Contacts of the helix formed by residues 257 - 272 (chain A) in PDB entry 3UZU
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 GLY 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A PRO* 3.6 23.7 - - - +
161A PHE* 4.3 2.5 - - - -
255A ASP 4.1 0.4 + - - -
256A ILE* 1.3 75.6 - - - +
258A VAL* 1.3 66.5 + - - -
259A ASP* 3.2 2.9 - - - -
260A GLU* 3.0 19.9 + - - +
261A TYR* 3.1 16.9 + - - -
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Residues in contact with VAL 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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161A PHE* 4.8 3.5 - - + -
166A VAL* 3.9 29.6 - - + +
169A GLN* 3.5 39.7 - - + +
170A TYR* 3.8 34.1 - - + +
214A LEU* 5.6 0.7 - - + -
257A GLY* 1.3 69.9 - - - -
259A ASP* 1.3 69.9 + - - +
261A TYR* 3.2 3.1 + - - +
262A VAL* 3.0 30.7 + - + +
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Residues in contact with ASP 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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257A GLY 3.2 0.6 - - - -
258A VAL* 1.3 83.4 - - - +
260A GLU* 1.3 62.6 + - + +
262A VAL* 3.4 10.6 + - - +
263A ARG* 3.2 20.3 + - - +
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Residues in contact with GLU 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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247A PHE* 3.4 14.0 - - + -
251A ARG* 2.8 42.6 + - - -
255A ASP 5.6 0.2 - - - +
256A ILE* 3.4 24.6 - - + +
257A GLY* 3.0 8.9 + - - +
259A ASP* 1.3 77.9 - - + +
261A TYR* 1.3 60.6 + - - +
263A ARG* 3.1 12.9 + - + +
264A VAL* 2.9 33.7 + - - +
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Residues in contact with TYR 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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166A VAL* 3.8 20.2 - - + -
214A LEU* 3.7 17.2 - - + +
217A VAL* 4.2 15.8 - - + +
218A VAL* 4.0 16.6 - - + -
221A ALA* 3.6 19.9 - - + +
222A PHE* 3.3 24.3 - + - -
229A LEU* 4.4 3.0 - - + +
233A LEU* 5.7 2.5 - - + -
247A PHE* 6.1 1.1 - + - -
253A ALA* 2.8 37.0 + - - +
256A ILE* 3.3 37.0 - - + +
257A GLY 3.1 22.9 + - - -
258A VAL 3.6 5.8 - - - +
260A GLU* 1.3 75.6 - - - +
262A VAL* 1.3 62.2 + - - +
264A VAL* 3.3 9.3 + - + +
265A ALA* 3.0 24.1 + - - +
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Residues in contact with VAL 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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170A TYR* 4.7 0.4 - - + -
207A PRO* 3.8 36.6 - - + -
209A VAL* 4.0 10.2 - - + +
214A LEU* 4.1 23.1 - - + -
258A VAL* 3.0 25.6 + - + +
259A ASP* 3.5 12.6 - - - +
260A GLU 3.2 0.2 - - - -
261A TYR* 1.3 75.8 - - - +
263A ARG* 1.3 58.3 + - - +
265A ALA* 3.3 4.3 + - - +
266A GLN* 2.9 54.4 + - - +
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Residues in contact with ARG 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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245A LEU 5.9 2.3 + - - -
247A PHE* 6.5 1.3 - - + -
259A ASP 3.2 12.4 + - - +
260A GLU* 3.1 15.1 + - - +
262A VAL* 1.3 78.7 - - - +
264A VAL* 1.3 57.1 + - + +
266A GLN* 3.3 17.7 + - + +
267A ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 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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217A VAL* 3.4 29.4 - - + -
233A LEU* 4.4 9.2 - - + -
236A TYR* 6.4 0.2 - - + -
242A PHE* 3.6 27.8 - - + -
247A PHE* 3.6 37.2 - - + -
256A ILE* 5.7 0.2 - - + -
260A GLU 2.9 20.3 + - - +
261A TYR* 3.6 13.5 - - + +
263A ARG* 1.3 75.6 - - + +
