Contacts of the helix formed by residues 184 - 198 (chain A) in PDB entry 3CBG
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 GLU 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TRP* 2.6 29.8 + - - -
176A LYS* 2.8 28.4 + - + +
179A GLU* 5.4 1.9 + - - +
182A PRO* 3.6 1.0 - - - +
183A GLN* 1.3 78.7 - - - +
185A ALA* 1.3 64.6 + - - +
186A GLN* 2.9 32.8 - - - +
187A THR* 3.3 14.5 + - - +
188A GLN* 3.2 22.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
147A ARG* 3.2 42.6 - - - +
183A GLN 3.6 3.2 + - - -
184A GLU* 1.3 74.0 - - - +
186A GLN* 1.3 66.3 + - - +
188A GLN* 3.1 16.3 + - - +
189A VAL* 2.9 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS* 3.8 32.5 - - + +
147A ARG* 4.4 16.9 - - - +
173A TRP* 3.7 17.3 - - + +
184A GLU* 2.9 37.1 - - - +
185A ALA* 1.3 86.9 - - - +
187A THR* 1.3 56.1 + - - +
189A VAL* 4.0 4.2 - - - +
190A LEU* 2.9 37.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
173A TRP* 3.4 21.7 - - + -
176A LYS* 3.3 44.9 - - + +
177A VAL* 4.2 3.1 - - + +
179A GLU* 4.2 2.6 + - - +
182A PRO* 3.4 22.2 - - + -
184A GLU* 3.3 22.7 + - - +
185A ALA 3.2 0.6 - - - -
186A GLN* 1.3 75.6 - - - +
188A GLN* 1.3 61.8 + - - +
190A LEU* 3.4 3.0 + - - +
191A GLN* 2.9 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 6.1 0.2 - - - +
182A PRO* 2.7 37.2 - - + +
183A GLN* 3.5 13.8 + - - +
184A GLU 3.3 13.2 - - - +
185A ALA* 3.1 16.4 + - - +
187A THR* 1.3 77.4 - - - +
189A VAL* 1.3 63.5 + - + +
191A GLN* 3.4 10.8 + - - +
192A GLN* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS 3.3 25.4 - - - +
147A ARG* 3.7 31.9 - - + +
149A TYR* 5.0 1.1 - - + -
150A PRO* 3.7 19.9 - - + +
185A ALA* 2.9 26.2 + - + +
186A GLN 4.0 4.5 - - - +
188A GLN* 1.3 79.4 - - + +
190A LEU* 1.3 58.7 + - + +
192A GLN* 3.6 4.6 + - - +
193A PHE* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS* 4.1 19.5 - - + +
149A TYR* 3.6 39.3 - - + -
170A ASN 3.5 19.5 - - - +
171A VAL* 5.2 2.9 - - + -
173A TRP* 3.4 42.0 - - + -
177A VAL* 4.8 4.5 - - + -
186A GLN 2.9 26.0 + - - +
187A THR* 3.9 3.8 - - - +
189A VAL* 1.3 75.7 - - + +
191A GLN* 1.3 60.9 + - - +
193A PHE* 3.5 7.3 - - + +
194A ASN* 2.9 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS 4.2 1.7 - - - +
177A VAL* 3.1 35.7 - - + +
179A GLU 3.1 22.3 - - - +
180A VAL 5.4 0.4 + - - -
182A PRO* 3.1 33.5 - - - +
187A THR* 2.9 23.1 + - - +
188A GLN* 3.7 6.7 + - - +
189A VAL 3.3 0.2 - - - -
190A LEU* 1.3 77.9 - - - +
192A GLN* 1.3 60.5 + - - +
194A ASN* 3.5 6.1 + - - +
195A ARG* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PRO* 6.6 0.2 - - + -
188A GLN 3.2 13.9 + - - +
189A VAL* 4.0 5.4 - - - +
191A GLN* 1.3 76.4 - - - +
193A PHE* 1.3 60.6 + - - +
195A ARG* 3.0 35.7 + - - +
196A ASP* 2.9 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 5.9 0.2 - - + -
149A TYR* 3.9 20.2 - + + -
150A PRO* 4.1 27.5 - - + +
153A TYR* 3.6 36.6 - + + -
168A ILE* 4.0 38.4 - - + -
171A VAL* 4.9 3.6 - - + -
189A VAL 3.0 18.9 + - - +
190A LEU* 3.5 10.8 - - + +
191A GLN 3.3 0.2 - - - -
192A GLN* 1.3 78.1 - - - +
194A ASN* 1.3 71.7 + - - +
196A ASP* 3.7 6.6 - - + +
197A LEU* 3.0 55.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
171A VAL* 2.8 46.3 + - - +
177A VAL* 4.4 9.1 - - - +
190A LEU* 2.9 25.1 + - - +
191A GLN* 4.0 4.8 - - - +
193A PHE* 1.3 87.5 - - - +
195A ARG* 1.3 65.1 + - - +
197A LEU* 3.4 5.8 + - - +
198A ALA* 3.0 25.1 + - - +
205A ILE* 5.6 0.9 - - - +
215A THR* 4.9 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLN 3.2 18.2 + - - +
192A GLN* 3.0 25.4 - - - +
194A ASN* 1.3 77.3 - - - +
196A ASP* 1.3 88.2 + - - +
198A ALA* 3.5 10.8 + - - +
199A GLN* 2.6 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLN* 2.9 39.9 + - - +
193A PHE* 3.7 6.8 + - + +
195A ARG* 1.3 111.6 + - - +
197A LEU* 1.3 60.4 + - - +
199A GLN* 3.4 6.5 + - - +
200A ASP* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.1 45.1 - - + +
168A ILE* 4.1 9.6 - - + -
193A PHE* 3.0 41.5 + - + +
194A ASN* 4.0 5.8 - - - +
195A ARG 3.3 0.2 - - - -
196A ASP* 1.3 72.9 - - - +
198A ALA* 1.3 64.1 + - - +
199A GLN 3.1 3.1 + - - -
200A ASP* 3.3 17.5 + - - +
203A VAL* 3.9 10.3 - - + -
205A ILE* 3.9 24.0 - - + +
215A THR* 3.7 30.7 - - + +
217A ALA* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASN 3.0 16.9 + - - +
195A ARG* 3.7 10.3 - - + +
196A ASP 3.3 0.6 - - - -
197A LEU* 1.3 76.4 - - - +
199A GLN* 1.3 58.8 + - + +
200A ASP 3.6 0.4 - - - -
205A ILE* 4.1 16.9 - - + +
----------------------------------------------------------
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