Contacts of the helix formed by residues 188 - 206 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I PHE* 5.1 6.3 - - + -
172I LEU* 5.8 2.7 - - + -
186I LEU* 3.5 17.1 + - + -
187I ASP* 1.3 72.2 + - - +
189I GLN* 1.3 64.6 + - - +
190I PRO 3.4 0.7 - - - -
191I SER* 3.1 14.7 + - - +
192I ILE* 3.0 32.4 + - + +
324I LEU* 4.0 15.0 - - + -
327I LEU* 4.7 5.4 - - + -
494I SER* 4.8 1.1 + - - +
495I PRO* 5.2 1.8 - - + +
497I LEU* 3.6 32.8 - - + -
499I PHE* 3.2 35.2 - - + -
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Residues in contact with GLN 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ASP* 3.0 14.1 + - - +
188I VAL* 1.3 77.1 - - - +
190I PRO* 1.3 75.5 - - + +
192I ILE* 3.9 0.2 - - - -
193I PHE* 2.9 53.6 + - + +
321I PHE* 4.0 16.7 - - - -
324I LEU* 3.7 24.6 - - + +
491I PRO* 5.2 4.2 - - - +
493I THR 5.6 0.7 - - - -
494I SER* 3.7 21.2 + - - +
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Residues in contact with PRO 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ASP* 3.6 25.8 - - + +
189I GLN* 1.3 100.6 - - + +
191I SER* 1.3 61.6 + - - +
193I PHE* 3.3 3.1 + - + +
194I HIS* 2.9 35.7 + - + +
224I LEU* 6.3 0.4 - - + -
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Residues in contact with SER 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I PHE* 3.6 27.6 - - - -
186I LEU* 4.9 8.3 - - - +
187I ASP 5.2 0.4 + - - -
188I VAL* 3.1 19.8 + - - +
190I PRO* 1.3 80.1 - - - +
192I ILE* 1.3 53.8 + - - +
194I HIS* 2.9 10.4 + - - +
195I TYR* 2.8 32.9 + - - +
212I VAL* 5.4 0.7 - - - +
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Residues in contact with ILE 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I PHE* 3.6 25.1 - - + -
188I VAL* 3.0 31.8 + - + +
189I GLN 3.9 2.7 - - - +
191I SER* 1.3 77.2 + - - +
193I PHE* 1.3 63.7 + - - +
195I TYR* 3.1 4.9 + - - +
196I THR* 3.0 22.0 + - - +
320I ALA* 3.8 31.2 - - + +
323I LEU* 4.0 16.8 - - + -
324I LEU* 4.2 11.9 - - + -
327I LEU* 4.1 23.1 - - + -
463I LEU* 3.7 20.9 - - + -
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Residues in contact with PHE 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I GLN* 2.9 42.2 + - + +
190I PRO* 3.7 5.6 - - + +
192I ILE* 1.3 77.1 - - - +
194I HIS* 1.3 59.4 + - - +
196I THR* 3.0 19.5 + - - -
197I ILE* 3.2 19.0 + - - +
224I LEU* 3.6 35.0 - - + -
316I VAL* 3.9 7.0 - - + +
317I ASP* 3.3 32.3 - - - -
320I ALA* 3.5 22.4 - - + -
321I PHE* 3.5 45.5 - + - -
324I LEU* 3.9 8.5 - - + -
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Residues in contact with HIS 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I PRO* 2.9 28.7 + - + +
191I SER* 2.9 11.3 + - - +
193I PHE* 1.3 73.4 - - - +
195I TYR* 1.3 65.2 + - - +
197I ILE* 3.5 6.9 + - + +
198I GLU* 3.0 24.9 + - - +
211I LEU* 4.0 32.6 + - + +
212I VAL* 4.0 3.8 - - + +
216I PRO* 3.3 34.3 - - + +
220I SER* 3.1 39.9 + - - -
221I LEU* 4.2 4.8 - - - +
224I LEU* 3.7 24.7 - - + +
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Residues in contact with TYR 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I VAL* 3.7 10.4 - - - +
164I VAL* 3.5 34.3 - - + -
165I ALA* 3.7 19.5 - - - +
168I PHE* 4.0 16.8 - - + -
191I SER 2.8 12.4 + - - +
192I ILE* 3.4 9.6 - - - +
194I HIS* 1.3 76.3 - - - +
196I THR* 1.3 65.4 + - + +
198I GLU* 3.1 1.0 + - - +
199I ALA* 2.7 47.4 + - + +
212I VAL* 3.7 11.3 - - + +
323I LEU* 3.9 11.4 - - + -
459I GLU* 2.6 47.3 + - + +
463I LEU* 3.7 33.6 + - + -
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Residues in contact with THR 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I ILE 3.0 12.7 + - - +
193I PHE* 3.0 15.2 + - - -
195I TYR* 1.3 87.6 - - + +
197I ILE* 1.3 57.5 + - - +
200I SER* 2.7 36.2 + - - -
315I SER 4.0 6.8 - - - +
316I VAL* 3.2 26.0 + - - +
319I THR* 4.2 8.1 - - + -
320I ALA* 3.8 26.0 - - - +
323I LEU* 4.2 7.6 - - + -
459I GLU* 3.9 15.0 - - - +
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Residues in contact with ILE 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193I PHE 3.2 15.5 + - - +
194I HIS* 3.8 8.7 - - - +
196I THR* 1.3 79.8 + - - +
198I GLU* 1.3 57.1 + - - +
200I SER* 4.0 2.0 - - - -
201I ASN* 3.1 28.6 + - - +
209I LEU* 3.9 2.0 - - + -
