Contacts of the helix formed by residues 255 - 268 (chain B) in PDB entry 2XWU
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 LEU 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B SER* 3.9 25.4 - - - +
219B ARG* 3.6 37.2 - - + +
220B GLN* 4.6 7.4 - - + +
223B LEU* 3.9 13.1 - - + +
249B ALA* 3.6 35.4 - - + +
252B ASP* 3.0 26.6 + - + +
254B GLU* 1.3 89.3 - - + +
256B PHE* 1.3 64.5 + - - +
257B ASP 3.4 1.8 - - - -
258B SER* 3.3 8.1 + - - +
259B SER* 3.1 22.3 + - - -
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Residues in contact with PHE 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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250B LEU* 3.5 38.8 - - + +
252B ASP 3.1 10.2 + - - +
253B SER* 3.5 17.8 + - - +
255B LEU* 1.3 75.5 - - - +
257B ASP* 1.3 77.5 + - - +
259B SER* 3.3 5.1 + - - -
260B VAL* 3.0 41.5 + - + +
292B GLN* 3.9 19.3 - - - -
303B GLU* 3.7 14.1 - - + -
304B THR* 3.5 50.5 - - + -
307B GLY* 4.2 4.3 - - - -
308B ILE* 4.3 8.5 - - + -
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Residues in contact with ASP 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 SER 4.9 0.6 + - - -
254B GLU 4.9 4.4 + - - +
255B LEU 3.4 0.8 - - - -
256B PHE* 1.3 87.7 - - - +
258B SER* 1.3 64.0 + - - +
260B VAL* 3.5 4.3 + - - +
261B GLU* 3.3 27.4 + - + +
303B GLU* 3.4 24.2 - - - +
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Residues in contact with SER 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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220B GLN* 4.5 12.1 - - - -
223B LEU* 3.4 32.3 - - - +
224B LYS* 4.8 15.0 - - - -
227B SER* 4.7 1.7 + - - -
254B GLU 5.5 0.2 + - - -
255B LEU* 3.3 6.9 + - - -
257B ASP* 1.3 78.0 - - - +
259B SER* 1.3 59.7 + - - +
261B GLU* 3.3 7.8 + - - +
262B ALA* 2.9 26.0 + - - +
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Residues in contact with SER 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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223B LEU* 3.7 19.0 - - - +
246B ALA* 3.3 26.8 + - - -
249B ALA* 4.4 2.5 - - - -
250B LEU* 3.1 26.7 + - - +
255B LEU 3.1 13.3 + - - -
256B PHE 3.3 5.2 + - - -
258B SER* 1.3 74.4 - - - +
260B VAL* 1.3 60.3 + - - +
262B ALA* 4.1 7.0 - - - -
263B ILE* 2.7 37.0 + - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU* 3.7 20.9 - - + -
256B PHE* 3.0 38.6 + - + +
257B ASP* 3.9 5.4 - - - +
259B SER* 1.3 76.2 + - - +
261B GLU* 1.3 60.0 + - - +
263B ILE* 3.8 1.0 - - - +
264B VAL* 2.9 34.9 + - + +
307B GLY* 4.0 23.6 - - - +
310B ARG* 3.8 31.9 - - - +
311B ILE* 3.8 16.8 - - + -
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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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21A PRO* 4.3 9.7 - - - +
110A LYS* 3.9 17.2 + - - -
114A LEU* 4.3 14.1 - - + +
227B SER* 4.9 3.1 - - - +
257B ASP* 3.3 14.2 + - + +
258B SER* 3.6 9.4 - - - +
259B SER 3.2 0.2 - - - -
260B VAL* 1.3 78.5 - - + +
262B ALA* 1.3 55.6 + - - +
264B VAL* 4.2 2.6 - - - +
265B ASN* 2.9 45.9 + - - +
310B ARG* 2.8 38.3 + - - -
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Residues in contact with ALA 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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223B LEU* 4.5 11.7 - - + +
226B PHE* 3.8 27.5 - - + -
