Contacts of the helix formed by residues 248 - 262 (chain B) in PDB entry 1WVV
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 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B ALA* 3.3 11.3 + - - +
243B ILE* 4.4 7.4 - - - -
246B ASN* 3.2 5.7 - - - +
247B ALA* 1.3 78.8 - - - +
249B PHE* 1.3 66.1 + - - +
250B GLY 3.0 2.9 - - - -
251B GLU* 3.0 19.1 + - - +
252B THR* 3.8 2.4 + - - +
290B PRO* 3.3 23.3 - - - -
291B ASN* 3.4 4.3 - - - -
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Residues in contact with PHE 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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135B ARG* 6.3 0.2 - - - +
139B ALA* 3.9 17.3 - - + -
142B ALA* 4.9 2.5 - - + -
143B ASN* 3.5 37.0 - - - -
243B ILE* 4.1 10.8 - - + +
248B GLY* 1.3 71.6 - - - -
250B GLY* 1.3 55.6 + - - +
252B THR* 2.6 38.6 + - - -
253B ILE* 3.2 22.7 + - + -
273B ARG* 3.8 22.4 - - + -
274B ILE* 4.0 6.1 - - + -
277B PHE* 3.5 63.0 - + + -
288B THR 4.8 2.2 + - - +
290B PRO 3.8 3.2 + - - -
291B ASN 3.5 1.8 + - - -
292B LEU* 3.5 25.1 - - + +
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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
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249B PHE* 1.3 78.6 - - - +
251B GLU* 1.3 57.5 + - - +
253B ILE* 3.2 9.9 + - - +
254B ARG* 3.1 20.6 + - - +
291B ASN 2.9 12.0 + - - -
292B LEU 3.3 17.7 + - - -
293B SER 3.3 22.0 - - - -
294B CYS* 3.6 10.6 - - - +
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Residues in contact with GLU 251 (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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236B THR* 4.3 7.2 + - - -
237B MET* 4.0 22.6 - - + +
242B ALA* 3.7 16.5 - - + +
247B ALA* 3.9 29.1 - - + +
248B GLY 3.0 10.4 + - - +
250B GLY* 1.3 72.4 - - - +
252B THR* 1.3 60.7 + - - +
254B ARG* 3.0 49.2 + - - +
255B SER* 3.0 33.6 + - - -
291B ASN 4.6 0.2 + - - -
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Residues in contact with THR 252 (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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143B ASN* 3.2 18.0 + - - -
228B TRP* 3.8 29.6 - - + -
239B PRO* 3.8 27.8 - - + +
242B ALA* 4.0 5.8 - - + -
243B ILE* 3.9 20.4 - - + -
249B PHE* 2.6 29.4 + - + +
251B GLU* 1.3 73.6 - - - +
253B ILE* 1.3 65.9 + - - +
255B SER 3.4 1.0 + - - -
256B ILE* 3.2 30.6 + - - +
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Residues in contact with ILE 253 (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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143B ASN* 4.9 0.4 - - - +
249B PHE* 3.2 26.8 + - + +
250B GLY* 3.2 9.2 + - - +
252B THR* 1.3 83.2 + - - +
254B ARG* 1.3 56.4 + - - +
256B ILE* 3.2 5.0 + - - +
257B ASN 2.8 27.9 + - - -
258B GLY 3.4 1.9 + - - -
261B GLU* 3.7 17.9 - - + +
262B CYS* 4.3 2.2 - - - -
270B VAL* 4.0 28.9 - - + +
273B ARG* 3.7 34.8 - - - +
274B ILE* 4.5 0.4 - - + -
292B LEU 3.7 22.2 - - - +
293B SER* 4.7 0.2 - - - -
294B CYS* 3.6 17.3 - - - -
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Residues in contact with ARG 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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234B PRO* 3.6 17.4 - - - +
235B GLY* 3.9 20.4 - - - -
236B THR* 4.9 5.8 - - - +
250B GLY 3.1 10.2 + - - +
251B GLU* 3.0 44.0 + - - +
253B ILE* 1.3 76.4 - - - +
255B SER* 1.3 60.8 + - - +
258B GLY* 2.9 25.3 + - - -
262B CYS* 3.6 35.5 - - + +
263B ASN* 4.0 15.2 + - - +
293B SER 5.2 1.0 + - - -
294B CYS* 3.8 21.4 + - - +
