Contacts of the helix formed by residues 246 - 266 (chain B) in PDB entry 4XQ2
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 THR 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B HIS* 4.2 4.0 - - - -
243B GLY* 3.1 7.8 + - - -
244B LEU 3.1 0.2 - - - -
245B HIS* 1.3 79.3 - - + +
247B LEU* 1.3 54.7 + - - +
248B SER 3.3 2.9 - - - -
249B LEU* 3.0 11.1 + - + -
250B ARG* 2.7 61.1 + - - +
202C HIS* 4.1 13.4 + - - +
246C THR* 3.7 31.6 - - - +
250C ARG* 3.9 25.1 - - + -
327C VAL* 5.1 0.2 - - + -
363C ILE* 4.1 9.4 - - + -
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.9 16.6 - - + -
177B SER* 4.5 1.3 - - - -
178B PRO* 3.9 24.9 - - + -
179B VAL* 3.6 20.9 - - + -
198B SER* 3.4 35.7 - - - +
199B ILE* 3.8 13.5 - - + +
243B GLY 3.4 2.8 + - - -
244B LEU* 3.1 25.3 + - + +
245B HIS 3.4 0.2 - - - -
246B THR* 1.3 76.5 - - - +
248B SER* 1.3 57.3 + - - +
250B ARG* 3.3 13.4 - - - +
251B VAL* 2.9 43.0 + - + +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.9 9.0 - - - -
7B GLY* 5.0 3.6 - - - -
10B LEU* 3.6 23.5 - - - +
179B VAL* 3.8 26.0 - - - -
245B HIS 5.0 0.2 + - - -
246B THR 3.3 0.4 - - - -
247B LEU* 1.3 77.1 - - - +
249B LEU* 1.3 75.0 + - - +
252B HIS* 3.2 33.0 + - - +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B HIS 5.4 0.9 + - - +
246B THR* 3.0 12.1 + - + +
248B SER* 1.3 87.8 + - - +
250B ARG* 1.3 60.5 + - - +
252B HIS* 4.4 1.1 - - - +
253B ARG* 3.3 22.2 + - - +
249C LEU* 3.6 36.5 - - + +
250C ARG* 3.9 11.2 - - + +
253C ARG* 3.7 28.0 - - + -
363C ILE* 3.9 42.6 - - + +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 2.7 21.2 + - - +
199B ILE 3.0 19.4 + - - -
200B ALA 4.0 1.1 + - - -
201B GLY* 3.4 17.3 + - - -
202B HIS* 3.8 4.8 - - - -
243B GLY 2.6 24.9 + - - -
246B THR* 2.7 34.2 + - - +
247B LEU* 3.3 18.6 - - - +
249B LEU* 1.3 71.9 - - - +
251B VAL* 1.3 60.8 + - - +
253B ARG* 3.2 3.5 + - - +
254B GLN* 2.8 40.8 + - - +
325B GLY 4.4 6.7 + - - -
327B VAL* 3.9 19.3 - - - -
363B ILE* 4.1 9.6 - - + -
246C THR* 3.8 17.9 - - + -
249C LEU* 3.8 21.3 - - + -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA 4.9 1.1 - - - +
177B SER* 3.8 22.0 - - - +
179B VAL* 4.0 12.6 - - + -
180B LEU* 3.7 40.4 - - + -
198B SER* 4.4 9.4 - - - +
247B LEU* 2.9 32.6 + - + +
248B SER 4.1 2.7 - - - +
249B LEU 3.4 0.2 - - - -
250B ARG* 1.3 77.9 - - + +
252B HIS* 1.3 59.8 + - - +
254B GLN* 3.1 14.3 + - - +
255B VAL* 2.8 32.9 + - + +
297B ALA* 6.3 0.2 - - - -
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.5 18.7 + - + +
180B LEU* 3.5 30.6 - - + +
248B SER* 3.2 25.3 + - - +
249B LEU* 4.7 1.1 - - - +
251B VAL* 1.3 73.1 - - - +
253B ARG* 1.3 61.0 + - - +
255B VAL* 3.7 10.6 - - - +
256B ALA* 3.0 29.3 + - - +
293B SER* 4.9 4.0 - - - -
294B ALA* 4.2 10.0 - - + +
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Residues in contact with ARG 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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249B LEU 3.3 15.9 + - - +
250B ARG 3.2 9.1 + - - +
