Contacts of the helix formed by residues 40 - 49 (chain A) in PDB entry 1Q0R
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 PRO 40 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.5 5.2 - - + +
38A GLY 3.3 10.3 - - - +
39A TRP* 1.3 83.6 - - - +
41A ASP* 1.3 66.9 + - - +
42A GLU 4.3 0.4 - - - +
43A PHE* 3.0 19.6 + - + +
44A ALA* 3.1 10.9 + - - +
201A TRP* 3.5 57.2 - - + +
278A LEU* 4.0 22.0 - - + +
283A HIS* 4.1 10.1 - - + +
2712A 1PE 3.9 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.8 8.8 - - + -
37A LEU* 3.6 10.4 - - - +
40A PRO* 1.3 70.7 - - - +
42A GLU* 1.3 59.4 + - - +
44A ALA* 3.2 3.5 + - - +
45A ARG* 2.9 62.6 + - - +
56A ARG* 2.9 37.0 + - - +
204A ARG* 3.7 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO 3.1 0.6 - - - -
41A ASP* 1.3 78.4 + - - +
43A PHE* 1.3 60.9 + - - +
45A ARG* 3.7 25.6 + - - +
46A ARG* 3.1 24.1 + - - +
201A TRP* 3.0 19.9 + - + -
204A ARG* 2.9 42.7 + - - -
280A SER* 6.2 1.1 - - - -
283A HIS* 4.2 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.4 4.3 - - + -
39A TRP* 3.8 38.4 - + + -
40A PRO* 3.0 18.0 + - + +
42A GLU* 1.3 76.4 - - - +
44A ALA* 1.3 68.2 + - - +
46A ARG* 3.2 4.5 + - + +
47A LEU* 3.1 52.4 + - + +
278A LEU* 5.2 3.8 - - + -
283A HIS* 3.7 51.9 + + + +
286A LEU* 3.9 28.3 - - + -
287A ALA* 4.2 5.2 - - + -
290A ILE* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.5 37.7 - - + -
28A LEU* 4.4 9.6 - - + -
39A TRP* 5.3 1.1 - - + -
40A PRO 3.1 8.7 + - - +
41A ASP 3.6 5.6 - - - +
43A PHE* 1.3 82.9 - - - +
45A ARG* 1.3 57.4 + - - +
47A LEU* 3.4 5.1 + - - +
48A ALA* 2.9 29.8 + - - +
54A VAL* 3.9 16.1 - - + +
56A ARG* 5.1 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.7 22.3 - - + -
41A ASP* 2.9 45.5 + - - +
42A GLU* 3.7 32.0 + - - +
44A ALA* 1.3 74.6 - - - +
46A ARG* 1.3 59.4 + - - +
48A ALA* 3.3 5.2 + - - -
49A ASP* 2.9 43.5 + - - +
204A ARG* 5.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU 3.1 13.0 + - - +
43A PHE* 3.5 11.0 - - + +
45A ARG* 1.3 79.4 - - - +
47A LEU* 1.3 64.0 + - - +
49A ASP* 3.6 10.6 + - - +
50A GLY 3.7 6.4 + - - -
280A SER 5.4 1.8 + - - -
283A HIS* 4.4 13.1 - - + +
284A GLY* 3.4 30.8 - - - +
287A ALA* 4.1 18.4 - - + -
291A LEU* 4.4 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.3 15.5 - - + -
28A LEU* 4.1 20.6 - - + -
43A PHE* 3.1 43.8 + - + +
44A ALA 3.6 7.4 - - - +
46A ARG* 1.3 74.9 - - - +
48A ALA* 1.3 64.3 + - - +
50A GLY* 3.0 15.4 + - - -
52A LEU* 4.1 9.1 - - + +
54A VAL* 4.0 9.2 - - + -
287A ALA* 3.8 26.6 - - + +
290A ILE* 3.8 31.9 - - + -
291A LEU* 3.8 18.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
18A PHE* 3.8 25.6 - - + -
19A GLY* 3.9 8.2 - - - +
20A ASP 5.7 0.2 + - - -
23A ASP* 4.8 1.6 - - - +
44A ALA 2.9 17.2 + - - +
45A ARG* 3.8 4.3 - - - +
47A LEU* 1.3 76.4 - - - +
49A ASP* 1.3 60.3 + - - +
50A GLY 3.0 0.2 - - - -
51A GLY* 2.9 19.6 + - - -
52A LEU 3.1 28.6 + - - +
54A VAL* 3.6 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY* 5.5 3.5 - - - -
45A ARG* 2.9 27.0 + - - +
46A ARG* 4.1 7.6 - - - +
47A LEU 3.2 0.4 - - - -
48A ALA* 1.3 79.7 - - - +
50A GLY* 1.3 57.2 + - - +
51A GLY 3.3 1.1 + - - -
----------------------------------------------------------
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