Contacts of the helix formed by residues 188 - 206 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B PHE* 4.9 5.8 - - + -
172B LEU* 5.7 2.2 - - + -
186B LEU* 3.4 21.3 + - + -
187B ASP* 1.3 70.9 + - - +
189B GLN* 1.3 66.2 + - - +
190B PRO* 3.4 2.0 - - - -
191B SER* 3.4 13.8 + - - +
192B ILE* 2.9 30.8 + - + +
324B LEU* 4.0 13.9 - - + -
327B LEU* 4.5 8.1 - - + -
494B SER* 5.8 0.7 - - - +
495B PRO 5.0 2.2 + - - +
497B LEU* 3.5 34.5 - - + -
499B PHE* 3.5 29.4 - - + -
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Residues in contact with GLN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 3.2 13.1 + - - +
188B VAL* 1.3 77.2 - - - +
190B PRO* 1.3 76.4 - - + +
192B ILE* 3.9 0.2 - - - -
193B PHE* 3.0 50.7 + - + -
321B PHE* 4.0 18.1 - - - -
324B LEU* 3.5 20.4 - - + +
491B PRO* 5.7 3.3 - - - +
493B THR 5.4 1.0 - - - +
494B SER* 3.7 21.4 + - - +
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Residues in contact with PRO 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 3.7 26.2 - - - +
188B VAL 3.7 0.2 - - - -
189B GLN* 1.3 97.8 - - + +
191B SER* 1.3 62.5 + - - +
193B PHE* 3.2 3.1 + - + +
194B HIS* 3.0 34.3 + - + +
216B PRO* 5.6 5.8 - - + -
224B LEU* 6.1 1.1 - - + -
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Residues in contact with SER 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.5 28.5 - - - -
186B LEU* 4.7 9.1 - - - +
187B ASP 5.4 0.2 + - - -
188B VAL* 3.4 17.8 + - - +
189B GLN 3.3 0.4 - - - -
190B PRO* 1.3 79.0 - - - +
192B ILE* 1.3 59.2 + - - +
194B HIS* 3.3 7.7 + - - +
195B TYR* 3.0 27.5 + - - +
212B VAL* 5.7 0.2 - - - +
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.6 24.9 - - + -
188B VAL* 2.9 32.8 + - + +
189B GLN 4.0 2.2 - - - +
191B SER* 1.3 73.0 - - - +
193B PHE* 1.3 65.2 + - - +
195B TYR* 3.5 3.5 + - - +
196B THR* 3.2 21.5 + - - +
320B ALA* 3.8 30.3 - - + +
323B LEU* 4.2 14.1 - - + -
324B LEU* 4.1 17.3 - - + -
327B LEU* 4.2 13.2 - - + -
463B LEU* 3.8 29.8 - - + -
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Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLN* 3.0 45.5 + - + +
190B PRO* 3.6 4.9 - - + +
192B ILE* 1.3 76.3 - - - +
194B HIS* 1.3 59.7 + - - +
196B THR* 2.8 21.0 + - - -
197B ILE* 3.0 19.2 + - - +
224B LEU* 3.6 37.0 - - + -
316B VAL* 3.8 7.8 - - + +
317B ASP* 3.4 33.2 - - - -
320B ALA* 3.5 19.1 - - + -
321B PHE* 3.4 44.9 - + - -
324B LEU* 4.0 4.3 - - + -
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Residues in contact with HIS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PRO* 3.0 31.1 + - + +
191B SER* 3.8 7.6 - - - +
192B ILE 3.3 0.2 - - - -
193B PHE* 1.3 75.2 - - - +
195B TYR* 1.3 59.7 + - - +
197B ILE* 3.4 8.1 + - + +
198B GLU* 2.9 30.0 + - - +
211B LEU* 3.5 34.0 - - + +
212B VAL* 4.6 0.2 - - - -
216B PRO* 3.4 43.4 - - + +
220B SER* 3.0 33.3 + - - -
221B LEU* 4.3 4.8 - - + +
224B LEU* 3.9 24.5 - - + +
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Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B VAL* 3.9 7.0 - - - +
164B VAL* 3.6 29.8 - - + -
165B ALA* 3.8 22.9 - - - +
168B PHE* 4.1 17.5 - - + -
191B SER 3.0 13.6 + - - +
192B ILE* 3.5 11.2 - - + +
194B HIS* 1.3 72.2 - - - +
196B THR* 1.3 69.3 + - + +
198B GLU 3.1 0.7 + - - -
199B ALA* 2.7 41.2 + - + +
212B VAL* 4.0 9.9 - - + +
323B LEU* 4.0 10.8 - - + -
459B GLU* 2.6 43.3 + - + -
463B LEU* 3.1 40.0 + - + +
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Residues in contact with THR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ILE 3.2 12.4 + - - +
193B PHE* 2.8 21.7 + - - -
195B TYR* 1.3 87.2 - - + +
197B ILE* 1.3 62.6 + - - +
199B ALA* 4.6 0.7 - - - +
200B SER* 2.7 29.9 + - - -
315B SER 3.9 10.1 - - - -
316B VAL* 3.4 23.7 + - - +
319B THR* 3.7 27.4 - - + -
320B ALA* 3.7 16.1 - - - +
323B LEU* 4.4 2.7 - - + -
459B GLU* 4.0 8.3 - - - +
