Contacts of the helix formed by residues 32 - 44 (chain C) in PDB entry 3REO
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 32 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 4.5 8.7 - - + +
35A PRO* 3.7 13.5 - - + +
36A MET* 4.1 25.6 - - + -
134A ALA 6.0 1.6 - - - +
135A THR* 6.1 1.1 - - + -
140A LEU* 4.5 13.0 - - + -
143A TRP* 6.0 0.2 - - - -
29C ALA 5.9 0.9 - - - +
30C SER 3.1 2.1 + - - -
31C ALA* 1.3 74.9 - - - +
33C VAL* 1.3 64.0 + - - +
34C LEU 3.1 0.6 + - - -
35C PRO* 3.3 13.1 - - + +
36C MET* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 3.5 20.9 - - + +
318A HIS* 4.3 11.7 - - + +
321A ALA* 3.4 20.2 - - + -
322A LEU* 3.4 38.8 - - + -
30C SER* 3.1 19.5 + - - +
32C ALA* 1.3 78.8 - - + +
34C LEU* 1.3 58.0 + - - +
36C MET* 4.6 1.1 - - - -
37C ALA* 2.9 26.9 + - - +
86C LEU* 3.3 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.5 34.3 - - + -
31A ALA* 5.0 7.4 - - + -
318A HIS* 5.6 2.5 + - - +
31C ALA 3.2 8.2 + - - +
32C ALA 3.1 1.0 - - - -
33C VAL* 1.3 77.4 - - - +
35C PRO* 1.4 73.6 - - + +
37C ALA* 3.8 0.7 - - - +
38C LEU* 3.0 21.7 + - + +
86C LEU* 4.3 10.6 - - + +
87C LEU* 3.8 24.5 - - + -
90C TYR* 3.8 55.2 - - + -
92C VAL* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.7 20.9 - - + +
29A ALA 4.6 1.1 - - - +
31A ALA* 3.8 12.1 - - + -
32A ALA* 3.7 24.5 - - + +
31C ALA 3.4 8.7 - - - +
32C ALA* 3.3 22.7 - - - +
34C LEU* 1.4 91.6 - - + +
36C MET* 1.3 64.3 + - + +
38C LEU* 3.7 7.2 - - + +
39C LYS* 2.8 30.5 + - - +
131C LEU* 4.4 1.6 - - + +
135C THR* 4.0 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 4.6 11.0 - - + -
140A LEU* 5.6 5.8 - - + +
143A TRP* 3.6 52.0 - - + +
144A PHE* 4.7 6.5 - - - -
32C ALA* 3.1 24.2 + - + +
33C VAL 4.0 0.9 - - - +
35C PRO* 1.3 89.7 - - + +
37C ALA* 1.3 58.1 + - - +
39C LYS* 3.4 11.3 + - - +
40C ALA* 3.1 25.5 + - - +
135C THR* 4.0 28.9 - - + +
140C LEU* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 4.2 13.0 - - + -
146A LEU* 4.7 4.9 - - - -
321A ALA* 5.6 0.9 - - + -
33C VAL 2.9 20.0 + - - +
34C LEU 3.8 1.3 - - - +
36C MET* 1.3 74.3 - - - +
38C LEU* 1.3 60.5 + - - +
40C ALA* 3.2 4.2 + - - +
41C ALA* 2.9 27.4 + - - +
83C VAL* 3.7 26.6 - - + +
86C LEU* 3.6 22.4 - - + -
87C LEU* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.9 37.5 - - + +
34C LEU* 3.0 17.6 + - + +
35C PRO* 3.7 6.1 - - + +
37C ALA* 1.3 72.6 - - - +
39C LYS* 1.3 67.4 + - - +
41C ALA* 3.2 4.9 + - + +
42C ILE* 2.9 40.9 + - + +
47C LEU* 4.4 6.5 - - + -
87C LEU* 3.9 22.1 - - + +
92C VAL* 4.0 23.1 - - + -
118C LEU* 4.2 11.7 - - + -
131C LEU* 3.3 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP 5.8 2.9 - - - +
144A PHE* 3.3 26.2 - - + -
35C PRO 2.8 21.6 + - - +
36C MET* 3.6 13.2 - - - +
37C ALA 3.3 0.2 - - - -
38C LEU* 1.3 73.1 - - - +
40C ALA* 1.3 63.9 + - - +
42C ILE* 3.1 3.6 + - - +
43C GLU* 2.9 51.1 + - - +
131C LEU* 3.8 10.3 - - + +
132C LEU* 3.7 21.3 - - + -
135C THR* 3.0 51.6 + - - +
136C ASP* 3.7 10.7 + - - +
137C LYS 4.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP 5.2 3.1 - - - +
146A LEU* 3.7 37.0 - - + -
147A LYS* 4.4 10.7 - - - +
150A ILE* 5.5 0.7 - - + -
36C MET 3.1 12.0 + - - +
37C ALA 3.2 7.1 + - - +
39C LYS* 1.3 77.7 - - - +
41C ALA* 1.3 61.7 - - - +
43C GLU* 3.3 12.2 + - - +
44C LEU* 3.0 32.8 + - + +
83C VAL* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ALA 2.9 17.2 + - - +
38C LEU* 3.2 10.7 + - + +
40C ALA* 1.3 72.1 - - - +
42C ILE* 1.3 60.8 + - - +
44C LEU* 3.4 2.0 + - - -
45C ASP 3.3 2.6 + - - -
46C VAL* 2.8 51.5 + - + +
47C LEU* 4.1 8.0 + - + -
83C VAL* 4.5 9.7 - - + +
84C LEU* 5.7 0.2 - - + -
87C LEU* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 2.9 28.5 + - + +
39C LYS 3.7 2.9 - - - +
41C ALA* 1.3 75.3 - - - +
43C GLU* 1.3 57.7 + - - +
45C ASP* 3.0 21.0 + - - +
47C LEU* 4.1 21.8 - - + +
118C LEU* 4.7 8.5 - - + +
128C ALA* 3.8 30.5 - - + -
131C LEU* 3.8 39.3 - - + -
132C LEU* 4.1 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP 5.7 1.2 - - - +
144A PHE* 5.3 5.4 - - - +
147A LYS* 3.1 49.6 + - + +
39C LYS* 2.9 50.8 + - - +
40C ALA* 3.9 10.2 - - - +
42C ILE* 1.3 76.0 - - - +
44C LEU* 1.3 60.0 + - - +
45C ASP* 3.1 2.4 + - - +
132C LEU* 3.8 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS* 3.9 24.9 - - + +
150A ILE* 3.8 31.6 - - + -
151A LEU* 3.8 38.1 - - + -
40C ALA* 3.0 24.8 + - + +
41C ALA* 3.4 1.3 + - - +
42C ILE 3.2 0.2 - - - -
43C GLU* 1.3 76.9 - - - +
45C ASP* 1.3 80.6 - - - +
46C VAL* 3.8 13.9 - - + -
69C LEU* 3.2 23.8 - - + +
80C LEU* 4.2 15.5 - - + -
----------------------------------------------------------
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