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Residues in contact with SER 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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227B TYR* 2.5 31.4 + - - -
232B ASN 3.2 20.7 + - - -
233B GLY* 3.3 8.8 + - - -
234B PRO* 3.5 2.2 - - - +
235B GLY* 3.7 8.3 - - - +
236B THR 4.2 0.2 + - - -
237B MET* 2.7 28.7 + - - +
239B PRO* 4.0 19.0 - - - -
251B GLU* 3.0 18.7 + - - -
252B THR 4.1 0.2 - - - -
253B ILE 3.3 0.2 - - - -
254B ARG* 1.3 74.1 - - - +
256B ILE* 1.3 52.6 + - - +
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Residues in contact with ILE 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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143B ASN* 3.5 39.5 - - + +
147B GLN* 4.4 11.0 - - - +
227B TYR* 3.8 20.4 + - + -
228B TRP* 4.0 15.9 - - + -
234B PRO* 4.3 6.4 - - - +
239B PRO* 4.4 4.5 - - + -
252B THR 3.2 19.1 + - - +
253B ILE 3.9 1.8 - - - +
254B ARG 4.2 0.2 - - - -
255B SER* 1.3 82.5 - - - +
257B ASN* 1.3 60.1 + - + +
258B GLY 4.0 0.4 - - - -
273B ARG* 4.1 23.3 - - - +
402B GOL 2.3 42.7 + - - +
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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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234B PRO* 4.4 4.8 - - - +
253B ILE 2.8 9.1 + - - +
256B ILE* 1.3 82.5 - - + +
258B GLY* 1.3 59.4 + - - +
259B ALA* 3.3 2.6 - - - +
260B LEU* 3.2 31.5 + - - +
261B GLU* 2.8 60.9 + - - +
273B ARG* 3.9 13.1 - - - +
402B GOL 4.8 3.1 + - - +
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Residues in contact with GLY 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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234B PRO* 3.8 5.2 - - - +
253B ILE 3.4 0.8 + - - -
254B ARG* 2.9 25.8 + - - -
257B ASN* 1.3 73.5 - - - +
259B ALA* 1.3 66.7 + - - +
262B CYS* 3.0 49.4 + - - +
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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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234B PRO* 3.8 20.1 - - + +
257B ASN* 3.3 1.2 + - - +
258B GLY* 1.3 78.0 - - - +
260B LEU* 1.3 69.3 + - + +
262B CYS 4.9 3.1 - - - +
265B GLY* 5.5 1.4 - - - -
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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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257B ASN* 3.2 33.8 + - - +
258B GLY 3.1 0.2 - - - -
259B ALA* 1.3 88.5 - - + +
261B GLU* 1.3 58.5 + - + +
265B GLY* 3.2 25.2 - - - +
266B ASN* 3.9 3.5 - - - +
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Residues in contact with GLU 261 (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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146B HIS* 4.4 1.7 + - - -
253B ILE* 3.7 10.4 - - + +
257B ASN* 2.8 42.0 + - - +
260B LEU* 1.3 80.8 - - + +
262B CYS* 1.3 66.3 + - - +
264B GLY* 4.2 2.1 + - - -
265B GLY 3.3 1.6 + - - -
266B ASN* 3.1 32.1 + - + +
267B PRO* 5.2 0.2 - - - +
269B GLN* 3.8 24.2 - - - +
270B VAL* 3.5 21.1 + - + +
273B ARG* 2.8 44.7 + - - -
294B CYS* 4.6 0.3 - - - +
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Residues in contact with CYS 262 (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 ILE* 4.3 2.2 - - - -
254B ARG* 3.6 27.6 - - + +
258B GLY* 3.0 35.7 + - - +
259B ALA 4.9 2.1 - - - +
260B LEU 4.9 0.3 - - - -
261B GLU* 1.3 77.1 + - - +
263B ASN* 1.3 76.1 + - - +
265B GLY* 2.9 11.8 + - - -
294B CYS* 2.0 54.3 - - + +
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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
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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