Contacts of the helix formed by residues 254 - 270 (chain B) in PDB entry 2DH3
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 ASP 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B VAL* 5.5 0.5 - - - +
252B LEU 3.5 0.2 + - - -
253B LYS* 1.3 101.7 + - - +
255B ALA* 1.3 66.1 + - - +
256B SER* 3.3 6.0 + - - -
257B SER* 3.3 19.4 + - - +
258B PHE* 3.1 26.9 + - + -
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Residues in contact with ALA 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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249B ILE* 3.6 29.4 - - + +
252B LEU* 3.3 30.4 + - + +
254B ASP* 1.3 75.4 - - - +
256B SER* 1.3 63.7 + - - +
258B PHE* 3.2 4.0 + - - +
259B LEU* 3.0 31.7 + - + +
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Residues in contact with SER 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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254B ASP* 4.7 3.5 + - - -
255B ALA* 1.3 78.7 - - - +
257B SER* 1.3 67.2 + - - +
259B LEU* 4.6 0.9 - - - -
260B ALA* 3.3 11.4 + - - +
291B LEU* 3.7 30.4 - - - +
292B GLU* 2.8 40.8 - - - +
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Residues in contact with SER 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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254B ASP* 3.3 16.8 + - - +
255B ALA 3.3 0.6 - - - -
256B SER* 1.3 79.5 + - - +
258B PHE* 1.3 69.3 + - - +
260B ALA* 3.4 7.8 + - - +
261B GLU* 3.2 21.7 + - - +
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Residues in contact with PHE 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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222B VAL* 4.3 16.4 - - + -
223B ASP* 4.3 17.0 - - - -
226B ALA* 3.3 31.6 - - + -
230B LYS* 4.4 6.7 - - - -
252B LEU* 4.3 11.2 - - + -
253B LYS 3.5 20.6 - - - -
254B ASP* 3.1 30.7 + - + -
255B ALA 3.2 5.2 + - - +
257B SER* 1.3 77.0 - - - +
259B LEU* 1.3 64.4 + - - +
261B GLU* 3.4 16.5 + - - +
262B TRP* 3.1 57.2 + + + -
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Residues in contact with LEU 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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246B VAL* 4.4 12.1 - - + -
249B ILE* 4.7 19.3 - - + -
252B LEU* 6.1 1.3 - - + -
255B ALA* 3.0 26.9 + - + +
256B SER* 3.9 4.7 - - - +
258B PHE* 1.3 77.4 - - - +
260B ALA* 1.3 51.1 + - - +
262B TRP* 3.3 20.1 + - + +
263B GLN* 2.8 37.6 + - - +
275B LEU* 4.1 6.9 - - + +
277B ALA* 4.1 29.6 - - + -
292B GLU* 3.9 27.1 - - + +
297B LEU* 4.1 16.6 - - + -
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Residues in contact with ALA 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 SER 3.3 11.9 + - - +
257B SER* 3.5 11.4 - - - +
258B PHE 3.3 0.2 - - - -
259B LEU* 1.3 77.9 - - - +
261B GLU* 1.3 61.2 + - - +
263B GLN* 3.4 7.5 + - - +
264B ASN* 3.2 34.6 + - - +
292B GLU* 3.8 12.7 + - - +
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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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230B LYS* 2.8 46.9 + - - +
257B SER 3.2 9.9 + - - +
258B PHE* 3.7 17.8 - - - +
259B LEU 3.3 0.2 - - - -
260B ALA* 1.3 77.1 - - - +
262B TRP* 1.3 64.9 + - + +
264B ASN* 3.4 9.1 + - - +
265B ILE* 3.3 37.9 + - + +
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Residues in contact with TRP 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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217B TRP* 4.2 23.3 - + - -
226B ALA* 4.0 21.8 + - + -
229B VAL* 3.5 34.2 - - + +
230B LYS* 4.1 14.6 - - + +
233B LEU* 3.4 32.2 - - + +
246B VAL* 4.8 12.1 - - + -
249B ILE* 6.4 0.2 - - + -
252B LEU* 3.9 21.3 - - + -
258B PHE* 3.1 42.1 + + + +
259B LEU* 4.0 20.9 - - + +
261B GLU* 1.3 78.6 - - + +
263B GLN* 1.3 59.7 + - - +
