Contacts of the helix formed by residues 246 - 260 (chain B) in PDB entry 2VXO
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 GLY 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B SER* 3.2 8.9 + - - -
245B GLY* 1.3 78.1 - - - +
247B VAL* 1.3 61.3 + - - -
249B SER* 3.6 0.2 - - - -
250B THR* 2.7 28.5 + - - -
438B PHE* 6.0 5.4 - - - -
1697B SO4 3.2 22.1 + - - -
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Residues in contact with VAL 247 (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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246B GLY* 1.3 70.7 - - - -
248B ASP* 1.3 55.6 + - - +
250B THR* 3.0 7.0 + - - -
251B VAL* 2.8 51.1 + - + +
416B LYS* 4.6 14.8 - - - +
419B VAL* 4.2 12.1 - - + +
420B ARG* 5.0 1.8 - - + -
432B LEU* 3.6 22.2 - - + +
433B VAL* 3.7 30.7 - - + +
435B ARG* 3.8 27.8 - - + +
436B HIS 5.5 1.1 - - - +
1697B SO4 3.8 2.0 + - - -
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLY 3.4 0.6 - - - -
247B VAL* 1.3 75.0 - - - +
249B SER* 1.3 58.5 + - - +
252B CYS* 2.9 32.4 + - - +
367B GLY* 3.1 25.8 - - - +
368B THR* 5.1 0.7 - - - -
369B LEU* 3.8 20.8 + - - +
411B LEU* 3.4 10.2 - - + +
416B LYS* 4.1 19.3 + - - +
419B VAL* 3.4 23.1 - - - +
1697B SO4 3.4 19.3 + - - +
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Residues in contact with SER 249 (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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241B VAL* 4.4 3.4 - - - +
242B LEU 3.1 14.6 + - - -
243B LEU* 3.3 8.7 - - - -
244B SER* 3.0 29.2 + - - -
245B GLY 4.2 0.2 - - - -
246B GLY 3.6 2.9 - - - -
248B ASP* 1.3 76.1 - - - +
250B THR* 1.3 54.0 + - - +
252B CYS* 3.6 5.7 + - - +
253B THR* 2.7 36.9 + - - -
367B GLY* 4.4 7.2 + - - +
1697B SO4 2.6 29.0 + - - -
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Residues in contact with THR 250 (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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243B LEU* 3.7 15.0 - - - +
245B GLY 3.6 10.0 + - - -
246B GLY 2.7 22.5 + - - -
247B VAL 3.5 3.4 - - - -
249B SER* 1.3 74.1 - - - +
251B VAL* 1.3 60.9 + - - +
253B THR* 3.3 3.1 + - - -
254B ALA* 3.0 27.4 + - - +
283B VAL* 4.1 6.6 - - + +
287B LEU* 4.1 19.3 - - + +
428B LEU* 3.7 27.8 - - + -
432B LEU* 3.7 22.4 - - + +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 2.8 31.7 + - + +
248B ASP 4.0 2.7 - - - +
250B THR* 1.3 68.7 - - - +
252B CYS* 1.3 60.7 + - - +
254B ALA* 3.3 2.1 + - - +
255B LEU* 2.8 28.8 + - + +
411B LEU* 4.1 9.9 - - + -
419B VAL* 3.7 38.8 - - + +
422B LEU* 4.0 22.4 - - + -
423B GLY* 3.9 14.6 - - - +
426B LEU* 3.9 10.4 - - + +
428B LEU* 4.0 13.0 - - + -
432B LEU* 6.2 0.2 - - + -
433B VAL* 4.7 3.1 - - + -
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Residues in contact with CYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 4.9 4.5 - - + -
248B ASP 2.9 18.6 + - - +
249B SER* 3.7 5.2 - - - +
251B VAL* 1.3 77.9 - - - +
253B THR* 1.3 55.6 + - - +
255B LEU* 3.2 8.3 + - - +
256B LEU* 2.9 35.3 + - - +
365B ALA* 4.2 14.8 - - - -
366B GLN 3.7 26.9 - - - -
367B GLY* 3.7 10.3 - - - +
410B PRO* 3.9 23.3 - - - -
411B LEU* 4.2 9.8 - - + +
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 3.4 27.6 - - + +
243B LEU* 3.6 12.9 - - + +
249B SER 2.7 22.4 + - - -
250B THR* 3.6 5.2 - - - -
251B VAL 3.3 0.2 - - - -
252B CYS* 1.3 76.0 - - - +
254B ALA* 1.3 62.2 + - - +
256B LEU* 3.4 3.3 + - - +
257B ASN* 3.1 22.5 + - - +
265B VAL* 4.5 4.9 - - + +
267B ALA* 3.7 28.9 - - + -
