Contacts of the helix formed by residues 188 - 206 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J PHE* 4.7 8.5 - - + -
172J LEU* 5.4 2.2 - - + -
186J LEU* 3.7 13.8 + - + +
187J ASP* 1.3 72.2 + - - +
189J GLN* 1.3 67.2 + - - +
190J PRO* 3.4 0.9 - - - -
191J SER* 3.0 18.9 + - - +
192J ILE* 2.9 36.6 + - + +
324J LEU* 3.9 15.3 - - + -
327J LEU* 4.8 3.1 - - + -
494J SER* 4.7 1.0 + - - +
495J PRO* 4.9 1.3 + - + +
497J LEU* 3.4 35.0 - - + -
499J PHE* 3.5 31.6 - - + -
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Residues in contact with GLN 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J ASP* 2.9 18.9 + - - +
188J VAL* 1.3 77.4 - - - +
190J PRO* 1.3 69.4 - - + +
192J ILE 3.8 0.3 - - - -
193J PHE* 2.9 54.3 + - + -
321J PHE* 4.5 15.2 - - - -
324J LEU* 3.7 24.6 - - + +
490J ARG* 6.1 0.4 - - - +
491J PRO* 5.3 1.7 - - - +
493J THR 4.9 2.8 - - - +
494J SER* 3.7 21.1 - - - +
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Residues in contact with PRO 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J ASP* 3.5 25.1 - - + +
188J VAL 3.6 0.4 - - - -
189J GLN* 1.3 96.9 - - + +
191J SER* 1.3 61.1 + - - +
193J PHE* 3.2 4.6 + - + +
194J HIS* 2.8 39.0 + - + +
216J PRO* 5.5 6.7 - - + -
224J LEU* 6.1 0.9 - - + -
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Residues in contact with SER 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J PHE* 3.9 19.6 - - - -
186J LEU* 4.7 7.7 - - - +
187J ASP 5.2 0.2 + - - -
188J VAL* 3.0 27.1 + - - +
190J PRO* 1.3 78.3 - - - +
192J ILE* 1.3 54.6 + - - +
194J HIS* 2.9 8.6 + - - +
195J TYR* 2.8 33.6 + - - +
212J VAL* 5.6 0.5 - - - +
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Residues in contact with ILE 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J PHE* 3.6 24.2 - - + -
188J VAL* 2.9 28.8 + - + +
189J GLN 3.8 2.9 - - - +
191J SER* 1.3 78.6 + - - +
193J PHE* 1.3 62.5 + - + +
195J TYR* 3.4 5.1 + - - +
196J THR* 3.2 21.3 + - - +
320J ALA* 3.9 29.4 - - + +
323J LEU* 4.2 16.6 - - + -
324J LEU* 3.9 20.2 - - + -
327J LEU* 4.1 19.3 - - + -
463J LEU* 3.7 21.8 - - + -
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Residues in contact with PHE 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J GLN* 2.9 51.7 + - + +
190J PRO* 3.6 6.5 - - + +
192J ILE* 1.3 78.9 - - + +
194J HIS* 1.3 61.2 + - - +
196J THR* 3.1 19.5 + - - -
197J ILE* 3.1 16.6 + - - +
224J LEU* 3.7 35.4 - - + -
316J VAL* 4.0 5.7 - - + +
317J ASP* 3.3 27.8 - - - -
320J ALA* 3.4 28.9 - - + -
321J PHE* 3.5 38.6 - + - -
324J LEU* 5.9 2.0 - - + -
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Residues in contact with HIS 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190J PRO* 2.8 28.5 + - + +
191J SER* 2.9 10.8 + - - +
193J PHE* 1.3 76.0 - - - +
195J TYR* 1.3 63.5 + - - +
197J ILE* 3.4 7.2 + - + +
198J GLU* 3.1 23.6 + - - +
211J LEU* 3.9 33.4 - - + +
