Contacts of the helix formed by residues 243 - 259 (chain B) in PDB entry 3V6R
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 ASN 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLU* 4.3 0.7 - - - +
241B LYS* 3.3 32.0 - - - +
242B GLU* 1.4 72.0 - - - +
244B VAL* 1.3 62.9 + - - +
245B ASP 3.2 2.2 - - - -
246B ILE* 3.1 24.5 + - + +
344B PRO* 2.7 38.2 + - - +
347B ARG* 2.9 39.6 + - - +
348B ILE 3.7 17.7 - - - +
349B SER* 4.4 10.0 - - - +
350B VAL* 5.5 1.1 - - - +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 3.4 32.1 - - + -
188B ARG* 4.1 11.5 - - + -
231B ALA* 3.4 33.7 - - + +
233B GLU* 3.5 22.2 - - + +
234B VAL* 3.5 22.9 - - + -
240B TYR* 4.0 11.7 - - + -
241B LYS 3.2 13.0 + - - +
242B GLU 3.0 1.2 + - - -
243B ASN* 1.3 77.7 + - - +
245B ASP* 1.3 65.6 + - - +
246B ILE 3.5 0.5 + - - -
247B TRP* 3.6 9.7 + - - +
248B SER* 4.0 6.1 + - - -
347B ARG* 3.6 0.9 - - - +
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Residues in contact with ASP 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 4.6 17.4 - - + +
181B HIS* 2.8 34.3 + - + +
186B ILE* 3.6 6.6 - - - +
187B HIS* 3.1 26.8 + - - +
188B ARG* 2.8 32.8 + - - -
189B ASP 4.5 0.2 + - - -
190B LEU* 5.0 5.4 - - + +
242B GLU 3.4 2.4 + - - +
243B ASN 3.2 0.4 - - - -
244B VAL* 1.3 75.5 - - - +
246B ILE* 1.4 62.6 + - - +
247B TRP 3.4 0.2 - - - -
248B SER* 3.4 11.7 + - - -
249B VAL* 3.2 26.1 + - - +
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 3.7 29.4 - - + -
177B ILE* 4.4 2.0 - - + -
243B ASN* 3.1 17.8 + - - +
245B ASP* 1.4 74.5 - - - +
247B TRP* 1.3 59.7 + - - +
249B VAL* 3.1 6.5 + - + +
250B GLY* 2.9 25.8 + - - -
339B MET* 3.8 25.5 - - + +
347B ARG* 3.7 15.5 - - + -
348B ILE* 3.4 24.2 - - + +
349B SER 3.7 22.7 - - - +
350B VAL* 3.7 18.4 - - + +
353B ALA* 4.2 4.9 - - + -
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Residues in contact with TRP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR 4.9 1.0 + - - -
229B TYR 3.5 13.9 - - - -
230B ARG 3.3 12.3 + - - -
231B ALA* 3.4 25.6 - - + -
232B PRO* 3.5 24.9 - - + -
235B ILE* 6.4 0.7 - - + -
243B ASN 3.7 2.2 + - - -
244B VAL 3.6 11.8 + - - +
246B ILE* 1.3 78.9 - - - +
248B SER* 1.4 55.2 + - - +
250B GLY* 3.2 2.8 + - - -
251B CYS* 2.9 42.5 + - - -
263B PHE* 3.5 24.5 - + - -
275B VAL* 3.9 14.6 - - + -
279B LEU* 3.6 22.2 - - + -
339B MET 4.0 11.2 - - - -
340B LEU* 4.1 7.8 - - + +
341B VAL 3.3 47.3 - - - -
342B ILE* 3.7 6.3 - - + -
347B ARG* 3.8 10.0 - - - +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ARG 5.0 4.0 + - - -
190B LEU* 3.5 38.1 + - - -
229B TYR* 2.8 26.9 + - - -
230B ARG* 4.7 2.1 - - - -
231B ALA 4.8 0.9 + - - -
244B VAL 4.0 9.2 + - - -
245B ASP* 3.4 13.3 + - - -
246B ILE 3.3 0.6 - - - -
247B TRP* 1.4 75.5 - - - +
249B VAL* 1.4 56.4 + - - +
251B CYS* 3.3 5.9 + - - +
252B ILE* 3.0 35.1 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 4.3 17.8 - - + +
173B MET* 4.4 14.6 - - + -
174B LEU* 4.5 15.5 - - + -
177B ILE* 3.8 24.9 - - + -
190B LEU* 4.4 15.3 - - + -
245B ASP 3.2 16.6 - - - +
246B ILE* 3.1 9.1 + - - +
248B SER* 1.4 70.9 - - - +
250B GLY* 1.3 60.4 + - - +
252B ILE* 3.4 9.0 + - - +
253B MET* 2.9 28.6 + - - +
339B MET* 4.0 21.5 - - + -
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Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE 2.9 13.0 + - - -
247B TRP 3.2 4.5 + - - -
249B VAL* 1.3 74.3 - - - +
251B CYS* 1.3 57.4 + - - +
253B MET 3.4 0.5 + - - -
254B GLY* 2.9 26.0 + - - -
336B LEU* 3.5 9.5 - - - +
339B MET* 3.7 27.7 - - - +
340B LEU* 3.6 16.1 - - - +
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Residues in contact with CYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR 4.0 10.1 - - - +
229B TYR* 3.6 23.1 - - + -
247B TRP* 2.9 46.0 + - - -
248B SER* 3.3 10.7 + - - +
250B GLY* 1.3 76.0 - - - +