265B ILE* 3.9 9.9 - - + +
266B THR* 2.6 35.2 + - - -
275B LEU* 3.9 12.3 - - + -
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Residues in contact with GLN 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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259B LEU 2.8 20.0 + - - +
260B ALA* 3.5 9.6 - - - +
262B TRP* 1.3 76.9 - - - +
264B ASN* 1.3 63.7 + - - +
266B THR* 3.4 3.1 + - - -
267B LYS* 3.1 60.9 + - + +
275B LEU* 3.7 16.6 - - - +
292B GLU* 5.4 3.4 - - - +
295B LYS* 3.4 19.2 - - + +
296B ASP 3.2 30.9 - - - +
297B LEU* 3.7 30.3 - - + +
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Residues in contact with ASN 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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260B ALA* 3.2 22.3 + - - +
261B GLU* 3.8 6.6 - - - +
262B TRP 3.3 0.2 - - - -
263B GLN* 1.3 83.4 - - - +
265B ILE* 1.3 60.2 + - + +
267B LYS* 4.6 3.4 - - - +
268B GLY* 2.9 27.5 + - - -
295B LYS* 5.6 5.2 - - - +
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Residues in contact with ILE 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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230B LYS* 4.8 14.1 - - + -
233B LEU* 4.4 22.9 - - + -
234B GLU* 4.0 35.2 - - + +
237B LEU* 4.2 6.7 - - + +
261B GLU* 3.3 34.4 + - + +
262B TRP* 3.9 13.7 - - + +
263B GLN 3.4 0.2 - - - -
264B ASN* 1.3 76.5 - - + +
266B THR* 1.3 63.2 + - - +
268B GLY* 4.0 1.2 - - - -
269B PHE* 3.4 19.4 + - - +
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Residues in contact with THR 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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233B LEU* 4.7 5.7 - - - +
237B LEU* 4.5 10.5 - - + -
243B GLY* 5.2 0.9 - - - -
244B PHE* 4.5 18.3 - - + -
262B TRP 2.6 23.4 + - - -
263B GLN* 3.7 6.7 - - - -
265B ILE* 1.3 79.4 - - - +
267B LYS* 1.3 61.3 + - + +
269B PHE* 3.5 10.7 + - - +
270B SER 3.4 8.7 - - - +
273B ARG* 3.4 36.5 - - + +
274B LEU 3.7 20.4 - - - +
275B LEU* 4.4 10.2 - - + +
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Residues in contact with LYS 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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116B LYS* 5.6 0.4 - - - +
118B TRP* 3.3 31.1 - - - -
263B GLN* 3.1 44.4 + - + +
264B ASN* 4.4 3.4 - - - +
266B THR* 1.3 74.9 - - - +
268B GLY* 1.3 63.6 + - - +
269B PHE 3.3 0.2 - - - -
270B SER* 3.1 21.3 + - - +
271B GLU* 3.9 19.0 + - + +
273B ARG 2.7 27.3 + - - +
274B LEU* 4.2 3.0 - - - +
275B LEU 5.2 1.3 - - - +
295B LYS* 5.0 9.6 - - + -
296B ASP* 3.9 19.4 + - - +
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Residues in contact with GLY 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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264B ASN 2.9 19.9 + - - -
265B ILE* 4.0 2.0 - - - -
266B THR 3.3 0.4 - - - -
267B LYS* 1.3 74.5 - - - +
269B PHE* 1.3 64.6 + - - +
270B SER* 3.6 0.5 + - - -
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Residues in contact with PHE 269 (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 GLU* 4.9 1.8 - - - -
237B LEU* 3.5 56.3 - - + -
238B GLN* 3.8 23.6 - - + -
265B ILE 3.4 12.2 + - - +
266B THR 3.6 10.1 - - - +
267B LYS 3.3 0.2 - - - -
268B GLY* 1.3 77.4 - - - +
270B SER* 1.3 68.5 + - - +
273B ARG* 4.2 27.1 - - + -
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Residues in contact with SER 270 (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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266B THR 3.4 4.2 + - - +
267B LYS* 3.1 23.9 - - - +
268B GLY 3.3 0.8 - - - -
269B PHE* 1.3 83.3 - - - +
271B GLU* 1.3 72.0 + - - +
272B ASP* 3.1 20.1 + - - +
273B ARG* 3.6 31.1 + - - +
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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