212J VAL* 4.7 3.1 - - + -
216J PRO* 3.3 38.4 - - + +
220J SER* 2.8 37.8 + - - -
221J LEU* 4.5 6.2 + - + -
224J LEU* 3.6 24.7 - - + +
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Residues in contact with TYR 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161J VAL* 3.8 10.4 - - - +
164J VAL* 3.7 21.3 - - + -
165J ALA* 3.7 33.8 - - - +
168J PHE* 4.1 15.9 - - + -
191J SER 2.8 12.2 + - - +
192J ILE* 3.4 9.6 - - - +
194J HIS* 1.3 75.2 - - - +
196J THR* 1.3 70.7 + - + +
198J GLU* 3.0 2.9 + - - +
199J ALA* 2.8 39.3 + - + +
212J VAL* 4.0 12.0 - - + +
323J LEU* 4.0 9.6 - - + -
459J GLU* 2.7 46.4 + - + -
462J LEU* 4.5 0.3 - - - +
463J LEU* 3.6 27.5 + - + -
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Residues in contact with THR 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J ILE 3.2 14.6 + - - +
193J PHE 3.1 13.7 + - - -
195J TYR* 1.3 87.8 - - + +
197J ILE* 1.3 55.6 + - - +
200J SER* 2.8 32.7 + - - -
315J SER 4.0 6.0 - - - +
316J VAL* 3.1 27.3 + - - +
319J THR* 3.9 14.8 - - + -
320J ALA* 3.8 28.2 - - - +
323J LEU* 4.3 4.3 - - + -
459J GLU* 3.6 13.5 - - - +
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Residues in contact with ILE 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193J PHE 3.1 12.7 + - - +
194J HIS* 3.8 12.3 - - + +
195J TYR 3.1 1.0 - - - -
196J THR* 1.3 75.9 - - - +
198J GLU* 1.3 58.4 + - - +
200J SER* 4.1 3.1 - - - -
201J ASN* 3.0 30.9 + - + +
209J LEU* 3.9 2.7 - - + -
211J LEU* 3.6 19.1 - - + -
220J SER* 4.3 15.7 - - - -
223J PHE* 4.3 13.9 - - + -
224J LEU* 3.5 34.3 - - + -
266J TYR* 3.6 23.3 - - + +
316J VAL* 3.8 23.6 - - + -
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Residues in contact with GLU 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J VAL* 3.5 23.6 - - + -
194J HIS 3.1 12.3 + - - +
195J TYR 3.0 6.5 + - - +
197J ILE* 1.3 74.4 - - - +
199J ALA* 1.3 67.1 + - - +
201J ASN* 3.0 5.7 + - - +
202J LEU* 2.9 24.8 + - - +
207J GLU 4.8 0.9 - - - +
208J ARG* 2.8 30.3 + - - +
209J LEU* 3.2 14.6 + - - +
210J GLY* 2.9 25.1 + - - -
211J LEU* 2.8 33.9 + - - +
212J VAL* 4.1 10.3 + - + -
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Residues in contact with ALA 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161J VAL* 4.3 13.9 - - + +
164J VAL* 3.8 13.3 - - + +
195J TYR* 2.8 38.9 + - + +
198J GLU* 1.3 72.9 - - - +
200J SER* 1.3 62.9 + - - +
202J LEU* 3.4 2.1 + - - +
203J ALA* 3.0 23.9 + - - +
459J GLU* 3.3 30.1 - - + +
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Residues in contact with SER 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J THR 2.8 20.4 + - - -
197J ILE* 4.1 3.4 - - - -
199J ALA* 1.3 75.3 - - - +
201J ASN* 1.3 57.7 + - - +
203J ALA* 3.2 4.7 + - - +
204J LEU* 2.8 39.7 + - - +
315J SER* 3.2 41.3 + - - -
316J VAL* 5.9 0.4 - - - -
455J LEU* 4.7 4.5 - - - +
459J GLU* 2.8 22.8 + - - -
601J HEM 5.5 0.2 - - - +