227B SER* 3.3 21.5 + - - +
230B VAL* 4.9 0.9 - - - +
246B ALA* 4.8 2.9 - - + -
258B SER 2.9 17.0 + - - +
259B SER* 3.6 8.5 - - - +
261B GLU* 1.3 73.9 - - - +
263B ILE* 1.3 67.4 + - - +
265B ASN* 3.4 1.8 + - - +
266B ALA* 2.9 25.9 + - - +
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Residues in contact with ILE 263 (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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226B PHE* 5.7 0.9 - - - -
243B ILE* 4.6 6.7 - - + +
246B ALA* 3.8 16.4 - - + +
247B PHE* 3.7 42.4 - - + +
250B LEU* 3.6 31.6 - - + -
259B SER 2.7 25.7 + - - +
260B VAL 3.8 2.2 - - - +
262B ALA* 1.3 71.7 - - - +
264B VAL* 1.3 64.4 + - - +
266B ALA* 3.0 6.5 + - - +
267B ILE* 2.9 37.9 + - + +
311B ILE* 3.6 31.6 - - + -
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Residues in contact with VAL 264 (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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19A ASP* 3.3 33.0 - - - +
110A LYS* 4.2 7.2 - - - +
260B VAL* 2.9 22.1 + - + +
261B GLU* 4.2 2.5 - - - +
263B ILE* 1.3 76.7 - - - +
265B ASN* 1.3 56.8 + - - +
267B ILE* 3.3 1.9 + - - +
268B SER* 2.6 43.7 + - - +
310B ARG* 4.0 43.3 - - + +
311B ILE* 4.1 11.7 - - + +
314B ALA* 4.4 11.2 - - + -
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Residues in contact with ASN 265 (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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110A LYS* 3.6 24.5 + - - +
227B SER* 4.1 14.7 + - - +
230B VAL* 3.5 16.7 - - + +
231B GLN* 4.3 26.7 + - - +
261B GLU* 2.9 39.9 + - - +
262B ALA* 4.0 2.7 - - - +
264B VAL* 1.3 76.4 - - - +
266B ALA* 1.3 64.3 + - - +
268B SER* 3.3 6.1 + - - -
269B GLN* 3.3 24.4 + - - +
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Residues in contact with ALA 266 (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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226B PHE* 4.4 2.7 - - + -
230B VAL* 3.5 23.3 - - + +
236B LEU* 4.0 9.3 - - + +
239B CYS* 5.2 1.1 - - + -
243B ILE* 4.1 29.6 - - + -
262B ALA 2.9 19.9 + - - +
263B ILE* 3.5 4.3 - - - +
265B ASN* 1.3 77.7 - - - +
267B ILE* 1.3 64.7 + - + +
269B GLN* 3.4 21.6 + - - +
272B ALA* 3.9 5.7 - - - +
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Residues in contact with ILE 267 (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 LEU* 5.2 3.4 - - + -
243B ILE* 5.5 1.1 - - + -
247B PHE* 5.0 3.1 - - + -
263B ILE* 2.9 38.9 + - + +
264B VAL 4.1 3.4 - - - +
266B ALA* 1.3 80.2 - - + +
268B SER* 1.3 59.1 + - - +
269B GLN 3.3 2.1 + - - +
272B ALA* 3.6 9.1 - - - +
279B LEU* 4.4 5.2 - - + -
282B LEU* 3.8 29.2 - - + -
311B ILE* 4.7 11.0 - - + +
314B ALA* 3.9 24.0 - - + +
315B LEU* 4.0 32.3 - - + -
318B ASN* 4.6 2.1 + - - -
319B HIS* 3.3 25.7 + - - +
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Residues in contact with SER 268 (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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19A ASP* 4.7 4.1 + - - +
264B VAL* 2.6 34.4 + - - +
265B ASN* 3.3 8.0 + - - -
267B ILE* 1.3 74.4 - - - +
269B GLN* 1.3 64.3 + - - +
270B PRO* 3.5 4.9 - - - +
314B ALA* 4.2 6.6 - - - +
318B ASN* 3.8 23.9 + - - +
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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