Contacts of the helix formed by residues 258 - 271 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D THR* 4.4 3.8 - - - +
39D ARG* 3.6 67.5 - - + +
42D ASN* 3.2 27.3 + - + +
43D ILE* 4.2 15.7 - - + -
253D LEU* 3.3 14.3 + - + +
256D LEU* 3.3 48.4 - - + +
257D ASN* 1.3 76.6 - - - +
259D GLU* 1.3 58.3 + - - +
260D ASP 3.4 2.5 - - - -
261D ALA* 3.3 15.6 + - + +
262D LEU* 2.9 28.9 + - - +
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Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D GLN* 5.4 0.5 - - - +
257D ASN* 2.8 45.8 + - - +
258D TYR* 1.3 74.4 - - - +
260D ASP* 1.3 61.9 + - - +
262D LEU* 3.3 19.3 + - - +
263D ASP* 2.9 40.7 + - - +
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Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D TYR 3.4 0.6 - - - -
259D GLU* 1.3 80.2 - - - +
261D ALA* 1.3 62.2 + - - +
263D ASP* 3.3 13.0 + - - +
264D LEU* 3.0 22.5 + - - +
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Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ARG* 5.6 6.1 - - - -
43D ILE* 5.2 2.0 - - + -
225D PRO* 3.6 24.5 - - + +
253D LEU* 3.9 21.3 - - + -
258D TYR* 3.3 18.2 + - + +
259D GLU 3.3 0.4 - - - -
260D ASP* 1.3 76.7 - - - +
262D LEU* 1.3 59.6 + - - +
264D LEU* 3.3 3.8 + - - +
265D PHE* 2.9 28.8 + - - +
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Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D GLU* 4.5 3.4 - - + +
253D LEU* 3.9 31.3 - - + +
254D GLN* 4.0 24.5 - - + +
258D TYR 2.9 15.2 + - - +
259D GLU* 3.6 21.8 - - - +
260D ASP 3.3 0.2 - - - -
261D ALA* 1.3 72.1 - - - +
263D ASP* 1.3 69.4 + - - +
265D PHE* 3.3 14.5 + - + +
266D TYR* 2.9 67.2 + - + +
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Residues in contact with ASP 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D GLU* 2.9 27.1 + - - +
260D ASP* 3.3 15.3 + - - +
262D LEU* 1.3 78.9 - - - +
264D LEU* 1.3 56.3 + - - +
266D TYR* 3.3 9.5 + - - +
267D ILE* 2.9 36.6 + - + +
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Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D PRO* 3.6 27.8 - - + +
226D SER* 3.7 13.7 - - - +
229D SER* 3.9 18.6 - - - +
233D LEU* 4.3 13.0 - - + -
260D ASP 3.0 16.1 + - - +
261D ALA* 3.7 6.1 - - - +
263D ASP* 1.3 72.3 - - - +
265D PHE* 1.3 67.2 + - - +
267D ILE* 3.2 21.4 + - + +
268D MET* 3.0 35.8 + - + +
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Residues in contact with PHE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TYR* 5.7 2.2 - - - -
225D PRO* 4.2 3.5 - - + +
246D LEU* 3.6 35.4 - - + -
249D LEU* 3.9 28.0 - - + -
250D GLU* 3.5 29.6 - - + -
253D LEU* 3.9 15.9 - - + -
261D ALA 2.9 14.1 + - - +
262D LEU* 3.3 13.2 - - + +
264D LEU* 1.3 76.4 - - - +
266D TYR* 1.3 89.9 + + - +
268D MET* 3.2 13.9 + - + +
269D VAL* 2.9 51.3 + - + +
274D LEU* 4.5 5.6 - - + -
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Residues in contact with TYR 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TYR* 5.8 2.0 - - - -
250D GLU* 2.4 37.2 + - - +
254D GLN* 3.6 13.4 + - - -
262D LEU* 2.9 56.0 + - + +
263D ASP* 3.8 7.4 - - - +
265D PHE* 1.3 87.1 - + - +
267D ILE* 1.3 61.4 + - - +
269D VAL* 4.3 6.7 - - + +
270D ASN* 2.8 59.3 + - - +
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Residues in contact with ILE 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ALA 6.1 0.7 - - - +
125C PRO* 4.2 23.3 - - + +
126C GLU* 4.1 9.0 - - - +
128C ALA* 4.5 10.1 - - + -
129C ALA* 3.5 30.8 - - + +
233D LEU* 4.3 12.1 - - + -
263D ASP* 2.9 23.6 + - + +
264D LEU* 3.2 23.1 + - + +
266D TYR* 1.3 76.0 - - - +
268D MET* 1.3 58.0 + - - +
270D ASN* 4.6 1.5 - - - +
271D GLY* 2.9 27.8 + - - +
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Residues in contact with MET 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D PRO* 3.6 36.3 - - + +
228D ILE* 3.9 7.6 - - + -
229D SER* 3.6 29.4 - - - -
232D ALA* 3.9 16.8 - - + -
233D LEU* 3.9 20.6 - - + -
264D LEU* 3.0 24.7 + - + +
265D PHE* 3.6 9.6 - - + +
267D ILE* 1.3 81.2 - - - +
269D VAL* 1.3 59.7 + - - +
272D LYS 3.3 2.4 + - - -
273D ARG* 2.8 38.4 + - + +
274D LEU* 3.1 27.6 + - + -
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Residues in contact with VAL 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TYR* 3.5 45.3 - - + +
246D LEU* 4.4 5.6 - - + -
265D PHE* 2.9 50.4 + - + +
266D TYR* 4.3 7.9 - - + +
268D MET* 1.3 73.6 - - - +
270D ASN* 1.3 71.5 + - - +
271D GLY 3.1 1.3 - - - -
272D LYS* 3.1 20.3 + - - +
274D LEU* 3.6 29.4 - - + +
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Residues in contact with ASN 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TYR* 5.9 0.7 - - - -
126C GLU* 5.6 3.3 - - + +
266D TYR* 2.8 49.2 + - - +
267D ILE* 4.6 1.3 - - - +
269D VAL* 1.3 79.1 - - - +
271D GLY* 1.3 55.6 + - - +
272D LYS* 2.8 26.8 + - - +
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Residues in contact with GLY 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LYS* 2.8 26.1 + - - -
126C GLU* 4.5 8.0 - - - +
129C ALA* 3.7 13.2 - - - -
267D ILE 2.9 21.6 + - - -
268D MET 3.6 0.4 - - - -
269D VAL 3.1 0.4 - - - -
270D ASN* 1.3 76.2 - - - +
272D LYS* 1.3 69.0 + - - +
273D ARG* 3.2 11.6 + - - +
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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