Contacts of the helix formed by residues 41 - 54 (chain A) in PDB entry 3DAG
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 HIS 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY 3.7 1.3 - - - -
10A CYS 3.3 15.4 - - - -
11A TYR* 3.3 49.7 + + + -
14A HIS* 4.3 0.6 + - - -
22A PHE* 4.2 2.2 - + + -
39A LEU 4.9 2.0 - - - -
40A THR* 1.3 77.3 - - - +
42A SER* 1.3 93.6 + - - +
44A ILE* 3.0 22.2 + - - +
45A THR* 3.3 6.6 + - - -
119A ILE 2.9 20.3 + - - -
120A HIS* 3.4 36.7 + + - -
121A LEU* 4.8 5.2 - - + -
207A GLU* 3.5 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA 4.0 5.4 - - - -
9A GLY* 4.2 2.0 - - - -
14A HIS* 3.1 21.0 + - - -
41A HIS* 1.3 98.0 + - - +
43A SER* 1.3 65.9 + - - -
45A THR* 3.2 15.0 + - - -
46A TYR* 3.3 7.8 + - - -
148A TRP* 3.4 26.0 + - - -
206A PRO* 3.4 26.4 - - - +
207A GLU* 3.0 12.1 + - - -
501A FEG 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.5 25.3 - - - +
7A GLY 2.6 29.6 + - - -
8A ALA* 3.3 13.2 + - - -
42A SER* 1.3 79.5 - - - +
44A ILE* 1.3 62.9 + - - +
45A THR 3.3 0.2 - - - -
46A TYR* 3.2 18.1 - - - +
47A GLY 3.0 21.0 + - - -
146A ILE* 5.7 0.2 - - - -
148A TRP* 3.8 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.7 13.5 - - + +
40A THR* 3.7 24.7 - - + -
41A HIS 3.0 8.8 + - - +
43A SER* 1.3 76.8 - - - +
45A THR* 1.3 59.6 + - - +
47A GLY* 3.2 0.5 + - - -
48A ALA* 2.8 29.1 + - - +
62A VAL* 4.0 31.2 - - + -
120A HIS* 3.5 29.8 - - + +
122A VAL* 5.2 3.4 - - + -
124A PRO* 3.6 30.1 - - + -
127A VAL* 4.0 7.6 - - + -
129A LEU* 3.9 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 4.6 12.1 - - + +
28A VAL* 5.6 0.7 - - + -
37A ILE* 5.8 1.8 - - + -
40A THR* 2.9 39.5 + - - +
41A HIS* 3.3 7.4 + - - -
42A SER 3.2 9.7 + - - -
44A ILE* 1.3 79.5 - - - +
46A TYR* 1.3 63.0 + - - +
48A ALA* 3.8 2.3 - - - +
49A GLU* 3.0 42.7 + - + +
206A PRO* 3.8 26.5 - - - +
207A GLU* 3.6 8.2 - - - +
235A ARG* 4.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.5 5.4 - - + -
42A SER 3.3 1.6 + - - -
43A SER* 3.2 23.3 + - - +
44A ILE 3.3 0.2 - - - -
45A THR* 1.3 79.1 - - - +
47A GLY* 1.3 56.6 + - - +
49A GLU* 3.4 5.8 + - - +
50A LEU* 3.0 41.1 + - + +
146A ILE* 3.9 17.3 - - + -
148A TRP* 3.7 24.0 - + - -
175A ALA* 5.3 0.2 - - + -
200A TYR* 2.9 49.0 + + - -
201A HIS 3.6 0.7 - - - -
202A PRO* 3.1 27.4 - - + +
206A PRO* 3.7 19.5 - - + -
212A VAL* 4.4 0.9 - - - +
235A ARG* 3.5 35.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.5 22.4 - - - -
43A SER 3.0 11.4 + - - -
44A ILE 3.2 2.4 + - - -
45A THR 3.2 0.2 - - - -
