Contacts of the helix formed by residues 250 - 268 (chain A) in PDB entry 4LQL
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 VAL 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TYR* 5.2 14.1 - - + -
242A GLY 3.0 6.0 + - - -
243A ASP* 3.2 19.7 - - - +
244A ASN 3.3 22.0 - - - +
245A ASP* 4.5 9.2 - - - -
246A HIS 5.3 0.9 - - - +
247A GLU 4.2 9.9 + - - +
248A LYS 3.6 1.8 - - - -
249A TYR* 1.3 73.8 - - - +
251A HIS* 1.3 58.3 + - - +
252A ASN 2.8 12.2 + - - -
253A VAL* 3.0 18.6 + - + +
254A ARG* 3.8 8.4 + - + +
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Residues in contact with HIS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU 5.4 0.4 + - - -
248A LYS 5.0 5.3 + - - +
249A TYR 3.3 1.3 - - - -
250A VAL* 1.3 77.0 - - - +
252A ASN* 1.3 62.1 + - - +
253A VAL 3.3 1.1 - - - -
254A ARG* 3.7 7.5 + - + +
255A TYR* 3.1 40.9 + + - -
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Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LYS 5.8 0.4 + - - -
249A TYR* 3.4 18.2 + - + +
250A VAL 2.8 1.8 + - - -
251A HIS* 1.3 86.3 - - - +
253A VAL* 1.3 58.2 + - - +
254A ARG 3.7 0.2 - - - -
255A TYR* 4.0 5.9 - - - +
256A GLN* 3.7 10.9 - - - +
287A GLN* 3.6 17.7 - - - +
364A GLU* 6.1 0.9 - - + -
374A ASP* 4.3 14.3 - - - +
375A ASP* 3.0 47.6 + - - +
377A ALA* 3.1 28.0 + - + +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TYR* 4.4 24.5 - - + +
234A GLU* 5.3 6.1 - - - +
243A ASP* 5.0 20.2 - - + +
249A TYR 4.8 4.7 - - - +
250A VAL* 3.0 15.0 + - + +
252A ASN* 1.3 81.9 - - - +
254A ARG* 1.3 61.3 + - - +
255A TYR 3.4 1.1 - - - -
256A GLN* 3.7 10.1 - - + -
257A LEU* 2.9 27.9 + - + +
291A LEU* 5.8 8.7 - - + -
362A ARG* 5.2 6.1 - - + -
364A GLU* 5.2 0.2 - - + -
377A ALA* 4.0 14.4 - - + -
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Residues in contact with ARG 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 3.7 27.8 - - + +
227A ASP* 4.7 10.1 - - - -
230A TYR* 4.4 19.7 - - + -
250A VAL* 3.8 9.6 + - + +
251A HIS* 3.7 9.1 + - + +
253A VAL* 1.3 79.9 - - - +
255A TYR* 1.3 58.1 + - + +
256A GLN 3.2 4.3 - - - -
257A LEU 4.2 1.6 - - - +
258A ARG* 3.2 30.8 + - - +
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Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A HIS* 3.1 38.7 + + - +
252A ASN* 4.0 6.3 - - - +
253A VAL 3.4 0.2 - - - -
254A ARG* 1.3 79.6 - - + +
256A GLN* 1.3 58.9 + - - +
258A ARG* 4.6 18.3 - - - +
259A GLU* 4.5 6.1 - - - +
285A LEU* 5.6 0.7 - - - +
286A GLU* 4.4 16.6 - - + +
287A GLN* 2.9 36.0 - - + +
374A ASP* 5.5 4.3 - - - +
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Residues in contact with GLN 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ASN 3.7 19.7 - - - +
253A VAL* 3.7 9.6 - - + +
255A TYR* 1.3 78.5 - - - +
257A LEU* 1.3 56.5 + - - +
258A ARG 3.0 1.3 - - - -
259A GLU* 2.5 43.5 + - - +
260A TYR 3.9 0.7 + - - -
287A GLN* 3.3 13.1 + - - +
288A LEU 5.8 0.7 - - - +
291A LEU* 6.1 4.7 - - + +
292A ALA* 4.5 7.3 - - + +
377A ALA 4.9 11.4 - - - +
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 4.3 26.0 - - + +
229A ALA* 5.1 10.5 - - + -
230A TYR* 6.0 1.6 - - + +
253A VAL* 2.9 23.6 + - + +
254A ARG* 4.5 0.2 - - - -
256A GLN* 1.3 74.2 - - - +
258A ARG* 1.3 62.2 + - - +
259A GLU 3.0 1.0 + - - -
260A TYR* 3.3 9.1 + - - +
261A LEU* 3.3 30.2 + - + +
292A ALA* 5.7 0.4 - - - -
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 3.0 42.4 - - + +
219A ASN* 4.0 33.9 + - - +
221A ILE* 4.1 20.5 + - + +
226A ILE* 5.2 10.5 - - + -
254A ARG 3.2 21.6 + - - +
255A TYR* 4.8 17.2 - - - +
256A GLN 2.8 3.6 + - - -
257A LEU* 1.3 74.5 - - - +
259A GLU* 1.3 61.2 + - - +
261A LEU* 5.6 0.4 - - - -
262A GLY* 3.2 12.7 + - - -
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 4.4 8.7 - - + -
