Contacts of the helix formed by residues 256 - 275 (chain B) in PDB entry 3H90
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 PRO 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B SER 3.3 4.9 - - - +
255B LEU* 1.3 88.4 - - + +
257B LEU* 1.3 67.9 + - - +
258B VAL* 4.5 5.6 - - + +
259B GLN* 3.0 38.9 + - + +
260B ALA* 3.0 18.2 + - - +
253D ASP 4.3 6.1 - - - +
254D SER* 3.8 17.7 - - - +
255D LEU 3.4 6.3 - - - +
256D PRO* 4.0 4.0 - - + -
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Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU 3.7 0.6 + - - -
256B PRO* 1.3 70.4 - - - +
258B VAL* 1.3 56.7 + - - +
260B ALA* 2.8 8.9 + - + -
261B HIS* 2.7 37.2 + - + +
284B GLN* 4.1 10.1 - - - +
251D MET* 4.1 20.4 - - + +
252D GLU 4.1 6.7 - - - +
253D ASP 3.6 8.6 + - - +
255D LEU 2.7 18.5 + - - +
257D LEU* 4.4 7.4 - - + +
260D ALA* 3.9 18.6 - - + -
284D GLN* 3.6 35.0 - - + +
285D ASP 3.8 22.9 - - - +
286D PRO* 3.9 13.5 - - + -
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 4.3 24.0 - - + +
274A ARG* 6.1 2.9 - - - +
256B PRO* 3.2 6.8 - - + -
257B LEU* 1.3 79.7 - - - +
259B GLN* 1.3 75.7 + - + +
261B HIS* 3.8 3.1 + - - +
262B MET* 3.4 26.3 + - + +
253D ASP* 3.2 43.4 + - + +
254D SER* 6.0 0.2 - - - -
286D PRO* 3.8 17.3 - - + -
287D CYS 6.1 0.4 - - - +
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Residues in contact with GLN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 6.1 3.1 - - - -
255B LEU* 4.1 20.8 - - + +
256B PRO* 3.0 33.1 + - + +
258B VAL* 1.3 89.2 - - + +
260B ALA* 1.3 64.8 + - - +
261B HIS 3.4 0.4 - - - -
262B MET* 3.4 9.4 + - - +
263B VAL* 3.3 24.0 + - - +
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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
----------------------------------------------------------
251B MET* 3.3 32.5 - - - +
255B LEU* 3.9 11.8 - - + +
256B PRO 3.0 11.1 + - - +
257B LEU* 2.8 9.7 + - - +
259B GLN* 1.3 75.2 - - - +
261B HIS* 1.3 64.0 + - - +
262B MET 3.1 0.2 - - - -
263B VAL 3.4 1.6 + - - -
264B ALA* 3.1 17.8 + - - +
284B GLN* 3.8 8.1 - - + +
257D LEU* 3.9 25.4 - - + -
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Residues in contact with HIS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 4.8 11.4 + - - -
257B LEU* 2.7 19.5 + - + +
258B VAL 3.9 2.8 + - - +
260B ALA* 1.3 72.7 - - - +
262B MET* 1.3 58.9 + - - +
264B ALA* 3.2 2.5 - - - +
265B ASP* 2.9 46.0 + - - +
284B GLN* 3.3 11.4 - - - +
5D ZN 2.0 34.0 - - - -
283D HIS* 3.2 18.8 + + - -
284D GLN 3.7 10.1 - - - +
285D ASP* 2.5 13.0 + - - -
286D PRO* 3.7 27.4 - - + +
288D SER* 4.3 11.0 + - - -
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Residues in contact with MET 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 4.7 8.3 - - + +
221A ILE* 3.6 40.4 - - + +
224A SER* 3.6 28.3 - - - +
225A TRP* 5.2 6.7 - - + -
270A ALA* 6.0 1.6 - - + -
274A ARG* 4.0 21.5 - - + +
258B VAL* 3.4 16.7 + - + +
259B GLN* 3.4 12.8 - - - +
