3 74.3 - - - +
17B VAL* 1.3 59.8 + - - +
19B LYS* 3.2 9.9 + - - +
20B VAL* 2.9 33.3 + - - +
147B PRO* 3.6 20.6 - - + -
177B ILE* 4.1 6.5 - - + -
182B TRP* 4.0 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 3.0 19.1 + - - +
14B GLY* 3.2 10.5 + - - +
16B ALA* 1.3 75.3 - - - +
18B ILE* 1.3 68.6 + - + +
20B VAL* 3.2 11.9 + - - +
21B LEU* 3.1 25.0 + - + +
40B ILE* 4.1 19.1 - - + -
107B LEU* 5.0 6.7 - - + -
146B LEU* 3.6 34.3 - - + -
147B PRO 4.3 7.9 - - - -
150B ILE* 3.9 30.1 - - + -
168B ILE* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY 3.2 15.2 + - - +
15B ALA* 3.4 6.7 + - - +
16B ALA 3.3 0.2 - - - -
17B VAL* 1.3 83.9 - - + +
19B LYS* 1.3 57.2 + - - +
21B LEU* 3.2 18.1 + - + +
22B GLU* 2.9 45.8 + - - +
40B ILE* 4.6 11.0 - - + +
43B ALA* 3.6 25.4 - - + -
44B LEU* 3.7 25.4 - - + +
47B GLU* 3.8 16.2 - - + -
51B ILE* 3.7 22.9 - - + -
107B LEU* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 5.0 7.9 - - + -
15B ALA* 3.1 17.6 + - - +
16B ALA 3.2 5.1 + - - +
18B ILE* 1.3 72.1 - - - +
20B VAL* 1.3 60.6 + - - +
22B GLU* 3.2 18.5 + - + +
23B ALA* 2.8 30.1 + - - +
47B GLU* 3.0 38.0 + - - -
50B ARG* 3.9 12.9 - - - +
182B TRP* 3.3 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA 2.9 18.6 + - - +
17B VAL* 3.2 9.4 + - - +
19B LYS* 1.3 73.6 - - - +
21B LEU* 1.3 64.9 + - - +
23B ALA* 3.2 2.4 + - - +
24B TRP* 3.2 34.9 + - + -
147B PRO* 3.9 27.6 - - + +
150B ILE* 4.1 4.3 - - + -
151B ASP* 3.9 34.8 - - + +
154B ILE* 4.0 7.2 - - + -
182B TRP* 3.9 15.5 - - + -
183B TYR 4.3 7.0 - - - +
184B ALA* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.1 20.2 + - + +
18B ILE* 3.2 26.7 + - + +
20B VAL* 1.3 75.6 - - - +
22B GLU* 1.3 62.8 + - - +
24B TRP* 3.3 2.8 + - - -
25B GLY 3.3 4.3 + - - -
26B VAL* 3.1 40.5 + - + +
29B LEU* 4.2 19.1 - - + -
51B ILE* 3.9 25.6 - - + -
78B VAL* 4.6 6.7 - - + -
105B LEU* 3.6 31.0 - - + -
107B LEU* 5.3 6.1 - - + -
150B ILE* 4.1 8.1 - - + -
154B ILE* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 2.9 31.1 + - + +
19B LYS* 3.2 26.2 + - + +
20B VAL 3.2 0.2 - - - -
21B LEU* 1.3 72.1 - - - +
23B ALA* 1.3 66.5 + - - +
25B GLY* 3.0 14.3 + - - +
26B VAL 4.8 5.4 - - - +
47B GLU* 2.6 34.8 - - - +
50B ARG* 3.3 33.8 + - + +
51B ILE* 3.9 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS 2.8 16.7 + - - +
20B VAL 3.2 1.5 + - - +
22B GLU* 1.3 76.8 - - - +
24B TRP* 1.3 56.6 + - - +
25B GLY* 3.4 3.3 + - - -
182B TRP* 5.9 0.9 - - + -
184B ALA* 3.4 32.8 - - + -
186B ALA* 3.2 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.2 26.9 + - + +
21B LEU 3.8 7.4 - - - +
22B GLU 3.2 0.6 - - - -
23B ALA* 1.3 74.1 - - - +
25B GLY* 1.3 60.5 + - - +
26B VAL* 3.3 8.6 + - + +
75B LYS* 4.4 8.5 + - - -
76B ILE* 5.2 2.3 - - + +
151B ASP* 2.8 21.8 + - - -
154B ILE* 3.5 35.0 - - + +
155B ARG* 4.1 28.5 - - + -
158B TYR* 3.6 41.4 + + - -
184B ALA* 4.4 2.0 - - + -
185B SER* 3.6 19.9 - - - +
186B ALA* 3.4 34.5 - - + +
189B TYR* 3.8 31.0 - + + -
----------------------------------------------------------
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