Contacts of the helix formed by residues 15 - 26 (chain D) in PDB entry 3BRW
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 GLY 15 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLY 3.2 1.2 + - - -
14D VAL* 1.3 81.1 - - - +
16D LYS* 1.3 62.3 + - - +
18D ALA* 3.8 0.6 - - - +
19D LEU* 2.9 38.3 + - - +
116D ASN* 3.9 2.0 - - - -
171D GDP 3.0 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.8 22.3 - - + +
9D LEU* 3.4 33.0 - - - -
10D GLY* 2.8 15.5 + - - +
11D SER 2.8 20.6 + - - -
14D VAL* 3.8 11.0 - - + -
15D GLY* 1.3 75.0 - - - +
17D SER* 1.3 62.7 + - - +
19D LEU* 4.0 3.2 - - - +
20D THR* 2.7 34.0 + - - -
57D ASP* 3.2 11.2 - - - +
58D THR* 3.5 20.0 - - - -
60D GLY 4.3 0.9 - - - +
81D VAL* 4.3 6.3 - - + -
170D BEF 2.6 32.8 - - - -
171D GDP 2.8 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LYS* 1.3 74.5 - - - +
18D ALA* 1.3 58.3 + - - +
20D THR* 3.2 1.8 + - - -
21D VAL* 2.9 41.9 + - - +
29D VAL* 5.6 5.4 - - - -
33D ASP 5.6 1.3 - - - -
35D THR* 3.2 10.4 - - - +
38D ASP* 5.4 0.9 - - - -
40D TYR* 5.7 1.1 - - - -
57D ASP* 2.6 23.9 + - - -
171D GDP 2.7 15.0 + - - -
172D MG 2.2 29.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLY 3.8 2.0 - - - +
17D SER* 1.3 72.2 - - - +
19D LEU* 1.3 64.2 + - - +
20D THR 3.0 0.5 + - - -
21D VAL* 3.5 9.4 - - - +
22D GLN* 2.9 26.9 + - - +
27D ILE 4.7 0.2 - - - +
28D PHE* 4.6 2.6 - - + -
29D VAL* 4.3 19.0 - - + +
148D ALA* 3.8 11.0 - - + -
171D GDP 2.7 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 5.6 3.1 - - + -
15D GLY 2.9 27.2 + - - +
16D LYS* 4.0 4.5 - - - +
18D ALA* 1.3 72.7 - - - +
20D THR* 1.3 60.6 + - - +
22D GLN* 4.1 2.2 - - - -
23D PHE* 3.3 21.7 + - - +
81D VAL* 4.0 20.2 - - + -
114D VAL* 4.0 10.5 - - + -
116D ASN* 3.3 40.6 - - + +
146D SER* 4.1 13.5 - - - -
148D ALA* 3.9 8.7 - - + +
154D VAL* 4.0 32.6 - - + +
157D ILE* 4.8 9.0 - - + -
158D PHE* 4.0 10.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.5 19.8 - - - +
16D LYS 2.7 22.6 + - - -
17D SER* 3.6 5.4 - - - -
18D ALA 3.0 1.0 - - - -
19D LEU* 1.3 76.3 - - - +
21D VAL* 1.3 60.9 + - - +
22D GLN 3.2 1.3 - - - -
23D PHE* 3.1 5.4 + - - +
24D VAL* 2.9 31.0 + - + +
40D TYR* 3.3 33.2 - - + -
55D ILE* 3.8 26.4 - - + +
57D ASP* 4.0 7.2 + - + -
158D PHE* 4.6 5.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D SER* 2.9 29.0 + - - +
18D ALA* 3.5 5.4 - - - +
20D THR* 1.3 68.0 - - - +
22D GLN* 1.3 62.4 + - - +
24D VAL* 4.0 7.4 - - - -
25D GLN* 2.8 44.7 + - - +
26D GLY 3.2 4.2 + - - -
27D ILE* 3.6 16.6 + - + +
29D VAL* 3.6 32.1 - - + +
40D TYR* 3.4 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ALA 2.9 20.7 + - - +
19D LEU* 4.1 5.2 - - - +
21D VAL* 1.3 78.6 - - - +
23D PHE* 1.3 57.5 + - - +
26D GLY* 2.9 37.1 + - - -
27D ILE* 3.0 33.4 + - - +
28D PHE* 3.3 12.1 - - - +
148D ALA* 3.6 24.0 + - + +
150D SER 5.5 0.9 - - - -
151D LYS* 2.8 35.5 + - + +
154D VAL* 3.8 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU 3.3 16.8 + - - +
20D THR 3.1 4.5 + - - +
22D GLN* 1.3 82.2 - - - +
24D VAL* 1.3 72.6 + - + +
26D GLY* 4.5 0.9 + - - -
42D LYS* 3.3 32.9 + - + +
44D VAL* 4.4 7.4 - - + -
53D LEU* 4.1 18.6 - - + -
55D ILE* 4.3 8.7 - - + -
154D VAL* 4.1 6.7 - - + +
155D ASN* 3.2 42.6 - - - +
158D PHE* 3.5 44.0 - + + -
159D TYR* 4.0 23.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D THR* 2.9 23.5 + - + +
21D VAL* 4.0 7.0 - - - -
23D PHE* 1.3 93.3 - - + +
25D GLN* 1.3 78.5 + - + +
26D GLY 3.6 0.2 - - - -
40D TYR* 3.8 42.2 - - + -
41D ARG 5.7 0.7 - - - -
42D LYS* 3.5 41.5 + - + +
55D ILE* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D VAL* 2.8 27.4 + - - +
24D VAL* 1.3 86.4 - - + +
26D GLY* 1.3 64.5 + - - +
27D ILE* 3.3 21.6 + - + +
40D TYR* 4.3 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D VAL 3.2 0.2 + - - -
22D GLN* 2.9 36.4 + - - +
23D PHE 4.4 0.6 + - - -
24D VAL 3.6 1.0 - - - -
25D GLN* 1.3 78.2 - - - +
27D ILE* 1.3 63.8 + - - +
151D LYS* 4.6 6.3 + - - -
----------------------------------------------------------
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