260B ALA 3.1 0.4 - - - -
261B HIS* 1.3 78.9 - - - +
263B VAL* 1.3 60.2 + - - +
265B ASP* 3.1 23.7 + - + +
266B GLN* 2.8 35.2 + - - +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B TRP* 4.6 2.2 - - + -
227B GLY* 3.9 31.9 - - - +
228B VAL* 4.1 20.4 - - + +
249B LEU* 4.3 0.2 - - + -
251B MET* 3.7 22.9 - - + -
255B LEU* 4.5 8.3 - - + -
259B GLN 3.3 16.6 - - - +
260B ALA* 3.5 10.1 - - - +
262B MET* 1.3 72.2 - - - +
264B ALA* 1.3 65.9 + - - +
266B GLN* 3.5 18.1 - - - +
267B VAL* 2.9 32.3 + - + +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 4.1 11.7 - - - -
251B MET* 4.0 6.0 - - + +
260B ALA 3.1 14.1 + - - +
261B HIS* 3.2 16.4 - - + +
263B VAL* 1.3 79.1 - - - +
265B ASP* 1.3 56.1 + - - +
267B VAL* 3.3 3.1 + - - +
268B GLU* 2.8 28.2 + - - +
282B ILE* 3.9 20.2 - - + +
284B GLN* 3.9 18.6 - - - +
283D HIS* 4.8 3.8 - - + -
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TRP* 5.2 1.1 - - + -
273A ARG* 4.0 13.9 + - - +
274A ARG* 5.1 3.8 + - - -
261B HIS* 2.9 45.3 + - - +
262B MET* 3.1 23.5 + - + +
264B ALA* 1.3 72.6 - - - +
266B GLN* 1.3 65.6 + - - +
268B GLU* 3.5 23.1 - - - +
269B GLN* 2.9 32.4 + - - +
5D ZN 4.1 2.1 - - - -
283D HIS* 5.5 1.1 - - - -
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Residues in contact with GLN 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.3 30.9 + - - +
225A TRP* 3.5 36.3 - - + +
226A PRO* 3.2 26.8 - - - +
225B TRP* 2.9 38.2 + - + +
226B PRO* 5.5 0.2 - - - +
227B GLY 5.4 1.2 + - - -
262B MET* 2.8 25.5 + - - +
263B VAL* 3.5 15.7 - - - +
265B ASP* 1.3 75.0 - - - +
267B VAL* 1.3 58.3 + - - +
269B GLN* 3.2 3.5 + - - +
270B ALA* 2.9 26.7 + - - +
273B ARG* 4.9 0.5 + - - -
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 5.4 0.4 - - + +
222B VAL* 3.9 29.8 - - + -
225B TRP* 3.9 16.2 - - + -
228B VAL* 3.7 28.3 - - + -
249B LEU* 3.9 14.1 - - + -
263B VAL 2.9 17.8 + - - +
264B ALA 3.6 4.3 - - - +
266B GLN* 1.3 71.3 - - - +
268B GLU* 1.3 67.9 + - - +
270B ALA* 3.0 9.3 + - + +
271B ILE* 3.0 44.6 + - + +
282B ILE* 4.7 4.5 - - + -
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 3.1 24.3 + - - +
264B ALA 2.8 17.2 + - - +
265B ASP* 3.1 21.9 + - - +
267B VAL* 1.3 77.5 - - - +
269B GLN* 1.3 56.9 + - - +
271B ILE* 3.4 7.2 + - - +
272B LEU* 3.0 34.4 + - + +
280B VAL* 3.2 41.9 + - + +
282B ILE* 4.3 9.1 - - + +
283D HIS* 5.8 3.8 + - - -
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Residues in contact with GLN 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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225A TRP* 3.8 12.1 - - - -
266A GLN 3.4 10.9 + - - -
269A GLN* 3.5 20.1 - - + +
270A ALA* 3.4 41.5 - - - +
273A ARG* 4.1 22.6 + - - +
265B ASP* 2.9 19.6 + - - +
266B GLN* 3.4 5.2 - - - +
268B GLU* 1.3 76.8 - - - +
270B ALA* 1.3 58.7 + - - +
272B LEU* 3.6 10.9 - - + +
273B ARG* 2.9 51.4 + - - +