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Residues in contact with ASN 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197J ILE* 3.0 21.4 + - + +
198J GLU 3.0 2.7 + - - +
200J SER* 1.3 75.7 - - - +
202J LEU* 1.3 57.1 + - - +
204J LEU* 4.7 0.9 - - - -
205J PHE* 2.8 39.4 + - - +
206J GLY 3.4 3.3 + - - -
207J GLU* 3.5 30.1 + - - +
209J LEU* 3.6 33.3 - - + +
266J TYR* 4.5 3.5 + - - +
270J CYS* 3.4 29.7 - - - -
273J LYS* 5.8 1.0 - - - +
312J THR* 5.7 1.2 - - - +
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Residues in contact with LEU 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160J MET* 3.4 53.3 - - + +
163J ALA* 5.0 4.7 - - + -
164J VAL* 3.5 18.6 - - + -
198J GLU 2.9 14.7 + - - +
199J ALA 3.8 3.4 - - - +
201J ASN* 1.3 75.7 - - - +
203J ALA* 1.3 62.1 + - - +
206J GLY* 2.7 41.1 + - - +
207J GLU 3.2 29.7 + - - +
208J ARG* 4.2 17.7 - - + +
288J GLY* 4.5 0.2 - - - -
178K GLN 5.0 4.7 - - - +
180K ALA* 5.5 2.9 - - + +
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Residues in contact with ALA 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J PHE* 4.2 13.7 - - + -
160J MET* 3.7 14.7 - - - +
161J VAL* 4.3 6.9 - - + +
199J ALA 3.0 18.0 + - - +
200J SER 3.8 2.9 - - - +
202J LEU* 1.3 76.3 - - - +
204J LEU* 1.3 58.1 + - - +
286J TYR* 4.4 0.2 + - - -
288J GLY* 3.1 7.4 - - - -
289J ILE* 2.8 29.6 + - + +
455J LEU* 3.8 32.3 - - + -
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Residues in contact with LEU 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200J SER* 2.8 24.0 + - - +
201J ASN* 5.3 0.2 - - - -
203J ALA* 1.3 78.6 - - - +
205J PHE* 1.3 76.1 + - + +
206J GLY 3.6 0.2 - - - -
288J GLY 3.7 2.1 - - - -
289J ILE* 3.2 37.4 + - + +
290J VAL* 3.0 36.1 + - + +
291J ALA 4.0 0.9 + - - -
308J SER 5.1 0.2 - - - +
311J LEU* 3.9 42.8 - - + +
312J THR* 4.0 22.7 - - - +
315J SER* 4.6 6.1 - - - +
455J LEU* 4.7 8.7 - - + -
601J HEM 5.4 1.8 - - + -
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Residues in contact with PHE 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201J ASN* 2.8 35.2 + - - +
204J LEU* 1.3 89.9 - - + +
206J GLY* 1.3 62.1 + - - +
207J GLU* 3.2 13.7 + - + +
267J GLY 4.7 1.8 - - - -
270J CYS* 3.4 41.1 - - + +
271J ILE* 4.1 4.7 - - - -
274J ILE* 3.8 24.5 - - + -
287J THR 3.6 6.7 - - - -
290J VAL* 4.1 17.3 - - + -
308J SER* 3.5 24.9 - - - -
312J THR* 3.6 20.9 - - + -
181K ARG* 2.8 30.3 + - - +
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Residues in contact with GLY 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J MET* 5.1 1.8 - - - -
202J LEU* 2.7 28.6 + - - +
204J LEU 3.6 0.2 - - - -
205J PHE* 1.3 78.0 - - - +
207J GLU* 1.3 59.4 + - - +
287J THR 3.6 18.8 + - - -
179K ASN* 3.6 2.8 - - - +
180K ALA* 2.9 36.9 + - - +
181K ARG* 4.4 2.2 + - - -
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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