Contacts of the helix formed by residues 183 - 194 (chain A) in PDB entry 1BSG
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 PRO 183 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 3.6 31.6 - - - +
46A VAL 3.8 24.2 - - - +
47A TYR* 3.6 6.3 - - + +
61A ARG 3.7 8.7 - - - +
62A ALA* 3.4 14.1 - - - +
64A GLU 3.4 14.4 - - - +
66A PHE* 3.9 8.3 - - + -
182A SER* 1.3 82.1 - - - +
184A ARG* 1.3 59.7 + - - +
186A ILE* 3.9 0.9 - - - +
187A THR* 2.8 30.8 + - - -
262A THR* 4.2 14.6 - - + -
264A LEU* 3.9 8.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.4 45.6 + - + +
58A ALA* 4.7 5.9 - - - +
62A ALA* 2.9 30.1 + - + +
63A ASP* 2.7 39.7 + - - +
182A SER* 4.1 1.3 - - - +
183A PRO* 1.3 79.2 - - - +
185A ALA* 1.3 62.7 + - - +
187A THR* 3.8 2.1 - - - -
188A ARG* 3.1 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 3.6 14.9 - - - +
159A VAL* 3.7 27.4 - - + -
181A THR* 3.8 8.5 - - - +
182A SER* 3.0 22.2 + - - +
184A ARG* 1.3 77.8 - - - +
186A ILE* 1.3 57.2 + - - +
188A ARG* 3.4 8.5 + - - +
189A THR* 3.0 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 4.4 3.1 - - - -
71A VAL* 3.7 26.0 - - + -
75A LEU* 4.1 26.9 - - + -
160A THR* 3.9 18.2 - - + +
181A THR* 3.7 17.7 + - + +
182A SER 3.1 13.8 + - - +
183A PRO* 3.9 0.4 - - + +
185A ALA* 1.3 74.4 - - - +
187A THR* 1.3 62.8 + - - +
189A THR* 4.4 4.9 - - - -
190A TYR* 2.8 49.1 + - + +
247A ALA* 4.7 3.8 - - + -
262A THR* 3.3 34.5 - - + +
264A LEU* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.2 34.0 + - + +
49A TYR* 4.9 4.9 - - + +
183A PRO 2.8 20.5 + - - -
184A ARG 3.8 0.7 - - - -
185A ALA 3.3 0.2 - - - -
186A ILE* 1.3 76.4 - - - +
188A ARG* 1.3 58.5 + - - +
190A TYR* 4.6 0.9 - - - -
191A GLY* 2.9 24.6 + - - -
260A VAL* 3.5 42.6 - - + +
262A THR* 2.7 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 5.8 0.8 - - + -
155A LEU* 3.0 30.1 + - - +
156A GLY* 3.6 23.9 + - - -
157A ASP* 3.7 11.7 - - - +
184A ARG* 3.1 19.9 + - + +
185A ALA* 3.7 7.0 - - - +
187A THR* 1.3 77.6 - - - +
189A THR* 1.3 67.3 + - - +
191A GLY* 3.3 2.4 + - - -
192A ARG* 3.0 45.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
75A LEU* 3.7 28.7 - - + -
152A VAL* 4.2 11.4 - - + -
155A LEU* 4.2 21.6 - - + +
157A ASP* 2.7 34.4 + - - +
185A ALA 3.0 12.0 + - - -
186A ILE* 3.9 7.0 - - + -
188A ARG* 1.3 78.8 + - - +
190A TYR* 1.3 67.2 + - - +
192A ARG* 3.2 9.2 + - - +
193A LEU* 3.1 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 2.7 32.4 + - + +
74A THR* 2.7 43.8 + - + -
75A LEU* 4.1 14.1 - - + -
186A ILE* 2.8 45.2 + - + +
187A THR* 4.0 3.1 - - - +
189A THR* 1.3 73.1 - - - +
191A GLY* 1.3 62.0 + - - +
193A LEU* 3.4 6.1 + - + +
194A VAL* 3.1 31.4 + - + +
211A LEU* 4.7 11.2 - - + -
234A LYS* 3.4 11.4 - - + +
247A ALA* 3.6 35.9 - - + -
248A GLY* 4.4 7.0 - - - -
249A VAL* 5.3 2.5 - - + -
260A VAL* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A THR 2.9 18.5 + - - -
188A ARG* 3.6 2.2 - - - -
190A TYR* 1.3 76.3 - - - +
192A ARG* 1.3 54.7 + - - +
194A VAL* 5.2 0.7 - - - -
195A LEU* 2.8 35.7 + - - +
196A GLY 3.1 5.2 + - - -
249A VAL* 5.4 0.4 - - - -
260A VAL* 4.1 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER 4.9 1.2 + - - -
155A LEU* 3.1 47.2 + - + +
188A ARG* 3.0 45.8 + - + +
189A THR* 3.2 8.9 + - - +
191A GLY* 1.3 74.8 - - - +
193A LEU* 1.3 62.4 + - - +
196A GLY* 3.2 30.7 - - - +
197A ASP* 3.6 23.6 + - - +
198A ALA* 3.4 30.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
74A THR* 4.4 10.5 - - + -
75A LEU* 4.0 26.0 - - + -
78A ALA* 3.9 22.9 - - + -
151A PHE* 4.0 15.9 - - + -
155A LEU* 4.0 15.3 - - + -
189A THR* 3.1 18.0 + - + +
190A TYR* 3.7 9.9 - - - +
192A ARG* 1.3 80.5 - - - +
194A VAL* 1.3 63.5 + - + +
196A GLY 4.5 0.5 - - - +
198A ALA* 3.8 20.4 - - + -
199A LEU* 4.2 20.1 - - + +
204A ARG* 3.6 18.9 - - - +
207A LEU* 3.9 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 6.0 0.7 - - + -
190A TYR* 3.1 20.1 + - + +
191A GLY 4.5 0.2 - - - +
193A LEU* 1.3 82.9 - - + +
195A LEU* 1.3 71.3 + - + +
204A ARG* 3.2 21.2 - - - +
207A LEU* 4.8 5.6 - - + -
208A THR* 3.7 22.7 + - + +
211A LEU* 3.6 31.0 - - + -
249A VAL* 4.1 25.4 - - + -
251A TRP* 4.4 15.7 - - + -
----------------------------------------------------------
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