211I LEU* 3.7 18.8 - - + -
220I SER* 4.3 16.2 - - - +
223I PHE* 4.0 15.9 - - + -
224I LEU* 3.8 31.4 - - + -
266I TYR* 3.7 23.1 - - + +
316I VAL* 3.8 23.8 - - + -
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Residues in contact with GLU 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I VAL* 3.8 17.3 - - + -
194I HIS 3.0 18.3 + - - +
195I TYR 3.7 2.5 - - - +
197I ILE* 1.3 76.4 - - - +
199I ALA* 1.3 66.6 + - - +
201I ASN* 3.2 6.6 + - - +
202I LEU* 3.1 22.7 + - - +
207I GLU 4.9 1.0 - - - +
208I ARG* 2.8 30.9 + - - +
209I LEU* 3.1 22.1 + - - +
210I GLY* 2.9 21.8 + - - -
211I LEU* 2.7 30.5 + - + +
212I VAL* 3.8 15.0 - - + +
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Residues in contact with ALA 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I VAL* 4.5 8.8 - - + +
164I VAL* 3.8 15.8 - - + +
195I TYR* 2.7 40.6 + - + +
198I GLU* 1.3 75.0 - - - +
200I SER* 1.3 64.2 + - - +
202I LEU* 3.2 1.9 + - - +
203I ALA* 3.1 23.3 + - - +
459I GLU* 3.2 30.7 - - + +
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Residues in contact with SER 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I THR 2.7 23.5 + - - -
197I ILE* 4.0 3.4 - - - -
199I ALA* 1.3 74.5 - - - +
201I ASN* 1.3 57.8 + - - +
203I ALA* 3.4 4.3 + - - +
204I LEU* 2.8 39.8 + - - +
315I SER* 3.1 43.9 + - - -
316I VAL* 5.7 0.7 - - - -
455I LEU* 4.8 3.6 - - - +
459I GLU* 2.8 20.8 + - - -
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Residues in contact with ASN 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ILE 3.1 19.7 + - - +
198I GLU 3.2 3.8 + - - +
200I SER* 1.3 74.1 - - - +
202I LEU* 1.3 61.0 + - - +
204I LEU* 5.3 0.4 - - - -
205I PHE* 2.9 39.4 + - - +
206I GLY 3.5 3.8 + - - -
207I GLU* 3.6 28.2 + - - +
209I LEU* 3.7 29.8 - - + +
266I TYR* 3.9 10.9 + - - -
270I CYS* 3.8 25.0 - - - +
273I LYS* 6.0 0.4 - - - +
312I THR* 5.3 2.3 - - - +
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Residues in contact with LEU 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I MET* 3.1 55.6 - - + +
163I ALA* 5.0 5.2 - - + -
164I VAL* 3.7 16.6 - - + -
198I GLU 3.1 14.8 + - - +
199I ALA 3.8 2.9 - - - +
201I ASN* 1.3 72.7 - - - +
203I ALA* 1.3 68.8 + - - +
206I GLY* 2.8 47.2 + - - +
207I GLU 3.3 16.1 + - - +
208I ARG* 4.2 18.2 - - + +
288I GLY* 4.3 0.2 - - - -
178L GLN 5.1 3.4 - - - +
180L ALA* 5.7 2.9 - - + +
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Residues in contact with ALA 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I PHE* 4.6 4.4 - - + +
160I MET* 3.7 14.9 - - - +
161I VAL* 4.4 9.3 - - + +
199I ALA 3.1 11.7 + - - +
200I SER 3.6 8.1 - - - +
202I LEU* 1.3 78.2 - - - +
204I LEU* 1.3 57.5 - - - +
288I GLY* 3.3 4.9 - - - -
289I ILE* 2.9 31.3 + - + +
455I LEU* 3.4 36.3 - - + -
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Residues in contact with LEU 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I SER* 2.8 25.6 + - - +
203I ALA* 1.3 76.1 - - - +
205I PHE* 1.3 81.2 + - + +
206I GLY 3.7 0.2 - - - -
288I GLY 3.9 0.9 - - - -
289I ILE* 3.5 30.2 + - + +
290I VAL* 2.8 44.5 + - + +
291I ALA 4.4 0.3 + - - -
308I SER* 6.0 0.2 - - - +
311I LEU* 3.8 52.5 - - + +
312I THR* 3.9 10.1 - - + +
315I SER* 4.3 8.5 - - - +
455I LEU* 4.7 9.6 - - + -
601I HEM 5.4 0.2 - - + -
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Residues in contact with PHE 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I ASN* 2.9 35.9 + - - +
204I LEU* 1.3 97.6 - - + +
206I GLY* 1.3 57.5 + - - +
207I GLU* 3.1 12.5 + - + +
270I CYS* 3.6 44.0 - - + +
271I ILE* 4.2 7.2 - - + -
274I ILE* 4.0 17.9 - - + -
287I THR 3.7 6.5 - - - -
290I VAL* 4.2 13.0 - - + -
308I SER* 3.4 27.1 - - - -
312I THR* 3.5 22.2 - - + -
181L ARG* 2.8 34.3 + - - +
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Residues in contact with GLY 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I MET* 5.2 1.6 - - - -
201I ASN 3.5 0.2 + - - -
202I LEU* 2.8 32.2 + - - +
205I PHE* 1.3 76.1 - - - +
207I GLU* 1.3 59.6 + - - +
287I THR 3.6 18.8 + - - -
179L ASN* 3.7 2.8 - - - +
180L ALA* 3.1 34.1 + - - +
181L ARG* 4.3 4.0 - - - -
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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