252B HIS* 1.3 74.3 - - - +
254B GLN* 1.3 64.0 + - - +
256B ALA* 3.4 25.9 + - - +
257B THR* 3.2 38.5 + - - +
260B VAL* 5.4 1.6 - - - +
362B GLY 4.8 0.2 - - - -
363B ILE* 3.9 31.6 - - + +
364B GLU 5.0 1.5 + - - -
366B PRO* 3.8 28.9 - - - +
249C LEU* 3.7 28.3 - - + -
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Residues in contact with GLN 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 4.9 4.6 + - - -
250B ARG* 2.8 35.3 + - - +
251B VAL* 3.3 14.7 - - - +
253B ARG* 1.3 73.8 - - - +
255B VAL* 1.3 61.9 + - - +
257B THR 3.4 0.2 + - - -
258B ALA* 3.0 20.7 + - - +
297B ALA* 3.1 25.4 - - + +
325B GLY* 3.0 33.1 + - - +
326B GLY 3.7 10.1 + - - -
327B VAL* 4.7 1.0 - - - +
361B VAL* 3.0 34.2 + - - +
362B GLY* 3.7 18.8 - - - +
363B ILE* 4.0 10.0 - - + +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 4.0 26.0 - - + -
251B VAL* 2.8 29.2 + - + +
252B HIS* 3.7 11.9 - - - +
253B ARG 3.3 0.2 - - - -
254B GLN* 1.3 72.2 - - - +
256B ALA* 1.3 63.4 + - - +
258B ALA* 3.0 11.8 + - - +
259B ARG* 2.9 44.6 + - - +
276B TYR* 4.1 2.5 - - - +
294B ALA* 4.2 10.5 - - + -
295B PRO* 3.9 12.8 - - + -
296B GLY 3.8 16.6 - - - +
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Residues in contact with ALA 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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252B HIS 3.0 17.9 + - - +
253B ARG* 3.4 23.8 - - - +
255B VAL* 1.3 75.5 - - - +
257B THR* 1.3 62.4 + - - +
259B ARG* 3.3 18.8 - - - +
260B VAL* 3.2 24.0 + - - +
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Residues in contact with THR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ARG* 3.2 33.0 + - - +
256B ALA* 1.3 73.6 - - - +
258B ALA* 1.3 66.2 + - - +
260B VAL* 3.0 11.8 + - - +
261B LEU* 3.0 32.7 + - + +
361B VAL* 3.5 26.0 - - + -
362B GLY 4.7 2.0 + - - -
364B GLU 4.3 5.0 + - - -
366B PRO* 3.8 19.4 - - + +
369B LEU* 3.7 21.8 - - + -
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Residues in contact with ALA 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 GLN 3.0 13.1 + - - +
255B VAL 3.0 10.4 + - - +
257B THR* 1.3 76.4 - - - +
259B ARG* 1.3 61.9 + - - +
261B LEU* 3.2 3.5 + - - +
262B VAL* 3.0 29.7 + - - +
276B TYR* 3.6 14.8 - - + +
296B GLY 3.6 18.8 - - - +
297B ALA* 4.6 2.0 - - - -
299B VAL* 4.0 11.2 - - + +
361B VAL* 4.2 15.6 - - + +
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Residues in contact with ARG 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 VAL* 2.9 27.7 + - - +
256B ALA* 3.3 18.4 - - - +
258B ALA* 1.3 73.2 - - - +
260B VAL* 1.3 62.5 + - + +
262B VAL* 3.6 5.9 + - - +
263B GLU* 3.3 27.3 + - - +
276B TYR* 3.1 31.2 + - + -
278B GLY 5.4 3.8 + - - -
295B PRO* 3.1 34.2 - - - +
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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
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253B ARG* 5.4 1.6 - - - +
256B ALA 3.2 16.4 + - - +
257B THR* 3.0 14.1 + - - +
259B ARG* 1.3 76.5 - - + +
261B LEU* 1.3 71.7 + - + +
