Contacts of the helix formed by residues 258 - 271 (chain A) in PDB entry 1FIU
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 TYR 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A THR* 4.8 1.9 - - - +
39A ARG* 3.7 49.5 - - + +
42A ASN* 3.2 31.9 + - - +
43A ILE* 3.8 27.1 - - + -
253A LEU* 3.3 14.8 + - + +
256A LEU* 3.3 42.1 - - + +
257A ASN* 1.3 72.7 - - - +
259A GLU* 1.3 58.5 + - - +
260A ASP 3.4 2.7 - - - -
261A ALA* 3.3 13.9 + - + -
262A LEU* 2.9 30.9 + - - +
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Residues in contact with GLU 259 (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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257A ASN* 3.0 31.7 + - + +
258A TYR* 1.3 71.3 - - - +
260A ASP* 1.3 62.9 + - - +
262A LEU* 3.3 18.4 + - - +
263A ASP* 2.9 40.3 + - - +
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Residues in contact with ASP 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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258A TYR 3.4 0.8 - - - -
259A GLU* 1.3 76.6 - - - +
261A ALA* 1.3 67.2 + - - +
263A ASP* 3.1 14.3 + - - +
264A LEU* 2.9 23.8 + - - +
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Residues in contact with ALA 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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39A ARG* 5.6 5.8 - - - -
43A ILE* 5.2 2.2 - - + -
225A PRO* 3.7 24.8 - - + +
253A LEU* 3.8 22.7 - - + -
258A TYR* 3.3 17.9 + - + +
260A ASP* 1.3 79.9 - - - +
262A LEU* 1.3 56.3 + - - +
264A LEU* 3.3 3.4 + - - +
265A PHE* 2.8 29.9 + - - +
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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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250A GLU* 4.6 1.1 - - + +
253A LEU* 3.5 41.7 - - + +
254A GLN* 3.9 31.4 - - + +
257A ASN* 4.7 3.1 - - - +
258A TYR 2.9 20.6 + - - +
259A GLU* 3.4 27.4 - - - +
261A ALA* 1.3 77.8 - - - +
263A ASP* 1.3 64.1 + - - +
265A PHE* 3.2 5.9 + - + +
266A TYR* 2.9 57.4 + - + +
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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 GLU* 2.9 26.6 + - - +
260A ASP* 3.1 15.9 + - - +
262A LEU* 1.3 77.7 - - - +
264A LEU* 1.3 59.0 + - - +
266A TYR* 3.4 6.2 + - - +
267A ILE* 3.0 38.2 + - + +
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Residues in contact with LEU 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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225A PRO* 3.7 7.2 - - + +
226A SER* 3.7 34.3 - - - +
229A SER* 3.9 18.6 - - - +
233A LEU* 4.5 14.8 - - + -
260A ASP 2.9 15.2 + - - +
261A ALA* 3.7 5.8 - - - +
263A ASP* 1.3 73.1 - - - +
265A PHE* 1.3 67.7 - - - +
267A ILE* 3.1 20.2 + - + +
268A MET* 3.0 36.4 + - + +
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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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225A PRO* 4.3 4.2 - - + +
246A LEU* 3.6 35.4 - - + -
249A LEU* 3.9 22.7 - - + -
250A GLU* 3.6 31.9 - - + -
253A LEU* 3.9 23.1 - - + -
261A ALA 2.8 18.3 + - - +
262A LEU* 3.4 4.3 - - + +
264A LEU* 1.3 76.0 - - - +
266A TYR* 1.3 91.3 + + - +
268A MET* 3.3 13.7 + - - +
269A VAL* 2.9 51.5 + - + +
274A LEU* 4.5 6.1 - - + -
167D TYR* 5.6 1.1 - - - -
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Residues in contact with TYR 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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250A GLU* 2.6 34.6 + - + +
254A GLN* 3.0 25.0 + - - -
262A LEU* 2.9 49.7 + - + +
263A ASP* 4.1 5.4 - - - +
265A PHE* 1.3 91.2 - + - +
267A ILE* 1.3 60.4 + - - +
269A VAL* 4.2 7.0 - - + +
270A ASN* 2.7 60.5 + - - +
167D TYR* 5.8 1.3 - - - -
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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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233A LEU* 4.3 10.1 - - + -
263A ASP* 3.0 27.8 + - + +
264A LEU* 3.1 18.1 + - + +
266A TYR* 1.3 75.8 - - - +
268A MET* 1.3 59.6 + - - +
270A ASN* 5.1 0.4 - - - -
271A GLY* 2.9 27.5 + - - -
121B ALA 6.1 0.2 - - - +
125B PRO* 4.5 16.2 - - + -
126B GLU* 4.3 18.5 - - - +
128B ALA* 3.9 19.5 - - + -
129B ALA* 3.6 28.6 - - + +
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Residues in contact with MET 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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225A PRO* 3.4 37.9 - - + +
228A ILE* 3.8 11.9 - - + -
229A SER* 3.6 27.8 - - - -
232A ALA* 3.8 17.9 - - + -
233A LEU* 3.9 20.0 - - + -
264A LEU* 3.0 25.5 + - + +
265A PHE* 3.7 9.9 - - + +
267A ILE* 1.3 76.1 - - - +
269A VAL* 1.3 62.1 + - - +
271A GLY 3.6 0.2 - - - -
272A LYS 3.3 2.6 + - - -
273A ARG* 2.8 38.9 + - + -
274A LEU* 3.2 22.1 + - + -
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Residues in contact with VAL 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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246A LEU* 4.5 4.7 - - + -
265A PHE* 2.9 55.3 + - + +
266A TYR* 4.3 7.6 - - + +
268A MET* 1.3 70.9 - - - +
270A ASN* 1.3 73.3 + - - +
272A LYS* 3.2 20.8 + - - +
274A LEU* 3.6 29.6 - - + +
167D TYR* 3.6 43.2 - - + +
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Residues in contact with ASN 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 TYR* 2.7 46.6 + - - +
267A ILE* 4.7 0.7 - - - +
269A VAL* 1.3 81.7 - - - +
271A GLY* 1.3 55.8 + - - +
272A LYS* 3.2 20.8 + - - +
126B GLU* 5.4 10.8 - - + +
167D TYR* 5.9 0.5 - - - -
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Residues in contact with GLY 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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267A ILE 2.9 22.3 + - - -
268A MET 3.6 0.4 - - - -
269A VAL 3.1 0.4 - - - -
270A ASN* 1.3 76.0 - - - +
272A LYS* 1.3 67.3 + - - +
273A ARG* 3.2 9.9 + - - -
126B GLU* 5.0 8.2 - - - +
129B ALA* 3.4 14.1 - - - -
210D LYS* 2.8 27.5 + - - +
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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