Contacts of the helix formed by residues 41 - 53 (chain D) in PDB entry 1SA0
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 ASP 41 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TYR* 3.7 5.7 - - - -
39D ASP 5.1 1.8 - - - +
40D SER* 1.3 77.4 - - - +
42D LEU* 1.3 77.9 + - + +
43D GLN* 4.0 2.6 - - - +
44D LEU* 4.0 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D SER* 5.9 0.2 - - - -
41D ASP* 1.3 85.9 - - + +
43D GLN* 1.3 55.5 + - + +
44D LEU* 2.3 22.0 + - - +
47D GLU* 3.0 33.8 + - + +
244D PHE* 3.7 30.1 - - + +
245D PRO* 4.2 15.7 - - + +
358D ILE* 5.5 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU 3.5 17.0 + - - +
28D HIS* 3.0 57.0 + - - +
29D GLY* 4.1 1.2 + - - -
36D TYR* 2.7 48.5 + - + +
38D GLY* 5.1 1.2 - - - -
40D SER* 2.9 26.2 + - - -
41D ASP 4.0 3.8 - - - -
42D LEU* 1.3 76.2 - - - +
44D LEU* 1.3 64.2 + - + +
47D GLU* 3.3 2.5 + - - +
48D ARG 4.0 2.8 + - - -
49D ILE 3.7 6.9 + - - -
243D ARG 4.2 3.5 - - - +
244D PHE* 3.9 17.7 - - + +
358D ILE* 4.4 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D HIS 5.0 2.9 - - - +
30D ILE* 5.3 1.3 - - + -
36D TYR* 3.6 46.7 - - + -
41D ASP* 4.4 8.7 - - - +
42D LEU 2.3 15.4 + - - +
43D GLN* 1.3 74.7 - - + +
47D GLU* 1.3 68.3 + - - +
48D ARG 3.5 0.2 - - - -
49D ILE* 3.0 29.8 - - + +
61D TYR* 3.9 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 3.0 29.2 + - + +
43D GLN 3.3 0.8 + - - -
44D LEU* 1.3 78.6 - - - +
48D ARG* 1.3 69.0 + - + +
49D ILE* 3.3 1.7 + - - +
50D ASN* 4.2 8.7 + - - +
244D PHE 4.1 18.8 - - - +
245D PRO 4.4 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 6.0 4.4 - - - +
43D GLN 4.0 4.8 + - - -
47D GLU* 1.3 85.9 - - + +
49D ILE* 1.3 59.1 + - - +
50D ASN* 2.9 10.8 - - - +
51D VAL* 3.2 28.6 + - + +
52D TYR 4.3 0.7 + - - -
241D CYS 3.3 13.1 + - - -
242D LEU 3.6 19.1 - - - +
243D ARG* 4.0 20.5 + - - +
244D PHE 3.6 4.0 + - - +
245D PRO* 2.8 42.3 + - - +
246D GLY* 3.2 31.3 - - - +
247D GLN 4.2 0.2 - - - +
248D LEU 4.4 0.4 + - - -
249D ASN* 3.5 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D HIS* 3.4 48.5 - - + +
30D ILE* 3.8 15.7 - - + -
43D GLN 3.7 3.4 + - - +
44D LEU* 3.0 39.6 + - + +
47D GLU 3.2 0.8 - - - +
48D ARG* 1.3 75.9 - - - +
50D ASN* 1.3 67.6 + - - +
51D VAL 3.3 0.3 + - - -
52D TYR* 3.4 2.1 + - - -
53D TYR* 3.0 39.9 + - + +
55D GLU* 6.1 2.5 - - + +
61D TYR* 3.6 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ARG 4.3 16.2 + - - -
3D GLU* 4.5 12.9 + - - +
47D GLU 4.3 8.5 - - - +
48D ARG* 4.1 7.2 - - - -
49D ILE* 1.3 83.2 - - - +
51D VAL* 1.3 65.4 + - + +
52D TYR 3.2 0.9 + - - -
53D TYR 3.2 10.7 + - - +
55D GLU* 5.0 9.4 - - - +
64D ARG* 3.1 25.4 + - - -
130D ASP* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ARG* 4.8 6.1 - - - +
3D GLU* 4.2 14.1 - - - +
4D ILE* 3.0 36.7 + - + +
48D ARG* 3.2 28.2 + - + +
50D ASN* 1.3 83.3 - - + +
52D TYR* 1.3 73.5 + - + +
64D ARG* 2.7 19.9 + - - +
133D GLN* 4.4 4.5 - - - +
242D LEU* 3.8 25.1 - - + +
243D ARG* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.3 28.4 - - + +
6D HIS* 5.0 4.3 - - + -
20D PHE* 3.9 16.2 - + - -
21D TRP* 3.1 39.5 - + + -
24D ILE* 4.2 11.4 - - + -
28D HIS* 5.8 1.3 - - - +
48D ARG 4.3 0.6 + - - +
49D ILE* 3.4 3.7 + - - +
50D ASN 3.3 0.4 - - - -
51D VAL* 1.3 86.8 - - + +
53D TYR* 1.3 73.5 + - + +
54D ASN 4.3 0.4 - - - -
64D ARG* 3.5 12.5 + - - +
136D GLN* 2.9 42.5 + - + -
239D THR* 3.4 13.5 - - + +
242D LEU* 3.9 15.2 - - + +
243D ARG* 3.5 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TRP* 3.7 16.1 - + - -
24D ILE* 3.4 28.1 - - + +
25D SER* 2.4 41.8 + - - -
28D HIS* 4.2 14.1 - + - -
30D ILE* 4.8 11.0 - - + -
49D ILE* 3.0 37.5 + - + +
50D ASN* 3.2 18.9 + - - +
52D TYR* 1.3 83.9 - - + +
54D ASN* 1.3 62.3 + - - +
55D GLU* 3.4 11.5 + - + +
61D TYR* 3.8 28.7 - + + +
62D VAL 4.0 2.0 - - - -
63D PRO* 3.7 27.8 - - + -
64D ARG* 3.9 1.0 + - - +
86D ILE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLU* 5.5 1.2 - - - +
53D TYR* 1.3 69.9 - - - +
55D GLU* 1.3 64.5 + - - +
61D TYR 2.8 2.1 - - - +
62D VAL* 2.4 36.6 + - + +
63D PRO 5.3 0.2 - - - -
64D ARG* 3.1 48.1 + - + +
88D ARG* 6.2 0.9 - - - +
125D GLU* 3.2 26.7 + - - +
128D SER* 4.1 18.5 + - - +
129D CYS* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 6.1 2.8 - - + +
50D ASN* 5.0 8.3 - - - +
53D TYR 3.7 10.5 - - - +
54D ASN* 1.3 79.7 + - - +
56D ALA* 1.3 62.3 + - - +
59D ASN 4.9 0.7 - - - +
60D LYS 3.9 2.7 - - - +
61D TYR* 3.6 45.4 + - + +
----------------------------------------------------------
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