Contacts of the helix formed by residues 184 - 199 (chain A) in PDB entry 2BTO
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 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 2.8 22.0 + - - +
183A VAL* 1.3 73.1 - - - +
185A GLU* 1.3 55.3 + - - +
186A PRO* 3.3 1.6 - - - -
187A TYR* 2.9 40.1 + - - +
188A ASN* 3.5 4.8 + - - -
399A PHE* 3.7 26.5 - - + -
402A TRP* 3.8 28.0 - - + +
403A TYR* 3.4 19.4 + - + +
92T ARG* 2.9 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY 3.3 24.6 - - - +
175A PRO* 3.7 23.2 - - + +
176A SER 4.2 3.1 - - - +
178A GLN* 3.8 17.3 + - - +
183A VAL* 3.6 27.0 - - + +
184A THR* 1.3 79.6 + - - +
186A PRO* 1.3 67.6 - - + +
188A ASN* 3.3 3.0 + - - +
189A THR* 3.0 28.7 + - - -
1433A GTP 3.1 33.1 + - - +
92T ARG* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 5.4 0.9 - - + -
183A VAL* 3.4 15.7 - - + +
184A THR 3.4 5.2 - - - -
185A GLU* 1.3 93.5 - - + +
187A TYR* 1.3 61.4 + - - +
189A THR* 3.5 5.2 + - - -
190A VAL* 3.1 29.8 + - - +
386A ILE* 4.5 6.5 - - + +
389A ASN* 4.0 19.7 - - + +
390A PHE* 3.8 30.1 - - + +
393A LEU* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 2.9 22.8 + - - +
186A PRO* 1.3 74.9 - - - +
188A ASN* 1.3 57.9 + - - +
190A VAL* 3.4 0.9 + - - +
191A PHE* 2.8 55.8 + + + -
390A PHE* 3.5 28.7 - + - -
393A LEU* 3.3 51.9 + - + +
394A TRP* 3.6 33.0 + + + -
398A ALA 3.5 13.0 + - - -
399A PHE* 3.6 27.1 + + + -
400A ALA 4.8 0.2 + - - -
403A TYR* 3.6 25.1 - + + +
413A ILE* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY 2.9 24.4 + - - -
105A PHE* 2.8 29.3 + - - +
143A ILE 3.5 5.3 - - - +
144A GLY 3.0 25.0 + - - +
145A GLY 3.0 24.0 + - - +
149A SER* 3.8 5.2 - - - +
184A THR* 3.8 8.0 + - - -
185A GLU 3.3 2.4 + - - +
187A TYR* 1.3 75.1 - - - +
189A THR* 1.3 56.9 + - - +
191A PHE* 3.2 2.6 + - - +
192A ALA* 2.9 31.4 + - - +
403A TYR* 2.6 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 3.2 36.9 + - + +
174A LEU* 4.5 1.1 - - + -
175A PRO* 3.4 23.7 - - + +
185A GLU 3.0 17.6 + - - -
186A PRO* 3.8 4.7 - - - -
188A ASN* 1.3 72.5 - - - +
190A VAL* 1.3 60.6 + - - +
192A ALA* 3.3 3.6 + - - +
193A LEU* 2.8 36.2 + - + +
386A ILE* 3.8 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO 3.1 18.2 + - - +
187A TYR 3.9 2.9 - - - +
189A THR* 1.3 74.1 - - - +
191A PHE* 1.3 66.5 + - + +
193A LEU* 3.2 17.3 + - + +
194A ASN* 3.4 11.4 + - - +
386A ILE* 3.7 20.2 - - + +
387A CYS* 4.7 7.0 - - - -
390A PHE* 3.7 29.6 - - + -
416A LEU 3.7 24.1 - - - +
417A ARG* 4.0 16.4 - - - +
420A ALA* 4.1 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.5 52.1 - + + -
187A TYR* 2.8 51.8 + + + +
188A ASN 3.2 0.4 + - - -
190A VAL* 1.3 76.8 - - + +
192A ALA* 1.3 62.4 + - - +
194A ASN* 3.5 15.8 + - - +
195A THR* 4.0 4.2 + - - -
390A PHE* 4.1 9.0 - + - -
403A TYR* 3.8 20.0 - + - -
408A MET* 4.2 4.3 - - + -
