Contacts of the helix formed by residues 32 - 48 (chain D) in PDB entry 1SL0
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 CYS 32 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C TYR* 4.1 1.9 - - - -
287C PRO* 4.7 1.8 - - - -
327C THR* 3.3 23.8 - - - -
29D ALA 3.0 4.8 + - - +
30D GLU 4.9 1.7 - - - -
31D TRP* 1.3 85.6 - - + +
33D GLY* 1.3 69.8 + - - +
34D PRO* 3.6 6.5 - - - -
35D CYS* 3.2 29.0 - - + +
36D LYS* 3.2 15.8 + - - +
75D ILE* 3.1 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C PHE* 5.0 3.4 - - - -
286C TYR* 3.3 35.9 - - - +
287C PRO* 4.9 1.6 + - - +
327C THR* 5.0 0.8 + - - -
31D TRP 3.7 0.4 + - - -
32D CYS* 1.3 69.4 - - - +
34D PRO* 1.3 64.1 - - - +
36D LYS* 2.7 35.4 + - - +
37D MET* 3.0 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C PHE* 4.2 12.3 - - + -
287C PRO 5.4 0.7 - - - +
289C ILE* 3.6 33.4 - - + -
325C PRO* 4.3 28.7 - - + +
327C THR* 4.3 0.7 - - - +
32D CYS* 3.6 9.2 - - - -
33D GLY* 1.3 87.8 - - - +
35D CYS* 1.3 56.7 + - - +
37D MET* 2.8 26.8 + - + +
38D ILE* 2.9 17.0 + - - +
75D ILE 4.4 1.3 - - - +
76D PRO* 3.9 17.5 - - + -
93D ALA* 4.0 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASP* 5.4 1.2 - - - +
28D TRP* 3.2 44.8 - - + +
29D ALA 3.8 8.5 - - - +
32D CYS* 3.2 19.3 - - + +
33D GLY 3.1 0.6 - - - -
34D PRO* 1.3 78.9 - - - +
36D LYS* 1.3 61.2 + - - +
38D ILE* 3.2 21.6 - - - +
39D ALA* 3.3 9.4 + - - +
57D LYS* 6.2 0.2 - - - +
75D ILE* 3.7 19.1 - - - -
76D PRO* 3.6 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C PRO* 4.8 14.7 - - - +
286C TYR* 4.2 21.3 - - + +
29D ALA 5.4 0.2 + - - -
30D GLU* 5.9 2.9 - - - +
32D CYS 3.2 8.4 + - - +
33D GLY* 2.7 22.9 + - - +
35D CYS* 1.3 74.5 - - - +
37D MET* 1.3 70.7 + - - +
39D ALA* 3.1 20.7 - - + +
40D PRO* 3.4 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C PRO* 4.6 16.2 - - + -
33D GLY 3.0 5.2 + - - +
34D PRO* 2.8 20.6 + - + +
36D LYS* 1.3 86.9 - - - +
38D ILE* 1.3 58.6 + - - +
39D ALA 2.8 10.1 + - - -
40D PRO* 2.9 20.3 - - - +
41D ILE* 4.1 5.7 - - - +
93D ALA* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASP* 4.8 2.5 - - - +
34D PRO 2.9 11.4 + - - +
35D CYS* 3.2 14.1 - - - +
37D MET* 1.3 71.5 - - - +
39D ALA* 1.3 69.4 + - - +
41D ILE* 3.1 18.9 - - + +
42D LEU* 3.1 35.8 + - + +
76D PRO* 3.5 22.9 - - + -
78D LEU* 3.3 46.2 - - + -
92D GLY 3.6 11.9 - - - +
93D ALA* 4.0 18.0 - - - +
94D LEU* 4.7 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 5.5 0.3 - - - +
26D ASP* 5.9 0.2 - - - -
35D CYS 3.3 11.6 + - - +
36D LYS* 3.1 22.0 - - + +
37D MET 2.8 2.0 + - - -