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE 3.0 19.2 + - - +
194B HIS* 3.7 14.8 - - - +
195B TYR 3.3 0.2 - - - -
196B THR* 1.3 76.9 + - - +
198B GLU* 1.3 58.5 + - - +
200B SER* 3.8 2.1 - - - -
201B ASN* 2.9 28.3 + - + +
209B LEU* 4.2 4.0 - - + -
211B LEU* 4.0 15.5 - - + -
220B SER* 3.9 19.7 - - - +
223B PHE* 4.3 12.3 - - + -
224B LEU* 3.8 29.4 - - + -
266B TYR* 3.5 25.1 - - + +
316B VAL* 3.9 24.0 - - + +
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL* 3.8 13.2 - - + -
194B HIS 2.9 17.3 + - - +
195B TYR 3.7 2.7 - - - +
197B ILE* 1.3 75.8 - - - +
199B ALA* 1.3 67.0 + - - +
201B ASN* 3.2 5.1 + - - +
202B LEU* 3.0 23.6 + - - +
207B GLU 4.6 1.0 - - - +
208B ARG* 2.7 36.4 + - - +
209B LEU* 3.2 15.3 + - - +
210B GLY* 2.9 22.7 + - - -
211B LEU* 2.6 34.5 + - - +
212B VAL* 3.8 14.4 - - + -
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL* 4.5 11.7 - - + +
164B VAL* 4.0 15.9 - - + +
195B TYR* 2.7 42.8 + - + +
196B THR* 4.7 0.2 - - - -
198B GLU* 1.3 74.0 - - - +
200B SER* 1.3 60.5 + - - +
202B LEU* 3.4 2.4 + - - +
203B ALA* 3.0 25.6 + - - +
459B GLU* 3.5 25.1 - - + +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B THR 2.7 21.7 + - - -
197B ILE* 3.8 3.6 - - - -
199B ALA* 1.3 75.7 - - - +
201B ASN* 1.3 58.0 + - - +
203B ALA* 3.8 3.0 - - - +
204B LEU* 2.8 37.8 + - - +
315B SER* 3.1 42.9 + - - -
316B VAL* 5.8 0.4 - - - -
455B LEU* 4.9 2.5 - - - -
459B GLU* 2.7 21.7 + - - -
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Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 2.9 20.0 + - + +
198B GLU 3.7 4.3 - - - +
200B SER* 1.3 76.5 - - - +
202B LEU* 1.3 60.4 + - - +
204B LEU* 4.6 0.9 - - - -
205B PHE* 2.8 52.1 + - - +
206B GLY 3.4 3.1 + - - -
207B GLU* 3.6 21.5 + - - +
209B LEU* 3.5 41.7 - - + +
266B TYR* 4.6 3.5 + - - -
270B CYS* 3.7 16.2 - - - -
273B LYS* 5.4 1.4 - - - +
312B THR* 5.6 1.6 - - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B MET* 3.5 53.5 - - + +
163B ALA* 4.9 5.2 - - + -
164B VAL* 3.7 16.2 - - + -
198B GLU 3.0 16.8 + - - +
199B ALA 3.9 3.4 - - - +
201B ASN* 1.3 76.7 - - - +
203B ALA* 1.3 59.2 + - - +
206B GLY* 2.8 48.3 + - - +
207B GLU 3.3 22.1 + - - +
208B ARG* 4.2 17.5 - - + +
178D GLN 5.0 4.7 - - - +
180D ALA* 5.3 4.5 - - + +
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PHE* 4.4 11.0 - - + -
160B MET* 3.7 13.5 - - - +
161B VAL* 4.5 6.9 - - + +
199B ALA 3.0 18.2 + - - +
200B SER 3.8 3.1 - - - +
202B LEU* 1.3 76.7 - - - +
204B LEU* 1.3 58.5 + - - +
288B GLY* 3.2 6.9 - - - -
289B ILE* 2.9 30.6 + - + +
455B LEU* 3.6 32.8 - - + -
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B VAL* 6.0 0.4 - - + -
200B SER* 2.8 28.2 + - - +
201B ASN* 5.2 0.2 - - - -
203B ALA* 1.3 75.5 - - - +
205B PHE* 1.3 73.3 + - + +
288B GLY 3.9 1.0 - - - -
289B ILE* 3.4 21.5 + - + +
290B VAL* 2.9 38.6 + - + +
291B ALA 4.3 0.3 + - - -
311B LEU* 3.4 63.0 - - + +
312B THR* 3.9 15.3 - - + +
315B SER* 4.0 10.3 - - - +
455B LEU* 4.6 10.8 - - + -
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ASN* 2.8 42.0 + - - +
204B LEU* 1.3 85.4 - - + +
206B GLY* 1.3 59.0 + - - +
207B GLU* 3.4 7.9 + - + +
267B GLY 4.8 1.1 - - - -
270B CYS* 3.6 46.4 - - + +
271B ILE* 4.2 9.4 - - + -
274B ILE* 3.5 18.3 - - + +
287B THR 3.6 6.1 - - - -
290B VAL* 3.8 28.9 - - + -
308B SER* 4.5 9.0 - - - -
312B THR* 3.4 26.5 - - + -
181D ARG* 2.9 33.3 + - - +
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B MET* 5.2 1.1 - - - -
202B LEU* 2.8 34.8 + - - +
205B PHE* 1.3 71.9 - - - +
207B GLU* 1.3 59.0 + - - +
287B THR 3.2 19.0 + - - -
179D ASN* 3.7 3.8 - - - +
180D ALA* 3.1 33.5 + - - +
181D ARG* 4.3 5.3 + - - -
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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) + - + + + + + -
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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