Contacts of the helix formed by residues 31 - 46 (chain D) in PDB entry 3O2Q
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 THR 31 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D MET* 1.3 75.3 - - - +
32D THR* 1.3 61.2 + - - +
33D SER* 3.0 10.1 + - - -
34D GLU* 2.7 48.3 + - + +
35D ARG* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D THR* 1.3 72.8 - - - +
33D SER* 1.3 61.7 + - - +
35D ARG* 3.2 7.0 + - - +
36D VAL* 3.0 36.1 + - + +
61D LEU* 4.2 39.0 - - + +
65D LYS* 4.5 14.9 - - + +
66D ASP* 4.5 12.1 + - + +
69D LEU* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D THR* 3.0 7.4 + - - -
32D THR* 1.3 78.8 - - - +
34D GLU* 1.3 61.8 + - - +
36D VAL* 3.6 1.6 + - - +
37D VAL* 3.2 31.6 + - - +
69D LEU* 3.7 28.2 - - - +
72D ASN* 6.1 0.2 - - - -
73D PHE* 3.9 16.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D MET* 3.3 27.5 + - - +
31D THR* 2.7 51.8 + - + +
33D SER* 1.3 75.9 - - - +
35D ARG* 1.3 61.1 + - - +
37D VAL* 3.4 5.6 + - - +
38D ASP* 3.3 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D MET* 3.7 30.0 - - + +
31D THR 2.9 19.3 + - - +
32D THR* 3.2 6.5 + - - +
34D GLU* 1.3 76.5 - - - +
36D VAL* 1.3 57.2 + - - +
38D ASP* 3.6 2.8 + - - +
39D LEU* 3.1 41.6 + - + +
57D GLN* 3.0 28.1 + - - -
61D LEU* 4.0 28.8 - - + +
65D LYS* 6.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D THR* 3.0 22.6 + - + +
33D SER* 3.9 3.8 - - - +
35D ARG* 1.3 72.9 - - - +
37D VAL* 1.3 54.3 + - - +
39D LEU* 3.0 10.4 + - - +
40D LEU* 2.8 42.7 + - + +
58D VAL* 3.8 22.9 - - + -
61D LEU* 4.0 21.8 - - + -
62D ILE* 3.7 22.4 - - + -
69D LEU* 5.4 0.4 - - + -
73D PHE* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D SER* 3.2 20.9 + - - +
34D GLU* 3.4 6.9 + - - +
36D VAL* 1.3 75.5 - - - +
38D ASP* 1.3 64.6 + - - +
40D LEU* 2.9 11.8 + - + +
41D ASN* 2.9 40.2 + - - +
73D PHE* 4.1 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D MET* 4.8 13.7 - - + +
34D GLU 3.3 12.7 + - - +
35D ARG 4.0 4.0 - - - +
37D VAL* 1.3 80.3 - - - +
39D LEU* 1.3 58.4 + - - +
41D ASN* 3.3 9.0 + - - +
42D GLN* 2.8 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 3.1 29.3 + - + +
36D VAL* 3.0 9.2 + - - +
38D ASP* 1.3 78.3 - - - +
40D LEU* 1.3 56.9 + - - +
42D GLN* 3.2 20.9 - - - +
43D ALA* 2.9 23.6 + - - +
54D VAL* 3.3 28.1 - - + +
57D GLN* 4.5 25.4 - - + +
58D VAL* 3.3 31.4 - - + +
61D LEU* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D VAL* 2.8 27.1 + - + +
37D VAL* 3.4 7.9 - - + +
39D LEU* 1.3 74.3 - - - +
41D ASN* 1.3 61.3 + - - +
43D ALA* 3.1 5.8 + - - +
44D ALA* 2.8 28.1 + - - +
55D LEU* 4.6 8.5 - - + -
58D VAL* 4.1 12.3 - - + -
73D PHE* 3.7 34.3 - - + -
76D GLU* 4.0 25.6 - - + +
77D ILE* 3.9 28.0 - - + -
80D PHE* 5.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 2.9 33.6 + - - +
38D ASP* 3.7 13.2 - - - +
40D LEU* 1.3 76.6 - - - +
42D GLN* 1.3 66.1 + - - +
44D ALA* 3.3 16.2 + - - +
45D LEU* 3.4 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASP* 2.8 32.0 + - - +
39D LEU* 3.2 29.9 - - - +
41D ASN* 1.3 76.0 - - - +
43D ALA* 1.3 61.2 + - - +
45D LEU* 3.5 4.1 + - - +
46D ILE* 3.4 39.0 + - + +
54D VAL* 4.3 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU 2.9 13.9 + - - +
40D LEU* 3.1 9.6 + - - +
42D GLN* 1.3 73.9 - - - +
44D ALA* 1.3 63.0 + - - +
45D LEU 3.1 2.9 + - - -
46D ILE* 3.5 22.1 + - - +
51D LYS* 4.2 14.1 + - + +
54D VAL* 4.3 8.5 - - + +
55D LEU* 3.7 32.1 - - + -
80D PHE* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU 2.8 15.4 + - - +
41D ASN* 3.3 10.3 + - - +
43D ALA* 1.3 76.8 - - - +
45D LEU* 1.3 70.8 + - + +
46D ILE 3.6 2.6 - - - +
47D THR* 5.8 1.2 - - - +
51D LYS* 5.7 0.7 + - - -
80D PHE* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASN 3.4 15.9 + - - +
42D GLN* 3.5 4.2 + - - +
43D ALA 3.1 0.6 - - - -
44D ALA* 1.3 88.3 - - + +
46D ILE* 1.3 64.4 + - - +
47D THR* 3.5 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D GLN* 3.4 26.6 + - + +
43D ALA* 3.5 5.0 + - - +
44D ALA 4.5 2.4 - - - +
45D LEU* 1.3 76.6 - - + +
47D THR* 1.3 61.9 + - - +
48D ASN* 3.4 25.6 - - - +
50D SER* 3.2 31.0 - - - +
51D LYS* 3.2 39.0 + - + +
54D VAL* 4.0 26.5 - - + -
----------------------------------------------------------
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