38D ILE* 1.3 85.3 - - - +
40D PRO* 1.4 66.3 - - + +
42D LEU* 3.1 16.4 + - - +
43D ASP* 3.1 10.7 + - - +
57D LYS* 4.7 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LYS* 3.4 7.4 - - - +
37D MET* 2.9 22.7 - - - +
39D ALA* 1.4 85.8 - - + +
41D ILE* 1.3 70.2 + - + +
43D ASP* 3.0 10.6 + - + +
44D GLU* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D MET 4.1 10.8 - - - +
38D ILE* 3.1 20.4 - - + +
40D PRO* 1.3 81.5 - - + +
42D LEU* 1.3 60.8 + - + +
44D GLU* 3.1 5.3 + - - +
45D ILE* 2.8 42.4 + - + +
94D LEU 3.8 22.0 - - - +
95D SER* 4.1 3.6 - - - +
96D LYS* 3.3 44.2 - - + +
99D LEU* 4.2 7.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
4D ILE* 3.5 10.7 - - + +
24D LEU* 3.3 39.7 - - + -
26D ASP* 3.6 31.6 - - + +
38D ILE* 3.1 46.0 + - + +
39D ALA* 3.5 7.6 - - - +
41D ILE* 1.3 80.8 - - + +
43D ASP* 1.3 63.6 + - - +
45D ILE* 3.2 9.4 + - + +
46D ALA* 2.9 18.9 + - - +
55D VAL* 4.0 16.7 - - + +
57D LYS* 5.0 6.5 - - + -
78D LEU* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS* 5.1 9.2 - - - +
4D ILE* 3.3 21.2 - - + +
39D ALA 3.1 11.1 + - - +
40D PRO* 3.0 16.2 + - + +
42D LEU* 1.3 77.3 - - - +
44D GLU* 1.3 62.1 + - - +
46D ALA* 3.2 18.2 + - - +
47D ASP* 3.5 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PRO 3.0 11.1 + - - +
41D ILE* 3.7 7.2 - - - +
43D ASP* 1.3 74.7 - - - +
45D ILE* 1.3 62.2 + - + +
47D ASP* 3.2 7.4 + - - +
48D GLU* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 4.7 9.0 - - + -
41D ILE* 2.8 40.2 + - + +
42D LEU* 3.3 14.8 - - + +
44D GLU* 1.3 79.3 - - + +
46D ALA* 1.3 58.6 + - - +
48D GLU* 3.7 6.0 + - + +
49D TYR* 3.0 29.3 + - + +
53D LEU* 4.0 22.4 - - + -
55D VAL* 4.5 4.2 - - + +
96D LYS* 4.2 20.0 - - + +
99D LEU* 4.5 15.3 - - + -
100D LYS* 4.8 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS* 4.9 10.8 - - + +
4D ILE* 3.4 28.9 - - + -
42D LEU 2.9 7.9 + - - +
43D ASP 3.2 12.6 - - - +
44D GLU 3.1 0.4 - - - -
45D ILE* 1.3 78.4 - - - +
47D ASP* 1.3 56.3 + - - +
49D TYR* 3.8 1.5 - - - -
50D GLN* 3.2 31.1 + - - +
53D LEU 4.6 4.0 - - - +
55D VAL* 3.6 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS* 6.4 1.1 - - + +
43D ASP* 3.5 6.3 + - - +
44D GLU* 3.2 9.9 + - - +
46D ALA* 1.3 75.6 - - - +
48D GLU* 1.3 58.7 + - - +
49D TYR 2.9 10.4 + - - -
50D GLN* 3.3 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU* 2.9 18.2 + - + +
45D ILE* 3.9 5.8 - - + +
47D ASP* 1.3 74.9 - - - +
49D TYR* 1.3 58.7 + - - +
50D GLN 3.9 0.2 - - - -
----------------------------------------------------------
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