Contacts of the helix formed by residues 18 - 29 (chain D) in PDB entry 6BCH
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 SER 18 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASN 3.7 2.2 + - - -
17D ILE* 1.3 81.2 - - - +
19D PRO* 1.3 76.5 - - - +
20D TRP* 3.2 19.1 + - - +
21D THR* 3.1 26.0 + - - -
22D ILE* 3.2 11.1 + - - +
70D TYR* 4.7 0.2 - - - -
173D ASP* 5.5 0.2 - - - -
175D ASN* 3.6 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE 3.9 0.4 - - - +
18D SER* 1.3 89.2 - - - +
20D TRP* 1.3 60.5 + - + +
22D ILE* 3.2 9.8 + - + +
23D THR* 2.9 29.4 + - - -
70D TYR* 3.2 36.3 - - + +
98D HIS* 3.6 9.5 + - + -
102D TYR* 3.4 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D SER* 3.2 10.8 + - - +
19D PRO* 1.3 78.3 - - + +
21D THR* 1.3 61.3 + - - +
23D THR* 4.1 7.4 - - + -
24D GLY 2.9 23.0 + - - -
101D LYS 4.7 2.5 - - - -
102D TYR* 3.7 34.4 - + + -
103D PRO* 3.2 48.0 - - + -
105D ILE* 5.0 1.8 - - + -
172D PRO* 3.4 43.1 + - + -
173D ASP* 3.8 26.0 - - + +
176D TRP* 3.3 36.4 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 3.8 23.1 - - + +
18D SER* 3.1 19.4 + - - -
20D TRP* 1.3 78.0 - - - +
22D ILE* 1.3 57.5 + - - +
24D GLY 3.4 0.7 + - - -
25D PHE* 2.9 29.3 + - - +
175D ASN* 3.2 32.8 + - - +
178D ALA* 4.8 5.0 - - + +
179D GLY* 3.6 18.4 - - - +
269D HIS 5.6 0.9 - - - +
271D ILE* 4.3 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 3.7 22.4 - - + -
18D SER 3.5 11.2 - - - +
19D PRO* 3.2 9.3 + - + +
21D THR* 1.3 76.5 - - - +
23D THR* 1.3 57.5 + - - +
25D PHE* 3.3 5.4 + - - +
26D ALA* 2.9 32.3 + - + +
54D ILE* 5.7 2.4 - - + +
67D ILE* 4.2 35.6 - - + +
70D TYR* 3.6 47.3 - - + -
71D LEU* 5.2 4.9 - - + -
98D HIS* 3.8 17.9 - - + +
99D PHE* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D PRO 2.9 12.8 + - - -
20D TRP* 3.8 11.7 - - + -
21D THR 3.3 0.2 - - - -
22D ILE* 1.3 77.2 - - - +
24D GLY* 1.3 57.3 + - - +
26D ALA 3.4 0.3 + - - -
27D ASP* 2.8 30.9 + - - +
98D HIS* 3.3 16.1 + - - -
99D PHE* 4.0 11.2 - - + -
102D TYR* 2.6 31.9 + - - +
103D PRO 3.3 22.4 - - - +
104D LEU* 3.6 15.7 - - + +
176D TRP* 4.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TRP 2.9 12.4 + - - -
21D THR 3.8 0.2 - - - -
23D THR* 1.3 77.9 - - - +
25D PHE* 1.3 55.9 - - - +
27D ASP* 3.0 5.9 - - - +
28D ALA 3.0 21.5 + - - -
176D TRP* 3.4 38.9 - - - -
180D PHE* 3.6 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 6.4 0.2 - - + -
21D THR 2.9 17.9 + - - +
22D ILE* 3.8 5.8 - - - +
24D GLY* 1.3 72.5 - - - +
26D ALA* 1.3 61.9 + - - +
28D ALA* 3.1 4.6 + - - +
29D ASP* 2.9 30.1 + - + +
54D ILE* 4.3 13.2 - - + -
56D LEU* 3.5 49.6 - - + -
60D ASP* 5.8 2.9 - - - -
63D ILE* 5.2 6.1 - - + -
67D ILE* 4.8 15.3 - - + -
179D GLY* 3.4 21.4 - - - +
182D ALA* 3.9 27.1 - - + -
183D GLY* 3.9 9.2 - - - -
271D ILE* 4.3 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 2.9 18.8 + - + +
23D THR 3.8 3.8 - - - +
25D PHE* 1.3 74.6 - - - +
27D ASP* 1.3 65.7 + - - +
28D ALA 3.0 0.2 - - - -
30D SER* 2.6 50.7 + - - +
52D PHE* 4.4 4.7 - - + -
54D ILE* 4.4 11.0 - - + +
99D PHE* 3.8 25.6 - - + -
104D LEU* 4.2 2.6 - - + +
108D LYS* 5.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D THR 2.8 9.2 + - - +
24D GLY* 3.0 15.0 - - - +
26D ALA* 1.3 77.1 - - - +
28D ALA* 1.3 57.0 + - - +
104D LEU* 3.4 24.5 - - - +
105D ILE 2.9 16.3 + - - -
106D THR* 2.4 60.6 + - + +
108D LYS* 4.6 5.8 - - - +
176D TRP* 2.9 24.9 + - + -
180D PHE* 4.2 7.8 - - + -
184D GLU* 4.6 0.7 - - - +
211D GLN* 4.8 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLY 3.0 12.3 + - - +
25D PHE* 3.4 8.3 - - - +
26D ALA 3.0 0.6 - - - -
27D ASP* 1.3 80.3 - - - +
29D ASP* 1.3 69.5 + - - +
30D SER 3.8 1.0 + - - +
180D PHE* 4.0 8.0 - - + +
183D GLY* 3.8 15.0 - - - -
184D GLU* 2.9 45.0 - - + +
211D GLN* 5.7 0.2 + - - -
15F C 5.0 2.3 + - - -
17G A 4.0 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D PHE* 2.9 21.8 + - + +
28D ALA* 1.3 86.8 - - - +
30D SER* 1.3 64.1 + - - +
54D ILE* 4.8 4.0 - - + -
55D GLY 4.2 9.0 + - - +
56D LEU* 3.3 31.9 - - + +
183D GLY* 4.0 15.1 - - - +
184D GLU* 3.8 10.4 - - - +
16E T 5.5 1.0 - - - +
16F G 4.5 1.7 + - - -
16G T 3.8 34.6 + - - +
17G A 4.2 12.6 + - - +
----------------------------------------------------------
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