Contacts of the helix formed by residues 187 - 201 (chain A) in PDB entry 3L6B
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 187 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 3.8 17.5 - - - -
185A GLY 3.2 2.2 - - - -
186A GLY* 1.3 78.7 - - - +
188A GLY* 1.3 57.4 + - - +
189A MET 3.4 1.8 - - - -
190A LEU* 3.9 3.8 - - - -
191A ALA* 2.9 34.9 + - - +
248A THR* 3.3 5.9 - - - +
252A ILE* 3.9 13.1 - - - +
350A PLP 2.8 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 3.5 26.0 - - - +
159A VAL* 5.9 0.2 - - - -
160A ILE* 3.6 14.4 - - - +
163A GLN* 4.1 12.5 - - - +
186A GLY 3.5 3.2 + - - -
187A GLY* 1.3 77.9 - - - +
189A MET* 1.3 54.6 + - - -
192A GLY* 3.0 24.9 + - - -
248A THR* 3.9 3.4 - - - -
350A PLP 2.8 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.5 47.3 - - + -
163A GLN* 3.6 12.4 - - + +
166A ILE* 3.7 24.7 - - + -
182A VAL* 3.7 10.8 - - + -
183A PRO* 3.4 40.6 - - + +
188A GLY* 1.3 72.1 - - - +
190A LEU* 1.3 66.9 + - - +
192A GLY 3.3 0.5 + - - -
193A ILE* 2.9 41.8 + - + +
311A VAL* 4.0 12.3 - - - -
313A SER* 4.1 1.6 - - - -
350A PLP 2.9 14.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
182A VAL* 3.9 29.3 - - + +
183A PRO 5.1 0.8 + - - +
184A VAL* 3.8 20.6 - - + -
187A GLY* 3.6 12.3 + - - +
189A MET* 1.3 78.5 - - - +
191A ALA* 1.3 59.2 + - - +
193A ILE* 3.8 2.1 - - - +
194A ALA* 2.9 30.7 + - - +
206A VAL* 3.9 13.7 - - + -
208A ALA* 3.6 36.1 - - + +
217A CYS* 4.4 1.1 - - - -
252A ILE* 3.7 27.8 - - + -
256A VAL* 3.7 22.4 - - + -
350A PLP 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 4.2 4.3 - - + -
187A GLY 2.9 20.6 + - - +
188A GLY 4.0 1.3 - - - +
190A LEU* 1.3 75.3 - - - +
192A GLY* 1.3 66.4 + - - +
194A ALA* 3.3 0.6 + - - -
195A ILE* 2.9 29.0 + - - +
248A THR* 3.9 18.2 - - + +
251A ILE* 3.6 38.1 - - + +
252A ILE* 4.6 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.1 7.6 - - - -
12A VAL* 4.4 0.7 - - - +
160A ILE* 3.6 29.4 - - - +
164A GLY* 3.4 10.0 - - - -
188A GLY 3.0 12.3 + - - -
189A MET 3.8 0.2 - - - -
191A ALA* 1.3 76.7 - - - +
193A ILE* 1.3 60.2 + - - +
195A ILE* 3.5 2.4 + - - +
196A THR* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN 4.3 12.6 - - - +
164A GLY* 3.7 1.1 - - - +
166A ILE* 4.2 11.9 - - + -
167A ALA* 4.1 16.8 - - + +
180A LEU* 3.8 23.8 - - + -
182A VAL* 3.8 27.1 - - + -
189A MET* 2.9 38.3 + - + +
190A LEU 3.9 2.7 - - - +
192A GLY* 1.3 74.3 - - - +
194A ALA* 1.3 59.9 + - - +
196A THR* 3.2 1.0 + - - -
197A VAL* 2.8 37.5 + - + +
206A VAL* 4.3 10.1 - - + -
311A VAL* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU 2.9 19.5 + - - +
191A ALA 3.3 3.8 + - - +
193A ILE* 1.3 76.6 - - - +
195A ILE* 1.3 63.9 + - - +
198A LYS* 3.0 30.3 + - - +
206A VAL* 4.3 13.5 - - + -
251A ILE* 4.1 6.1 - - + -
255A LEU* 4.0 27.8 - - + +
256A VAL* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.8 22.4 - - + -
7A ILE* 3.9 33.7 - - + +
8A SER* 3.7 8.3 - - - -
9A PHE* 3.5 29.8 - - + +
12A VAL* 4.5 2.2 - - + -
191A ALA 2.9 21.4 + - - +
192A GLY 3.8 4.0 - - - +
194A ALA* 1.3 75.9 - - - +
196A THR* 1.3 57.7 + - - +
198A LYS* 4.0 0.7 - - - +
199A ALA* 3.1 28.4 + - - +
251A ILE* 3.9 13.7 - - + -
255A LEU* 3.8 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 4.0 13.2 - - + -
12A VAL* 3.3 24.8 - - - +
164A GLY 3.6 2.2 + - - +
167A ALA* 3.7 22.7 - - + -
168A LEU* 3.7 35.0 - - + +
171A LEU* 5.0 0.2 - - + -
192A GLY 2.8 21.1 + - - -
193A ILE 3.6 3.4 - - - -
194A ALA 3.2 0.4 - - - -
195A ILE* 1.3 75.3 - - - +
197A VAL* 1.3 66.0 + - - +
199A ALA* 3.2 4.0 + - - +
200A LEU* 3.1 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 3.9 18.8 - - + -
171A LEU* 4.4 15.3 - - + -
180A LEU* 4.2 15.0 - - + -
193A ILE* 2.8 32.5 + - + +
196A THR* 1.3 71.8 - - - +
198A LYS* 1.3 59.6 + - + +
201A LYS 2.8 37.2 + - - +
204A VAL* 3.6 45.8 - - + +
206A VAL* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA* 3.0 22.1 + - - +
195A ILE 4.5 1.3 - - - +
197A VAL* 1.3 77.9 - - + +
199A ALA* 1.3 58.7 + - - +
202A PRO* 3.0 48.8 + - + +
204A VAL 2.9 23.2 + - - +
205A LYS* 4.1 1.4 - - - +
206A VAL* 4.1 8.1 - - - -
255A LEU* 3.3 50.5 - - + +
257A ASP* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.6 32.5 - - + -
195A ILE 3.1 19.1 + - - +
196A THR 3.6 3.6 - - - +
197A VAL 3.2 0.2 - - - -
198A LYS* 1.3 79.2 - - - +
200A LEU* 1.3 63.9 + - - +
202A PRO* 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.7 41.5 - - + -
168A LEU* 3.7 18.2 - - + -
171A LEU* 3.8 29.4 - - + -
196A THR* 3.1 11.5 + - + +
199A ALA* 1.3 82.0 - - - +
201A LYS* 1.3 61.6 + - + +
202A PRO* 4.0 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 5.0 11.6 - - + +
175A PRO 5.2 10.3 - - - +
177A VAL* 4.4 7.0 + - + +
178A ASP* 5.6 2.6 + - - +
197A VAL* 2.8 17.2 + - - +
200A LEU* 1.3 78.7 - - + +
202A PRO* 1.4 63.0 - - + +
203A SER* 2.9 32.2 + - - +
204A VAL* 3.0 47.0 + - + +
----------------------------------------------------------
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