Contacts of the helix formed by residues 255 - 270 (chain A) in PDB entry 4OQZ
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 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A VAL* 3.3 32.8 - - - +
248A ASN* 3.7 9.6 - - + -
249A ALA* 3.5 25.8 - - + +
253A VAL 3.5 2.0 + - - +
254A ASP* 1.3 72.9 + - - +
256A ALA* 1.4 54.1 + - - +
258A PRO* 3.3 9.6 - - - +
259A ARG* 2.8 67.6 + - - +
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASP* 3.3 22.9 + - - +
255A THR* 1.4 75.8 - - - +
257A PHE* 1.3 62.3 + - - +
259A ARG* 3.6 10.4 - - - +
260A ALA* 3.2 23.4 + - - +
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Residues in contact with PHE 257 (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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178A PRO* 3.8 29.8 - - + -
181A LEU* 3.7 34.3 - - + -
182A SER* 3.4 30.7 - - - -
185A GLN* 3.6 30.1 + - + +
254A ASP* 4.7 1.4 + - - -
256A ALA* 1.3 75.2 - - - +
258A PRO* 1.4 69.6 - - + +
260A ALA* 3.3 18.8 + - + +
261A VAL* 3.3 29.6 + - + +
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Residues in contact with PRO 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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185A GLN* 3.5 39.0 - - + +
241A MET* 3.1 28.0 - - + +
244A VAL* 3.9 13.2 - - + -
245A VAL* 3.7 13.9 - - + -
248A ASN* 4.2 10.3 - - + +
255A THR* 3.3 18.8 - - - +
257A PHE* 1.4 91.0 - - + +
259A ARG* 1.4 55.6 + - - +
261A VAL* 3.4 3.0 + - + -
262A LEU* 3.0 24.4 + - - +
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Residues in contact with ARG 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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245A VAL* 3.7 28.8 - - + +
249A ALA* 5.6 3.2 - - - +
255A THR* 2.8 57.8 + - - +
256A ALA* 3.6 13.0 - - - +
258A PRO* 1.4 69.5 - - - +
260A ALA* 1.3 55.1 + - - +
262A LEU* 3.1 11.4 + - + +
263A ASP* 2.6 49.9 + - - +
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Residues in contact with ALA 260 (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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256A ALA 3.2 13.5 + - - +
257A PHE* 3.3 17.5 - - + +
259A ARG* 1.3 76.7 - - - +
261A VAL* 1.4 60.8 + - + +
263A ASP* 3.5 12.7 - - - +
264A ALA* 3.4 19.9 + - - +
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Residues in contact with VAL 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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241A MET* 3.9 27.1 - - + -
257A PHE* 3.3 36.7 + - + +
258A PRO* 3.7 7.9 - - + +
259A ARG 3.2 0.6 - - - -
260A ALA* 1.4 74.6 - - + +
262A LEU* 1.4 65.2 + - - +
264A ALA* 3.2 17.0 + - - +
265A PHE* 3.3 28.6 + - + -
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Residues in contact with LEU 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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238A VAL* 3.5 28.5 - - + +
241A MET* 4.0 15.0 - - + +
242A GLU* 3.7 27.8 - - + +
245A VAL* 3.9 27.6 - - + -
258A PRO 3.0 14.7 + - - +
259A ARG* 3.4 17.3 - - + +
261A VAL* 1.4 74.7 - - - +
263A ASP* 1.4 58.2 + - - +
265A PHE* 3.1 5.8 + - - +
266A HIS* 2.8 52.3 + - + +
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Residues in contact with ASP 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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259A ARG* 2.6 41.6 + - - +
260A ALA* 3.5 12.0 - - - +
262A LEU* 1.4 75.5 - - - +
264A ALA* 1.4 56.4 + - - +
266A HIS* 4.0 5.7 - - - +
267A ARG* 2.9 34.4 + - - +
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Residues in contact with ALA 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 ALA 3.4 8.5 + - - +
261A VAL* 3.2 11.9 + - - +
263A ASP* 1.4 73.4 - - - +
265A PHE* 1.3 59.7 + - + +
267A ARG* 2.2 40.9 - - - +
281A VAL* 3.1 19.3 - - + +
285A MET* 5.4 9.6 - - + -
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Residues in contact with PHE 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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234A LEU* 3.8 22.7 - - + +
237A GLY* 3.7 20.2 - - - -
238A VAL* 3.5 27.2 - - + +
241A MET* 3.6 33.0 - - + -
261A VAL* 3.3 21.7 + - + -
262A LEU* 3.1 8.1 + - - +
264A ALA* 1.3 80.8 - - + +
266A HIS* 1.4 64.3 + - - +
267A ARG 3.1 5.2 - - - +
269A ALA 3.5 10.4 + - - -
278A PHE* 3.9 32.8 - + - -
281A VAL* 4.3 13.2 - - + -
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Residues in contact with HIS 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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238A VAL* 3.6 28.5 - - + +
242A GLU* 3.2 22.1 + - - -
262A LEU* 2.8 31.9 + - + +
263A ASP* 4.0 6.3 - - - +
265A PHE* 1.4 67.5 - - - +
267A ARG* 1.4 62.7 + - - +
269A ALA* 3.2 19.5 + - + +
270A ASP* 3.3 21.3 + - - +
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Residues in contact with ARG 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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263A ASP 2.9 16.5 + - - +
264A ALA* 2.2 47.3 - - - +
265A PHE 3.1 3.3 - - - +
266A HIS* 1.4 71.0 - - - +
268A GLY* 1.3 60.6 + - - +
270A ASP* 4.0 11.0 - - + +
281A VAL* 3.5 2.5 - - - +
284A LEU* 4.3 36.6 + - + +
285A MET* 5.2 8.1 - - - +
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Residues in contact with GLY 268 (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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234A LEU* 3.6 9.0 - - - -
265A PHE 4.1 0.7 - - - -
266A HIS 3.4 0.4 + - - -
267A ARG* 1.3 77.7 - - - +
269A ALA* 1.4 52.5 + - - +
270A ASP* 3.0 10.7 - - - +
271A ALA* 3.0 13.4 + - - +
274A GLY 2.7 27.9 + - - -
280A SER 6.3 0.2 - - - -
281A VAL* 3.8 9.0 - - - -
284A LEU* 3.5 23.6 - - - +
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Residues in contact with ALA 269 (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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234A LEU* 3.5 12.1 - - + +
235A SER* 5.9 2.9 - - - -
238A VAL* 4.6 11.0 - - + -
265A PHE 3.5 11.1 + - - +
266A HIS* 3.2 18.6 + - - +
268A GLY* 1.4 74.6 - - - +
270A ASP* 1.3 59.0 + - - +
271A ALA 3.1 12.7 + - - +
274A GLY* 4.3 6.8 - - - -
275A ALA* 4.5 8.7 + - + +
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Residues in contact with ASP 270 (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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266A HIS* 3.3 22.3 + - - +
267A ARG* 4.0 9.6 - - - +
268A GLY 3.0 6.7 - - - +
269A ALA* 1.3 78.1 - - - +
271A ALA* 1.4 56.0 + - - +
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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