Contacts of the helix formed by residues 188 - 206 (chain A) in PDB entry 4DVQ
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 VAL 188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 5.0 7.9 - - + -
172A LEU* 5.7 2.9 - - + -
186A LEU* 3.5 16.7 + - + -
187A ASP* 1.3 72.8 + - - +
189A GLN* 1.3 67.8 + - - +
190A PRO 3.3 1.6 - - - -
191A SER* 3.2 17.6 + - - +
192A ILE* 3.0 30.9 + - + +
324A LEU* 4.0 14.1 - - + -
327A LEU* 4.4 4.3 - - + -
495A PRO 5.1 1.7 + - - +
497A LEU* 3.5 35.4 - - + -
499A PHE* 3.4 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 3.3 12.9 + - - +
188A VAL* 1.3 77.6 - - - +
190A PRO* 1.3 76.6 - - + +
192A ILE* 3.8 0.2 - - - +
193A PHE* 3.0 56.4 + - + -
321A PHE* 4.0 17.2 - - - -
324A LEU* 4.1 19.6 - - + +
491A PRO* 5.7 1.9 - - - +
493A THR 5.4 0.9 - - - +
494A SER* 3.4 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 3.7 27.6 - - + +
188A VAL 3.8 0.2 - - - -
189A GLN* 1.3 97.4 - - + +
191A SER* 1.3 60.8 + - - +
193A PHE* 3.4 3.7 + - + +
194A HIS* 2.8 39.1 + - + +
216A PRO* 5.5 7.0 - - + -
224A LEU* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.6 28.5 - - - -
186A LEU* 4.8 6.8 - - - +
187A ASP 5.1 0.6 + - - -
188A VAL* 3.2 22.5 + - - +
190A PRO* 1.3 78.7 - - - +
192A ILE* 1.3 55.9 + - - +
194A HIS* 3.4 6.7 + - - +
195A TYR* 2.9 28.1 + - - +
211A LEU 5.5 0.2 - - - +
212A VAL* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.9 17.7 - - + -
188A VAL* 3.0 31.9 + - + +
189A GLN 3.8 2.7 - - - +
191A SER* 1.3 74.7 - - - +
193A PHE* 1.3 65.9 + - - +
195A TYR* 3.2 4.7 + - - +
196A THR* 2.9 22.7 + - - +
320A ALA* 3.6 28.3 - - - +
323A LEU* 3.9 17.7 - - + -
324A LEU* 3.8 16.4 - - + -
327A LEU* 4.1 14.4 - - + -
463A LEU* 3.6 32.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
189A GLN* 3.0 53.3 + - + +
190A PRO* 3.8 5.6 - - + +
192A ILE* 1.3 76.4 - - - +
194A HIS* 1.3 58.5 + - - +
196A THR* 2.9 20.1 + - - -
197A ILE* 3.0 20.4 + - - +
224A LEU* 3.5 36.6 - - + -
316A VAL* 3.9 5.8 - - + +
317A ASP* 3.7 26.9 - - - -
320A ALA* 3.6 26.5 - - + -
321A PHE* 3.5 37.0 - + - -
324A LEU* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PRO* 2.8 32.0 + - + +
191A SER* 3.9 6.5 - - - +
193A PHE* 1.3 73.4 - - - +
195A TYR* 1.3 60.2 + - - +
197A ILE* 3.3 8.7 + - + +
198A GLU* 2.9 31.5 + - - +
211A LEU* 3.5 35.9 - - + +
216A PRO* 3.5 36.1 - - + +
220A SER* 2.7 36.8 + - - -
221A LEU* 4.4 5.1 - - + +
224A LEU* 3.6 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL* 3.8 10.7 - - - +
164A VAL* 3.7 26.2 - - + -
165A ALA* 3.8 19.2 - - - +
168A PHE* 4.0 17.7 - - + -
191A SER 2.9 15.8 + - - +
192A ILE* 3.3 9.6 - - - +
194A HIS* 1.3 75.5 - - - +
196A THR* 1.3 68.6 + - + +
198A GLU* 3.2 1.2 + - - +
199A ALA* 2.8 37.0 + - + +
212A VAL* 4.0 10.2 - - + +
323A LEU* 4.0 13.2 - - + -
459A GLU* 2.7 45.7 + - + -
463A LEU* 3.4 31.1 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
192A ILE 2.9 18.2 + - - +
193A PHE* 2.9 22.0 + - - -
195A TYR* 1.3 86.9 - - + +
197A ILE* 1.3 63.1 + - - +
200A SER* 2.9 30.2 + - - -
315A SER 4.0 7.6 - - - -
316A VAL* 3.4 23.0 + - - +
319A THR* 3.8 16.6 - - + -
320A ALA* 3.8 24.9 - - - +
323A LEU* 4.4 2.9 - - + -
459A GLU* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE 3.0 20.8 + - - +
194A HIS* 3.6 24.0 - - + +
196A THR* 1.3 76.7 + - - +
198A GLU* 1.3 56.2 + - - +
200A SER* 4.1 2.3 - - - -
201A ASN* 3.0 28.5 + - + +
