Contacts of the helix formed by residues 250 - 261 (chain B) in PDB entry 2WWR
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 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B GLY* 5.0 7.0 + - - +
226B CYS 3.1 7.8 + - - +
227B ASN* 4.0 15.2 - - + +
231B PHE* 4.4 1.0 - - - -
248B VAL 4.1 0.6 + - - -
249B VAL* 1.3 68.8 - - - +
251B GLN* 1.3 61.7 + - - +
252B ASP* 3.8 8.5 + - - +
253B ASP* 3.1 44.5 + - + +
254B LEU* 2.9 26.7 + - - +
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Residues in contact with GLN 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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246B GLY* 4.3 7.3 - - - +
249B VAL* 3.6 17.8 - - + +
250B ASN* 1.3 72.2 + - - +
252B ASP* 1.3 58.7 + - - +
254B LEU* 3.6 8.4 - - - +
255B TYR* 2.9 29.1 + - - +
268B LEU* 4.7 7.1 - - - +
270B VAL 4.8 0.5 - - - +
271B THR* 4.0 8.2 - - - -
272B SER* 2.9 49.7 + - - +
276B LEU* 4.0 6.3 - - - +
280B HIS* 3.9 22.6 + - + +
282B LEU* 4.0 26.8 - - + +
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Residues in contact with ASP 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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250B ASN* 3.3 7.1 + - - +
251B GLN* 1.3 75.5 - - - +
253B ASP* 1.3 63.7 + - - +
255B TYR* 3.2 6.5 + - - +
256B GLN* 2.8 31.2 + - - +
280B HIS* 5.7 2.4 + - - -
281B PRO* 5.3 1.6 - - - +
14C ARG* 3.0 33.5 + - - -
35C ASP 3.8 5.0 - - - +
36C SER* 2.8 34.2 + - - +
37C ASP* 3.1 25.8 + - - +
38C GLU* 4.1 5.5 - - + +
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Residues in contact with ASP 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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227B ASN* 3.5 8.5 - - - +
228B LYS* 2.9 48.1 + - - +
231B PHE* 4.0 3.6 - - - -
250B ASN* 3.1 32.5 + - + +
252B ASP* 1.3 77.1 - - - +
254B LEU* 1.3 63.0 + - - +
256B GLN* 3.4 8.1 + - - +
257B ALA* 3.0 24.3 + - - +
1328B MG 2.2 30.9 - - - -
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Residues in contact with LEU 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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231B PHE* 3.6 34.8 - - + -
240B PHE* 4.4 4.5 - - + -
249B VAL* 3.8 17.0 - - + -
250B ASN 2.9 12.9 + - - +
251B GLN 3.6 5.8 - - - +
253B ASP* 1.3 76.8 - - - +
255B TYR* 1.3 56.0 + - - +
257B ALA* 3.1 4.0 + - - +
258B LEU* 2.9 49.5 + - + +
263B ILE* 4.3 8.1 - - + -
266B ALA* 4.0 14.4 - - + -
268B LEU* 3.8 35.0 - - + -
282B LEU* 4.0 15.7 - - + -
288B CYS* 5.0 0.4 - - - -
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Residues in contact with TYR 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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251B GLN 2.9 18.1 + - - +
252B ASP* 3.2 6.5 + - - +
254B LEU* 1.3 76.1 - - - +
256B GLN* 1.3 58.6 + - - +
258B LEU* 3.3 1.4 + - - +
259B ALA* 2.9 39.9 + - + +
280B HIS* 6.2 0.2 - - + -
281B PRO* 3.8 31.9 - - + -
282B LEU* 3.9 13.7 - - + +
284B THR* 4.0 4.1 + - - -
285B LEU* 3.4 43.2 - - + +
34C TRP* 3.6 28.9 - + - -
36C SER* 4.6 4.7 - - - -
38C GLU* 4.1 25.6 - - + -
39C PRO 4.9 3.1 - - - -
41C PRO* 3.7 18.9 - - - +
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Residues in contact with GLN 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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228B LYS* 6.2 0.3 - - - +
252B ASP 2.8 16.9 + - - +
253B ASP* 3.7 8.4 - - - +
255B TYR* 1.3 81.1 - - - +
257B ALA* 1.3 53.6 + - - +
259B ALA* 3.9 4.0 - - - +
260B SER* 2.6 57.8 + - - -
262B LYS* 3.5 23.9 + - - +
38C GLU* 3.4 33.8 + - - +
139D THR* 3.8 24.7 - - + +
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Residues in contact with ALA 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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231B PHE* 3.8 29.2 - - + -
253B ASP 3.0 13.7 + - - +
254B LEU* 3.1 8.9 + - - +
256B GLN* 1.3 80.9 + - - +
258B LEU* 1.3 58.3 + - - +
260B SER* 3.9 4.3 - - - -
261B GLY* 3.0 24.8 + - - -
262B LYS* 3.1 24.1 + - + -
263B ILE* 3.7 13.1 + - + -
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Residues in contact with LEU 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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254B LEU* 2.9 44.6 + - + +
257B ALA* 1.3 75.3 - - - +
259B ALA* 1.3 65.7 + - - +
261B GLY* 4.0 5.5 + - - -
263B ILE* 4.3 9.0 - - + -
264B ALA 4.4 0.7 - - - -
265B ALA* 3.6 9.4 - - - +
266B ALA* 3.6 22.7 - - + +
282B LEU* 4.2 1.8 - - + -
285B LEU* 3.6 28.0 - - + +
287B ASN* 3.2 59.5 + - - +
288B CYS* 3.9 13.2 - - + -
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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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255B TYR* 2.9 31.3 + - + +
256B GLN* 3.9 6.1 - - - +
258B LEU* 1.3 79.4 - - - +
260B SER* 1.3 61.5 + - - +
285B LEU* 4.4 17.2 - - + +
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Residues in contact with SER 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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256B GLN* 2.6 44.1 + - - -
257B ALA 3.6 3.1 + - - -
259B ALA* 1.3 77.6 - - - +
261B GLY* 1.3 59.8 + - - +
262B LYS* 3.7 16.6 - - - +
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Residues in contact with GLY 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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236B GLU* 3.6 26.9 - - - +
257B ALA 3.0 6.8 + - - -
258B LEU 4.0 3.3 + - - -
259B ALA 3.5 2.4 - - - -
260B SER* 1.3 78.9 - - - +
262B LYS* 1.3 66.3 + - - +
263B ILE 3.1 12.5 + - - +
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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