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Residues in contact with ALA 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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221B ILE* 3.6 26.7 - - + +
225B TRP* 3.8 28.3 - - + -
266B GLN 2.9 12.8 + - - +
267B VAL* 3.0 11.4 + - - +
269B GLN* 1.3 73.7 - - - +
271B ILE* 1.3 64.7 + - - +
273B ARG* 3.6 14.0 - - - +
274B ARG* 3.4 17.2 + - - +
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Residues in contact with ILE 271 (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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218B ILE* 4.1 18.2 - - + -
221B ILE* 4.4 17.3 - - + -
222B VAL* 3.9 13.0 - - + -
245B ILE* 3.8 24.0 - - + -
247B ILE* 5.6 1.3 - - + -
267B VAL* 3.0 46.5 + - + +
268B GLU* 3.6 8.7 - - - +
270B ALA* 1.3 73.4 - - - +
272B LEU* 1.3 58.1 + - + +
274B ARG* 3.0 4.3 + - - +
275B PHE* 2.8 43.3 + - + +
278B SER* 5.1 0.7 - - - -
280B VAL* 3.7 24.0 - - + -
282B ILE* 4.7 9.0 - - + -
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Residues in contact with LEU 272 (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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273A ARG* 3.6 36.6 - - - +
268B GLU* 3.0 24.7 + - - +
269B GLN* 3.4 9.6 + - + +
271B ILE* 1.3 76.1 - - - +
273B ARG* 1.3 63.0 + - - +
275B PHE 3.7 3.6 - - - +
276B PRO* 3.2 24.8 - - - +
277B GLY 5.7 2.7 - - - +
278B SER* 3.5 33.4 - - - +
280B VAL* 3.9 24.2 - - + +
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Residues in contact with ARG 273 (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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225A TRP* 4.7 3.8 - - - -
262A MET* 3.7 27.2 - - - +
265A ASP* 5.5 2.0 + - - -
266A GLN* 4.0 36.5 - - - +
269A GLN* 4.3 13.1 - - - +
225B TRP* 5.0 2.2 - - - -
266B GLN 4.9 0.8 + - - -
269B GLN* 2.9 58.8 + - - +
270B ALA* 3.6 15.3 - - - +
272B LEU* 1.3 79.6 - - - +
274B ARG* 1.3 63.1 + - + +
275B PHE 3.4 0.2 + - - -
276B PRO* 3.6 10.0 - - - +
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Residues in contact with ARG 274 (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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213B GLU* 5.4 1.2 + - - +
214B GLU* 5.9 0.6 - - - +
217B GLU* 2.6 40.3 + - - -
221B ILE* 3.6 28.5 - - + -
270B ALA 3.4 3.5 + - - +
271B ILE 3.0 4.2 + - - +
273B ARG* 1.3 78.4 - - - +
275B PHE* 1.3 86.3 + - + +
276B PRO* 3.7 5.4 - - - +
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Residues in contact with PHE 275 (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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214B GLU* 3.7 39.3 - - + -
217B GLU* 3.4 28.7 - - + -
218B ILE* 3.7 28.0 - - + -
221B ILE* 4.5 2.7 - - + -
243B ARG* 3.6 30.5 - - - +
245B ILE* 5.1 1.3 - - + -
271B ILE* 2.8 26.6 + - + +
272B LEU* 3.2 9.4 - - - +
274B ARG* 1.3 103.4 - - + +
276B PRO* 1.3 68.3 - - - +
278B SER* 3.3 30.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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