209A LEU* 4.1 3.8 - - + -
211A LEU* 3.9 17.3 - - + -
220A SER* 4.3 9.4 - - - -
223A PHE* 4.3 13.5 - - + -
224A LEU* 3.8 27.4 - - + -
266A TYR* 3.6 25.4 - - + +
316A VAL* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL* 3.6 18.6 - - + -
194A HIS 2.9 16.1 + - - +
195A TYR 3.6 3.4 - - - +
197A ILE* 1.3 74.9 - - - +
199A ALA* 1.3 66.8 + - - +
201A ASN* 3.2 4.5 + - - +
202A LEU* 2.9 22.9 + - - +
207A GLU 4.7 1.0 - - - +
208A ARG* 2.8 31.5 + - - +
209A LEU* 3.1 15.1 + - - +
210A GLY* 2.8 24.7 + - - -
211A LEU* 2.7 32.5 + - - +
212A VAL* 3.8 15.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
161A VAL* 4.4 11.7 - - + +
164A VAL* 4.0 14.3 - - + +
195A TYR* 2.8 36.8 + - + +
198A GLU* 1.3 73.7 - - - +
200A SER* 1.3 63.9 + - - +
202A LEU* 3.3 1.9 + - - +
203A ALA* 3.0 25.5 + - - +
459A GLU* 3.5 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR 2.9 18.0 + - - -
197A ILE* 4.1 3.8 - - - -
199A ALA* 1.3 77.0 - - - +
201A ASN* 1.3 59.9 + - - +
203A ALA* 3.7 3.3 - - - +
204A LEU* 2.8 41.5 + - - +
315A SER* 2.9 41.8 + - - -
316A VAL* 5.7 0.4 - - - -
455A LEU* 5.0 2.7 - - - -
459A GLU* 2.7 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 3.0 20.7 + - + +
198A GLU 3.9 2.5 - - - +
200A SER* 1.3 74.5 - - - +
202A LEU* 1.3 61.7 + - - +
204A LEU* 5.1 0.9 - - - -
205A PHE* 2.9 41.5 + - - +
206A GLY 3.5 2.4 + - - -
207A GLU* 3.4 30.7 + - - +
209A LEU* 3.6 30.2 - - + +
266A TYR* 4.1 5.0 + - - -
270A CYS* 3.6 26.4 - - - -
312A THR* 5.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A MET* 3.6 41.7 - - + +
163A ALA* 5.2 3.1 - - + -
164A VAL* 3.7 18.6 - - + -
198A GLU 2.9 16.3 + - - +
199A ALA 3.8 2.9 - - - +
201A ASN* 1.3 77.8 - - - +
203A ALA* 1.3 59.1 + - - +
206A GLY* 2.7 56.4 + - - +
207A GLU 3.4 16.5 + - - +
208A ARG* 3.7 29.4 - - + +
288A GLY* 4.5 0.2 - - - -
178C GLN 5.2 2.5 - - - +
180C ALA* 5.4 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 4.2 11.9 - - + -
160A MET* 3.7 12.1 - - + +
161A VAL* 4.2 11.2 - - + +
199A ALA 3.0 16.6 + - - +
200A SER 4.0 1.8 - - - +
202A LEU* 1.3 76.1 - - - +
204A LEU* 1.3 59.3 + - - +
286A TYR* 4.2 1.2 + - - -
288A GLY* 3.3 5.9 - - - -
289A ILE* 2.9 32.2 + - + +
455A LEU* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 5.9 0.2 - - + -
200A SER* 2.8 33.5 + - - +
201A ASN* 5.1 0.7 - - - -
203A ALA* 1.3 74.1 - - - +
205A PHE* 1.3 75.4 + - + +
288A GLY 3.8 0.9 - - - -
289A ILE* 3.2 28.8 + - + +
290A VAL* 2.9 36.6 + - + +
291A ALA 4.3 0.9 + - - -
308A SER 5.2 0.2 - - - +
311A LEU* 3.8 57.7 - - + +
312A THR* 4.0 16.8 - - + +
315A SER* 4.3 7.0 - - - +
455A LEU* 4.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASN* 2.9 40.2 + - - +
204A LEU* 1.3 90.6 - - + +
206A GLY* 1.3 61.1 + - - +
207A GLU* 3.4 6.2 + - + +
267A GLY 4.9 1.8 - - - -
270A CYS* 3.6 46.2 - - + +
271A ILE* 4.2 8.5 - - + -
274A ILE* 4.0 16.2 - - + -
287A THR 3.8 4.7 - - - -
290A VAL* 4.1 15.5 - - + -
308A SER* 3.3 27.1 - - - -
312A THR* 3.4 23.3 - - + -
181C ARG* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A MET* 5.3 1.1 - - - -
202A LEU* 2.7 35.7 + - - +
204A LEU 3.7 0.2 - - - -
205A PHE* 1.3 72.3 - - - +
207A GLU* 1.3 57.4 + - - +
287A THR 3.5 19.7 + - - -
179C ASN* 3.8 2.8 - - - +
180C ALA* 3.0 35.9 + - - +
181C ARG* 4.3 3.9 + - - -
----------------------------------------------------------
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