255A TYR 4.5 6.7 - - - +
256A GLN* 2.5 24.2 + - - +
258A ARG* 1.3 69.8 - - - +
260A TYR* 1.3 52.3 + - - +
262A GLY* 2.5 7.1 + - - -
263A ILE* 2.4 45.3 + - + +
285A LEU* 4.3 24.9 - - + -
287A GLN* 5.5 1.1 - - + -
288A LEU 4.7 4.3 - - - +
289A PRO* 4.5 27.4 - - + -
292A ALA* 3.7 13.9 - - + -
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Residues in contact with TYR 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.3 10.3 + - - +
259A GLU* 1.3 76.1 - - - +
261A LEU* 1.3 74.2 + - + +
263A ILE* 4.4 4.0 - - - +
264A LYS* 2.6 46.7 + - + +
292A ALA* 3.2 39.3 - - + +
295A LEU* 3.9 21.5 - - + -
296A LEU* 4.6 2.2 - - + +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ILE* 3.3 22.4 - - + +
225A GLU* 3.7 34.8 - - + +
226A ILE* 5.3 1.8 - - - -
229A ALA* 4.8 14.1 - - + -
257A LEU* 3.3 15.6 + - + +
258A ARG* 5.6 0.2 - - - -
260A TYR* 1.3 97.3 - - + +
262A GLY* 1.3 57.9 + - - +
263A ILE 3.4 0.2 - - - -
264A LYS* 4.5 22.2 - - + +
265A LYS* 3.1 28.6 - - + +
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Residues in contact with GLY 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.4 9.4 - - - +
217A VAL* 3.1 25.3 - - - +
218A VAL* 3.8 14.4 - - - -
221A ILE* 3.7 12.7 - - - +
258A ARG 3.2 17.3 + - - -
259A GLU 2.5 15.5 + - - -
261A LEU* 1.3 73.6 - - - +
263A ILE* 1.3 55.6 + - - -
265A LYS 4.5 0.7 - - - -
266A PHE* 3.4 5.1 - - - +
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 4.4 12.6 - - + -
214A LEU* 3.6 32.3 - - + -
218A VAL* 5.1 0.2 - - + -
259A GLU* 2.4 30.3 + - + +
260A TYR 4.0 1.3 - - - +
262A GLY* 1.3 72.8 - - - +
264A LYS* 1.3 58.0 + - - +
265A LYS 3.1 1.3 - - - -
266A PHE* 2.7 25.2 + - - +
267A LEU* 3.1 21.4 + - + +
275A PHE* 4.8 10.1 - - + -
289A PRO* 5.7 6.7 - - + -
292A ALA* 6.2 0.4 - - + -
293A VAL* 6.2 1.3 - - + -
296A LEU* 4.3 15.3 - - + -
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A TYR* 2.6 26.7 + - + +
261A LEU* 4.5 21.9 - - + +
263A ILE* 1.3 72.4 - - - +
265A LYS* 1.3 60.6 + - + +
266A PHE 3.2 4.3 + - - -
267A LEU* 3.4 3.9 + - - +
268A ASP* 3.3 31.5 + - - -
295A LEU 5.6 0.7 - - - +
296A LEU* 3.9 25.9 - - + +
299A ASP* 5.0 15.0 - - - -
301A TYR* 4.1 13.8 + - + +
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL* 4.9 6.1 - - + +
221A ILE* 5.4 2.7 - - + -
261A LEU* 3.1 23.7 + - + +
262A GLY 4.6 1.6 - - - -
263A ILE 3.1 1.4 - - - -
264A LYS* 1.3 82.4 - - + +
266A PHE* 1.3 57.1 + - - +
268A ASP* 5.0 2.5 - - - +
269A ASP* 3.1 29.0 - - - +
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Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ALA* 5.1 1.1 - - + -
181A PHE* 3.2 35.0 - + - -
209A TYR* 3.8 21.5 - + + -
213A GLU* 4.9 14.4 - - + -
214A LEU* 3.5 21.3 - - + -
217A VAL* 4.1 22.9 - - + -
262A GLY 3.4 16.8 - - - +
263A ILE 2.7 13.5 + - - +
265A LYS* 1.3 74.5 - - - +
267A LEU* 1.3 68.1 + - + +
269A ASP* 4.6 2.5 - - + -
270A ASN* 3.1 39.0 + - + +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ALA* 4.9 4.3 - - + -
181A PHE* 4.2 13.2 - - + -
263A ILE* 3.1 19.7 + - + +
264A LYS 3.8 3.1 - - - +
266A PHE* 1.3 96.6 - - + +
268A ASP* 1.3 64.8 + - - +
269A ASP 3.1 0.9 - - - -
270A ASN 4.9 0.7 - - - -
271A GLY* 3.1 8.0 + - - -
272A TYR* 2.9 54.7 + - + +
274A ALA 4.5 11.0 - - - +
275A PHE* 3.5 31.9 - - + -
296A LEU* 4.5 1.3 - - + -
301A TYR* 3.8 26.2 - - + -
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LYS* 3.3 18.9 + - - +
265A LYS* 5.1 1.3 - - - -
267A LEU* 1.3 79.3 - - - +
269A ASP* 1.3 66.8 + - - +
270A ASN 3.6 0.3 + - - -
271A GLY* 3.8 6.8 + - - -
272A TYR 4.3 2.9 + - - -
301A TYR* 3.2 24.9 - - - -
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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