263B GLU* 3.1 9.5 + - - +
264B ARG* 3.0 24.2 + - + +
366B PRO* 4.3 14.8 - - + -
367B GLN* 4.0 28.5 - - - +
370B ALA* 4.4 6.5 - - + -
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Residues in contact with LEU 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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257B THR* 3.0 23.9 + - + +
258B ALA* 3.2 4.9 + - - +
260B VAL* 1.3 76.7 - - + +
262B VAL* 1.3 56.6 + - - +
264B ARG* 3.1 5.3 + - - +
265B LEU* 2.7 41.8 + - + +
299B VAL* 5.4 2.2 - - + -
318B PHE* 3.9 27.4 - - + -
359B LEU* 4.5 12.6 - - + -
361B VAL* 4.0 23.6 - - + -
366B PRO 4.4 3.1 - - - +
369B LEU* 4.2 3.4 - - + +
370B ALA* 3.7 40.4 - - + +
373B LEU* 4.4 13.2 - - + +
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Residues in contact with VAL 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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258B ALA 3.0 21.0 + - - +
259B ARG* 3.8 7.2 - - - +
260B VAL 3.3 0.2 - - - -
261B LEU* 1.3 76.5 - - - +
263B GLU* 1.3 64.1 + - - +
265B LEU* 3.3 8.2 + - - +
266B ARG* 2.8 46.3 + - - +
274B VAL* 4.1 10.5 - - + -
276B TYR* 3.7 27.4 - - + -
279B LEU* 4.2 17.3 - - + -
299B VAL* 3.7 26.9 - - + -
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Residues in contact with GLU 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 ARG* 3.3 14.2 + - + +
260B VAL* 3.1 9.8 + - - +
262B VAL* 1.3 80.0 - - - +
264B ARG* 1.3 66.5 + - - +
266B ARG* 3.5 29.7 + - - +
267B ALA* 3.5 19.8 + - - +
279B LEU* 4.6 6.6 - - - +
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Residues in contact with ARG 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 VAL* 3.0 13.1 + - + +
261B LEU* 3.1 12.5 + - - +
263B GLU* 1.3 74.1 - - - +
265B LEU* 1.3 64.4 + - - +
267B ALA* 3.1 16.7 + - - +
268B SER* 3.5 10.1 + - - -
367B GLN* 4.1 13.7 - - - +
370B ALA* 3.4 41.9 + - + +
371B GLU* 4.3 15.4 + - - +
373B LEU* 4.7 11.7 - - + -
374B SER* 2.8 46.5 + - - +
377B LEU* 6.1 2.5 - - + -
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Residues in contact with LEU 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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261B LEU 2.7 24.2 + - - +
262B VAL* 3.5 5.8 - - - +
264B ARG* 1.3 69.1 - - - +
266B ARG* 1.3 56.8 + - - +
267B ALA 3.0 10.9 + - - -
268B SER* 3.1 14.1 + - - +
271B VAL* 3.6 28.0 - - + +
274B VAL* 3.9 17.0 - - + -
299B VAL* 3.8 25.4 - - + -
301B PHE* 3.7 52.3 - - + -
359B LEU* 4.2 10.1 - - + -
373B LEU* 3.8 18.2 - - + -
377B LEU* 4.0 6.3 - - + -
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL* 2.8 40.8 + - + +
263B GLU* 3.8 27.9 + - - +
264B ARG 3.4 0.4 - - - -
265B LEU* 1.3 72.2 - - - +
267B ALA* 1.3 57.6 + - - +
268B SER 3.5 1.6 - - - +
274B VAL* 4.2 19.5 - - + -
279B LEU* 4.1 20.8 - - + +
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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
------------------------------------------------------------
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