252B ILE* 1.4 55.3 + - - +
254B GLY 3.5 0.2 + - - -
255B GLU* 3.1 29.3 + - - +
262B LEU* 3.7 17.1 + - + +
263B PHE* 3.9 24.5 - - + -
340B LEU* 3.6 1.3 - - - +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.8 27.6 - - + -
157B ILE* 4.7 2.1 - - + +
173B MET* 3.9 23.3 - - + -
190B LEU* 4.1 15.5 - - + +
191B LYS* 4.2 14.6 - - - +
192B PRO* 3.9 18.4 - - + -
195B ILE* 4.1 22.9 - - + -
229B TYR* 4.2 7.2 - - + -
248B SER 3.0 27.1 + - - +
249B VAL* 3.7 6.3 - - - +
251B CYS* 1.4 71.2 - - - +
253B MET* 1.3 58.9 + - - +
255B GLU* 3.3 8.9 + - - +
256B MET* 3.0 31.3 + - + +
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Residues in contact with MET 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 3.8 24.5 - - + -
170B LEU* 3.7 35.2 - - + +
249B VAL 2.9 21.0 + - - +
250B GLY 3.7 4.0 - - - +
252B ILE* 1.3 68.7 - - - +
254B GLY* 1.3 64.4 + - - +
256B MET* 3.1 17.9 + - - +
257B VAL* 3.1 14.8 + - - +
332B ALA* 3.3 36.1 - - + +
335B LEU* 3.9 14.1 - - + -
336B LEU* 3.7 18.4 - - + -
339B MET* 3.5 24.0 - - + -
358B TYR* 4.0 3.1 - - + -
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Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B GLY 2.9 16.4 + - - -
251B CYS 3.9 1.6 - - - -
253B MET* 1.3 75.9 - - - +
255B GLU* 1.3 50.6 + - - +
257B VAL* 3.3 2.6 + - - +
258B ARG* 2.8 39.8 + - - +
262B LEU* 3.9 11.9 - - - -
313B PHE* 3.6 23.3 - - - -
336B LEU* 3.6 6.9 - - - +
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Residues in contact with GLU 255 (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 ILE* 3.1 38.2 - - + +
192B PRO* 4.6 0.2 - - - +
229B TYR* 2.6 39.7 + - - -
251B CYS 3.1 12.2 + - - +
252B ILE 3.4 10.5 - - - +
253B MET 3.2 0.2 - - - -
254B GLY* 1.3 73.9 - - - +
256B MET* 1.4 56.2 + - - +
259B HIS* 2.6 35.7 + - - +
260B LYS* 3.6 26.2 - - - +
261B ILE* 3.7 22.4 + - - +
262B LEU* 4.3 2.0 + - - +
403B CQQ 4.8 2.9 - - - -
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Residues in contact with MET 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.3 13.2 - - + -
156B VAL* 5.9 2.7 - - + -
157B ILE* 3.7 21.9 - - + +
159B MET 4.5 1.7 - - - +
161B LEU* 4.8 13.6 + - + +
166B MET* 4.0 32.7 - - + +
169B LEU* 4.4 20.9 - - + -
170B LEU* 4.1 17.5 - - - -
173B MET* 3.6 30.3 - - + -
252B ILE* 3.0 25.6 + - + +
253B MET* 3.1 8.5 + - - +
255B GLU* 1.4 74.4 - - - +
257B VAL* 1.3 57.8 + - - +
259B HIS* 3.0 27.7 - - - -
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Residues in contact with VAL 257 (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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166B MET* 3.7 27.4 - - + -
253B MET 3.1 13.1 + - - +
254B GLY 3.6 7.2 - - - +
256B MET* 1.3 76.6 - - - +
258B ARG* 1.4 58.7 + - - +
259B HIS* 3.6 14.3 + - - -
313B PHE* 3.9 14.8 - - + -
317B LEU* 3.8 46.8 - - + +
318B PHE* 3.8 32.1 - - + -
336B LEU* 4.4 9.6 - - + -
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Residues in contact with ARG 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLY 2.8 23.4 + - - +
257B VAL* 1.4 71.3 - - - +
259B HIS* 1.4 65.3 + - - +
260B LYS* 3.0 26.7 + - + +
261B ILE 4.2 5.7 + - - -
262B LEU* 3.4 33.9 + - - +
278B GLN* 3.2 28.2 + - - -
307B LEU* 5.9 1.2 - - - +
312B LEU* 3.4 32.0 + - - +
313B PHE* 3.6 19.5 - - + -
317B LEU* 4.0 15.6 - - + +
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Residues in contact with HIS 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 2.6 27.3 + - - +
158B GLN* 3.6 25.6 + - + +
159B MET 3.1 28.3 - - - -
160B GLU* 3.9 23.9 + - + -
161B LEU 5.1 0.9 - - - -
255B GLU* 2.6 27.9 + - - +
256B MET 3.0 21.0 + - - -
257B VAL 3.6 13.0 + - - -
258B ARG* 1.4 71.2 - - - +
260B LYS* 1.4 55.6 + - - +
317B LEU* 5.5 4.3 + - + -
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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