265A ALA* 1.3 57.3 + - - +
267A ALA* 3.2 7.5 + - - +
268A VAL* 2.9 32.4 + - - +
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Residues in contact with ALA 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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209A VAL* 3.6 20.0 - - + -
213A VAL* 3.5 18.3 - - + +
214A LEU* 3.8 28.0 - - + +
217A VAL* 4.2 7.4 - - + +
261A TYR 3.0 16.8 + - - +
262A VAL 3.6 4.5 - - - +
264A VAL* 1.3 74.1 - - - +
266A GLN* 1.3 66.5 + - - +
268A VAL 3.3 0.5 + - - -
269A ALA* 3.0 22.7 + - - +
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Residues in contact with GLN 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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207A PRO* 5.3 0.4 - - - +
208A ALA* 2.8 36.4 + - - +
209A VAL* 4.2 8.5 - - + -
262A VAL* 2.9 31.8 + - - +
263A ARG* 3.6 21.7 - - + +
265A ALA* 1.3 76.8 - - - +
267A ALA* 1.3 57.5 + - - +
269A ALA* 3.5 5.9 + - - +
270A SER* 3.0 30.4 + - - -
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Residues in contact with ALA 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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240A VAL* 4.2 5.3 - - + +
242A PHE* 4.1 16.8 - - + -
245A LEU* 4.5 18.8 - - + -
263A ARG 2.9 13.5 + - - +
264A VAL* 3.2 11.0 + - - +
266A GLN* 1.3 74.9 - - - +
268A VAL* 1.3 59.1 + - - +
270A SER* 3.3 6.6 + - - -
271A ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 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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213A VAL* 4.0 10.5 - - + -
216A GLU* 4.7 0.4 - - - +
217A VAL* 3.9 16.8 - - + -
236A TYR* 4.0 17.5 - - + -
239A LEU* 3.9 7.9 - - + -
240A VAL* 4.2 8.7 - - + -
242A PHE* 4.0 20.0 - - + -
264A VAL 2.9 20.3 + - - +
265A ALA 3.3 4.5 + - - +
267A ALA* 1.3 75.8 - - - +
269A ALA* 1.3 63.0 + - - +
271A ALA* 3.3 4.3 + - - +
272A ARG* 3.2 57.5 + - - +
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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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209A VAL* 6.6 0.2 - - + -
210A ASP* 5.6 6.3 - - + +
213A VAL* 4.4 16.1 - - + +
265A ALA 3.0 16.8 + - - +
266A GLN* 3.8 6.5 - - - +
268A VAL* 1.3 77.0 - - - +
270A SER* 1.3 62.7 + - - +
272A ARG* 3.2 18.8 + - - +
273A ALA* 3.2 13.9 + - - +
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Residues in contact with SER 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 GLN 3.0 18.8 + - - -
267A ALA* 3.6 8.1 - - - -
269A ALA* 1.3 75.0 - - - +
271A ALA* 1.3 63.3 - - - +
273A ALA* 3.1 23.3 + - - +
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Residues in contact with ALA 271 (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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239A LEU* 3.7 38.3 - - + +
240A VAL* 3.8 11.9 - - + -
267A ALA 2.9 16.8 + - - +
268A VAL 3.3 6.3 + - - +
270A SER* 1.3 78.0 - - - +
272A ARG* 1.3 58.7 + - - +
273A ALA 3.7 1.7 + - - +
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Residues in contact with ARG 272 (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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213A VAL* 4.3 14.1 - - - +
216A GLU* 2.7 42.4 + - - -
236A TYR* 3.9 11.7 - - - -
239A LEU* 3.9 22.3 - - + +
268A VAL* 3.2 29.0 + - - +
269A ALA* 3.2 10.9 + - - +
270A SER 3.1 0.8 - - - -
271A ALA* 1.3 77.6 - - - +
273A ALA* 1.3 64.1 + - - +
274A SER* 3.7 3.1 + - - -
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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