287B LEU* 4.7 9.4 - - + -
292B ILE* 4.0 17.7 - - + -
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Residues in contact with ALA 254 (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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250B THR 3.0 17.6 + - - +
251B VAL 3.7 3.6 - - - +
253B THR* 1.3 76.3 - - - +
255B LEU* 1.3 57.6 + - - +
257B ASN* 3.4 3.5 + - - +
258B ARG* 3.0 28.9 + - - +
287B LEU* 4.6 2.2 - - + +
290B LEU* 5.6 1.6 - - + -
292B ILE* 3.7 21.5 - - + +
426B LEU* 4.1 22.2 - - + +
428B LEU* 4.0 21.5 - - + -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 4.0 28.0 - - + +
226B CYS* 4.1 17.5 - - - -
227B ILE* 4.2 14.4 - - + -
230B ILE* 4.3 8.7 - - + -
251B VAL* 2.8 17.2 + - + +
252B CYS 3.4 5.2 - - - +
254B ALA* 1.3 76.5 - - - +
256B LEU* 1.3 63.3 + - + +
258B ARG* 3.2 5.2 + - - +
259B ALA* 3.0 21.5 + - - +
410B PRO* 3.9 18.4 - - + -
411B LEU* 3.8 26.7 - - + -
414B PHE* 5.1 0.7 - - + -
422B LEU* 4.5 9.0 - - + -
426B LEU* 3.8 20.3 - - + +
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Residues in contact with LEU 256 (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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230B ILE* 3.9 29.2 - - + -
239B VAL* 3.6 21.1 - - + -
241B VAL* 4.2 18.8 - - + -
252B CYS* 2.9 23.2 + - - +
253B THR 3.4 3.8 + - - +
255B LEU* 1.3 75.1 - - - +
257B ASN* 1.3 59.2 + - - +
259B ALA* 3.2 3.6 + - - +
260B LEU* 3.0 38.8 + - + +
265B VAL* 3.7 13.0 - - + -
365B ALA* 3.4 30.3 - - + -
408B ILE* 4.8 2.7 - - + -
410B PRO* 4.0 20.6 - - + -
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Residues in contact with ASN 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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253B THR 3.1 16.4 + - - +
254B ALA 3.6 4.9 - - - +
256B LEU* 1.3 77.4 - - - +
258B ARG* 1.3 56.0 + - - +
260B LEU 2.9 23.2 - - - +
261B ASN 4.6 2.7 - - - +
262B GLN* 4.5 21.6 + - - +
265B VAL* 3.7 28.2 + - - +
290B LEU 5.0 1.2 - - - +
291B GLY 4.2 8.4 + - - +
292B ILE* 3.5 44.2 - - + +
293B GLN 5.3 0.6 - - - +
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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
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223B GLU* 4.8 4.3 + - - +
224B LEU* 3.9 24.4 - - - +
227B ILE* 3.9 32.1 - - + +
231B LYS* 5.5 4.6 - - - +
254B ALA 3.0 17.2 + - - +
255B LEU 3.2 4.5 + - - +
257B ASN* 1.3 76.1 - - - +
259B ALA* 1.3 56.1 + - - +
260B LEU 3.5 1.8 - - - +
426B LEU* 3.8 23.3 - - + -
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Residues in contact with ALA 259 (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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227B ILE* 3.8 40.2 - - + +
230B ILE* 4.2 21.5 - - + -
231B LYS* 3.3 29.8 - - - +
255B LEU 3.0 14.5 + - - +
256B LEU 3.2 4.7 + - - +
258B ARG* 1.3 78.0 - - - +
260B LEU* 1.3 61.2 + - + +
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Residues in contact with LEU 260 (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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230B ILE* 4.2 19.3 - - + -
231B LYS* 4.4 13.9 - - + -
234B VAL* 3.8 12.1 - - + -
235B GLY 4.4 2.5 - - - +
239B VAL* 3.8 30.1 - - + -
256B LEU* 3.0 22.5 + - + +
257B ASN 2.9 15.3 - - - +
258B ARG 4.4 1.7 - - - +
259B ALA* 1.3 88.5 - - + +
261B ASN* 1.3 69.8 + - - +
264B GLN* 3.7 35.4 - - + +
265B VAL* 4.1 10.8 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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