46A TYR* 1.3 72.3 - - - +
48A ALA* 1.3 65.6 + - - +
50A LEU* 3.3 4.2 + - - +
51A LEU* 3.0 26.9 + - - +
60A VAL* 4.0 10.2 - - - +
129A LEU* 3.6 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 5.2 1.1 - - - +
37A ILE* 3.9 37.5 - - + -
40A THR* 4.7 1.6 - - + -
44A ILE 2.8 20.9 + - - +
45A THR* 3.8 4.7 - - - +
47A GLY* 1.3 73.0 - - - +
49A GLU* 1.3 56.8 + - - +
52A HIS* 3.0 44.8 + - + +
127A VAL* 4.2 13.9 - - + -
129A LEU* 3.9 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.9 23.4 + - - +
28A VAL* 3.8 22.3 - - + +
37A ILE* 6.1 0.2 - - + -
45A THR* 3.0 23.7 + - + +
46A TYR* 3.6 12.0 - - - +
48A ALA* 1.3 75.0 - - + +
50A LEU* 1.3 59.2 + - - +
53A LEU* 2.8 42.0 + - + +
54A VAL* 3.8 0.9 + - - +
200A TYR* 5.1 0.3 + - - -
234A ALA* 3.0 30.1 - - + +
235A ARG* 2.7 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.9 28.9 - - + -
5A ILE* 4.8 1.6 - - + -
46A TYR* 3.0 29.0 + - + +
47A GLY* 3.8 6.5 - - - +
49A GLU* 1.3 74.6 - - - +
51A LEU* 1.3 62.6 + - - +
54A VAL* 3.2 30.9 + - + +
57A VAL* 3.3 12.6 - - + +
60A VAL* 4.3 3.6 - - + -
146A ILE* 3.5 31.4 - - + -
200A TYR* 4.0 10.1 - - + +
230A ILE* 3.4 33.2 - - + -
234A ALA* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY 3.0 16.4 + - - +
48A ALA 4.2 2.2 - - - +
50A LEU* 1.3 77.5 - - - +
52A HIS* 1.3 77.1 + - + +
54A VAL 4.1 4.7 - - - +
57A VAL* 3.8 27.6 - - - +
58A LYS 3.9 20.4 - - - +
59A GLU* 4.3 2.7 - - - +
60A VAL* 3.9 15.5 - - + +
127A VAL 4.1 1.1 - - - +
128A GLY* 3.3 39.3 - - - +
129A LEU* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 5.7 0.7 - - + -
32A VAL* 4.0 30.7 - - + +
34A LYS* 3.8 36.3 - - + +
37A ILE* 3.9 16.4 - - + +
48A ALA* 3.0 31.8 + - - +
51A LEU* 1.3 97.1 + - + +
53A LEU* 1.3 62.2 + - + +
54A VAL 3.6 0.7 - - - -
127A VAL 2.8 30.7 + - - -
128A GLY* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 3.8 11.0 - - - +
28A VAL* 4.4 10.1 - - + -
31A GLU* 4.1 20.0 - - + -
32A VAL* 3.6 26.5 - - + -
49A GLU* 2.8 26.6 + - + +
52A HIS* 1.3 78.1 - - + +
54A VAL* 1.3 59.1 + - - +
55A PRO* 3.5 8.9 - - - +
233A ILE* 3.3 34.8 - - + +
234A ALA* 3.3 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 6.1 0.4 - - + -
50A LEU* 3.2 29.1 + - + +
51A LEU 4.1 4.5 - - - +
52A HIS 5.3 0.4 - - - -
53A LEU* 1.3 79.0 - - - +
55A PRO* 1.3 74.3 - - + +
56A ASP* 4.3 9.4 - - + +
57A VAL* 3.1 30.6 + - + +
230A ILE* 4.2 22.4 - - + +
233A ILE* 3.9 20.2 - - + -
234A ALA* 3.8 28.7 - - + +
----------------------------------------------------------
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