Contacts of the helix formed by residues 260 - 272 (chain A) in PDB entry 4X5O
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 ALA 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A GLY 3.7 1.8 + - - -
259A LEU* 1.3 73.6 - - - +
261A PRO* 1.3 61.9 - - + +
262A GLU* 2.8 26.9 - - + +
263A VAL* 2.5 45.3 + - + +
264A ALA* 3.1 8.0 + - - -
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Residues in contact with PRO 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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250A LYS* 5.2 5.0 - - - -
254A VAL* 4.7 20.6 - - + -
259A LEU 3.3 7.4 - - - +
260A ALA* 1.3 83.3 - - + +
262A GLU* 1.3 62.0 + - + +
263A VAL 3.2 0.7 - - - -
264A ALA* 3.6 10.8 + - + +
265A ASP* 3.3 33.1 + - - +
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Residues in contact with GLU 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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260A ALA* 3.7 19.0 - - + +
261A PRO* 1.3 84.2 - - + +
263A VAL* 1.3 59.4 + - + +
265A ASP* 4.3 3.8 - - - +
266A ARG* 2.7 52.8 + - - +
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Residues in contact with VAL 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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224A CYS* 3.8 11.3 - - - +
225A GLY* 3.3 35.4 - - - +
226A VAL* 4.1 7.6 - - + -
259A LEU* 3.6 25.8 - - + -
260A ALA* 2.5 37.9 + - + +
262A GLU* 1.3 73.6 - - + +
264A ALA* 1.3 62.2 + - - +
265A ASP 3.2 2.5 + - - -
266A ARG* 3.6 5.6 + - - +
267A ILE* 3.2 26.9 + - - +
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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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246A TRP* 3.0 25.1 - - - -
250A LYS* 4.5 8.5 - - + -
253A MET* 4.2 8.7 - - + -
254A VAL* 4.4 7.4 - - + -
257A LYS* 3.0 30.5 - - - +
259A LEU* 4.2 6.2 - - - +
260A ALA 3.1 6.0 + - - +
261A PRO* 3.9 12.1 - - + +
262A GLU 3.6 0.2 - - - -
263A VAL* 1.3 78.4 - - - +
265A ASP* 1.3 57.5 - - + +
266A ARG 3.5 0.2 - - - -
267A ILE* 3.5 7.1 - - - +
268A GLY 3.3 6.9 + - - -
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Residues in contact with ASP 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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246A TRP* 3.6 19.1 + - - -
250A LYS* 2.6 38.2 + - - -
261A PRO* 3.3 15.6 + - - +
262A GLU* 5.1 3.4 - - - -
263A VAL 3.2 0.6 - - - +
264A ALA* 1.3 75.7 - - - +
266A ARG* 1.3 61.6 + - - +
267A ILE 3.4 0.4 - - - -
268A GLY* 3.8 3.5 - - - +
269A ASP* 2.8 27.4 + - - +
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Residues in contact with ARG 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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223A ILE 5.7 0.9 - - - -
224A CYS* 3.8 31.2 - - - +
262A GLU* 2.7 43.0 + - - +
263A VAL* 4.1 5.2 - - - +
264A ALA 3.5 0.2 - - - -
265A ASP* 1.3 74.1 - - - +
267A ILE* 1.3 66.5 + - - +
268A GLY 3.2 0.2 - - - -
269A ASP* 3.2 19.2 + - - +
270A TYR* 3.5 20.1 + - + -
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Residues in contact with ILE 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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220A MET* 5.2 1.8 - - + -
221A PHE* 4.4 17.0 - - + -
224A CYS* 3.8 20.6 - - + -
226A VAL* 3.9 24.7 - - + -
234A ILE* 4.2 12.8 - - + -
238A VAL* 4.2 22.2 - - + -
246A TRP* 4.9 4.5 - - + -
253A MET* 5.3 4.0 - - + -
259A LEU* 4.0 15.5 - - + -
263A VAL 3.2 17.5 - - - +
264A ALA* 3.5 9.9 - - - +
266A ARG* 1.3 77.7 - - - +
268A GLY* 1.3 57.0 + - - +
270A TYR* 3.0 7.0 + - - +
271A VAL* 2.9 37.2 + - + +
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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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246A TRP* 3.5 35.4 - - - -
264A ALA 3.3 7.5 + - - -
265A ASP* 3.8 4.0 - - - -
266A ARG 3.2 1.0 - - - -
267A ILE* 1.3 79.8 - - - +
269A ASP* 1.3 61.8 + - - +
270A TYR 3.1 0.7 + - - -
271A VAL* 4.7 0.7 - - - -
272A GLN* 3.2 34.9 + - - +
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Residues in contact with ASP 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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265A ASP 2.8 19.9 + - - +
266A ARG* 3.2 13.5 + - - +
267A ILE 3.2 1.2 - - - -
268A GLY* 1.3 76.9 - - - +
270A TYR* 1.3 61.5 + - + +
272A GLN* 5.4 0.2 - - - -
273A GLN* 3.2 26.7 + - - +
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Residues in contact with TYR 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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220A MET* 3.4 32.1 - - + -
223A ILE* 4.6 10.6 - - + +
224A CYS* 3.7 24.0 - - - -
266A ARG* 3.5 18.8 + - + -
267A ILE 3.0 4.9 + - - +
269A ASP* 1.3 85.4 - - + +
271A VAL* 1.3 61.8 + - - +
272A GLN 3.2 2.0 - - - -
273A GLN* 3.1 30.1 + - - +
283A LEU* 4.1 18.2 - - + -
286A ASP* 2.7 42.2 + - - -
288A LYS* 5.0 3.1 - - - +
289A LEU* 3.8 21.5 + - + +
322A LEU* 3.6 16.1 - - + +
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Residues in contact with VAL 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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217A LEU* 6.1 0.2 - - + -
220A MET* 4.0 16.6 - - + -
221A PHE* 5.3 0.2 - - + -
238A VAL* 4.4 26.7 - - + +
241A LEU* 3.6 30.9 - - + +
246A TRP* 4.9 12.1 - - + -
249A VAL* 6.4 0.2 - - + -
267A ILE* 2.9 23.0 + - + +
270A TYR* 1.3 70.3 - - - +
272A GLN* 1.3 65.8 + - + +
273A GLN 3.1 13.0 + - - +
321A ASP* 4.3 0.9 - - - +
322A LEU* 3.3 30.5 - - - +
323A SER* 3.8 16.4 + - - -
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Residues in contact with GLN 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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241A LEU* 4.3 10.3 - - + -
246A TRP* 3.0 55.9 + - + +
268A GLY* 3.2 22.9 + - - +
270A TYR 3.2 0.8 - - - -
271A VAL* 1.3 79.9 - - + +
273A GLN* 1.3 61.7 + - + +
274A HIS* 4.0 12.8 + - - -
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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
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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