413A ILE* 3.6 43.3 - - + -
416A LEU* 3.4 39.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.7 7.7 - - - -
141A HIS* 5.8 0.7 - - + -
143A ILE* 3.8 31.6 - - + -
149A SER* 3.9 18.6 - - - +
153A ALA* 4.6 3.9 - - + +
188A ASN 2.9 16.4 + - - +
189A THR 3.7 3.8 - - - +
191A PHE* 1.3 74.5 - - - +
193A LEU* 1.3 65.3 + - - +
195A THR* 3.0 8.3 + - - -
196A LEU* 3.0 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 4.1 10.5 - - + -
174A LEU* 5.1 0.9 - - + -
189A THR* 2.8 32.9 + - + +
190A VAL* 3.2 13.4 + - + +
192A ALA* 1.3 75.8 - - - +
194A ASN* 1.3 56.5 + - - +
196A LEU* 3.7 14.6 - - + +
197A ARG* 2.9 33.3 + - - +
205A ILE* 4.9 4.5 - - + -
271A PHE* 3.8 33.0 - - + -
383A LEU* 3.7 28.3 - - + +
386A ILE* 4.7 11.0 - - + -
387A CYS* 5.9 0.9 - - - -
420A ALA* 4.8 18.4 - - + -
423A LEU* 4.8 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU* 5.1 4.2 + - - -
190A VAL 3.4 7.2 + - - +
191A PHE 3.6 11.0 + - - +
192A ALA 3.1 0.4 - - - -
193A LEU* 1.3 78.2 - - - +
195A THR* 1.3 63.5 + - - +
197A ARG* 3.4 2.2 + - - +
198A ARG* 3.0 55.9 + - - +
416A LEU* 3.2 33.6 - - + +
419A SER* 2.7 38.3 + - - +
420A ALA 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 5.5 0.9 - - - -
109A TYR* 4.8 1.7 - - - -
153A ALA* 3.4 44.1 - - - +
156A ILE* 3.9 17.0 - - + -
157A GLU* 2.8 32.7 + - + -
191A PHE 4.0 3.5 + - - -
192A ALA 3.0 9.2 + - - -
194A ASN* 1.3 78.6 + - - +
196A LEU* 1.3 60.5 + - + +
197A ARG 3.0 2.2 - - - -
198A ARG* 4.4 1.1 - - - +
199A SER* 2.8 35.0 + - - +
200A ALA 3.5 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A HIS* 4.0 13.0 - - + -
143A ILE* 4.0 30.3 - - + -
153A ALA* 6.4 0.9 - - - -
156A ILE* 5.1 8.7 - - + -
170A SER* 3.2 32.5 - - - +
172A ALA* 4.2 5.8 - - + -
192A ALA* 3.0 20.3 + - + +
193A LEU* 3.2 15.5 + - + +
195A THR* 1.3 77.5 - - + +
197A ARG* 1.3 52.3 + - - +
200A ALA* 3.4 19.8 + - + +
203A CYS* 3.8 20.3 - - + +
270A HIS* 2.7 28.6 + - - -
271A PHE* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU 2.9 17.0 + - - +
194A ASN* 3.5 2.2 - - - +
196A LEU* 1.3 81.0 - - - +
198A ARG* 1.3 79.0 + - - +
267A PRO 4.5 2.9 - - - +
268A SER* 5.8 11.8 + - - +
270A HIS* 3.0 24.4 - - + +
271A PHE* 4.2 4.3 - - + -
419A SER* 3.0 41.6 + - - -
422A GLU* 2.8 48.6 + - - +
423A LEU* 3.8 32.1 - - + +
426A SER* 5.1 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASN* 3.0 38.0 + - - +
195A THR* 5.1 0.9 - - - -
197A ARG* 1.3 105.3 - - - +
199A SER* 1.3 66.3 + - - +
200A ALA 4.8 1.2 - - - +
270A HIS* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 4.0 13.5 - - - -
157A GLU* 3.7 24.5 + - - +
160A LYS* 3.3 36.1 - - - +
195A THR* 2.8 23.3 + - - +
198A ARG* 1.3 80.5 + - - +
200A ALA* 1.3 64.7 + - - +
201A ASP* 3.7 1.7 + - - +
----------------------------------------------------------
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