Contacts of the helix formed by residues 287 - 305 (chain B) in PDB entry 5FLZ
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 ILE 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU* 5.4 2.0 - - + -
264B TYR* 3.6 41.1 - - + +
267B PHE* 4.3 21.1 - - + -
271B LEU* 4.8 14.1 - - + -
283B LEU* 3.2 35.3 + - + +
284B TYR* 3.6 7.2 - - + +
285B ARG 3.4 0.4 + - - -
286B GLU* 1.3 78.2 - - + +
288B TYR* 1.4 62.4 + - - +
289B GLU* 3.3 5.3 + - - -
290B ASN* 3.5 21.7 + - + +
291B ILE* 3.7 23.2 + - + +
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Residues in contact with TYR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 4.9 6.5 + - - -
147A GLU* 2.4 38.8 + - + -
151A LEU* 3.0 34.3 - - + +
223B LEU* 6.6 0.2 - - + -
284B TYR* 3.1 30.1 - + + +
285B ARG* 3.3 21.9 + - - +
286B GLU 3.6 1.2 - - - -
287B ILE* 1.4 77.4 - - - +
289B GLU* 1.3 68.6 + - + +
291B ILE* 3.0 28.6 + - + +
292B ILE* 3.2 18.4 + - + +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 4.1 11.2 - - + -
285B ARG 4.0 4.7 - - - +
286B GLU* 2.9 30.3 - - - +
288B TYR* 1.3 80.8 + - + +
290B ASN* 1.4 69.7 + - - +
292B ILE* 3.1 17.9 + - - +
293B ARG* 3.1 48.9 + - - +
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Residues in contact with ASN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASN* 3.2 13.1 - - - +
264B TYR* 3.3 24.6 - - + -
267B PHE* 3.0 44.1 - - - -
287B ILE* 3.5 23.3 - - + +
289B GLU* 1.4 81.6 + - - +
291B ILE* 1.4 58.2 + - + +
293B ARG* 3.7 15.5 - - + +
294B LEU* 3.0 42.9 + - + +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU 5.8 1.8 - - - +
227B ALA* 5.3 14.8 - - + -
230B LEU* 5.1 18.8 - - + +
284B TYR* 5.4 11.7 - - + +
287B ILE* 3.7 22.2 - - + +
288B TYR* 3.0 22.7 + - + +
290B ASN* 1.4 74.1 - - + +
292B ILE* 1.3 63.0 + - + +
294B LEU* 4.6 2.4 - - - +
295B ARG* 3.2 28.8 + - + +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 4.8 17.7 - - + +
140A TYR* 4.3 30.7 - - + -
143A ARG* 6.3 2.7 - - + -
144A ARG* 6.5 0.9 - - + -
288B TYR* 3.6 16.6 - - + +
289B GLU* 3.1 14.3 + - - +
291B ILE* 1.3 78.4 - - + +
293B ARG* 1.4 67.3 + - - +
295B ARG* 3.7 4.3 - - - +
296B ILE* 3.3 33.9 + - + +
327B ILE* 6.0 1.6 - - + -
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU* 4.2 13.2 - - - +
263B ASN* 3.8 30.7 + - - +
267B PHE* 3.8 16.4 - - - -
289B GLU* 3.1 31.9 + - - +
290B ASN* 3.5 31.8 - - - +
292B ILE* 1.4 78.9 - - - +
294B LEU* 1.3 76.6 + - + +
296B ILE* 3.0 21.8 + - - +
297B TYR* 3.1 13.2 + - - +
326B THR* 6.3 0.6 - - - +
330B ILE* 4.4 21.6 - - + +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 6.1 9.4 - - + -
231B TYR* 5.7 2.7 - - + -
234B LEU* 4.4 35.2 - - + +
257B ILE* 5.6 3.4 - - + -
260B GLU* 4.5 24.9 - - + +
261B LEU* 5.1 7.4 - - + -
263B ASN* 5.7 1.8 - - - +
264B TYR* 4.6 17.9 - - + -
290B ASN* 3.0 33.0 + - + +
291B ILE* 4.6 2.5 - - - +
293B ARG* 1.3 83.4 - - + +
295B ARG* 1.3 61.6 + - - +
297B TYR* 3.2 11.9 + - + +
298B CYS* 3.2 26.8 + - - -
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 4.5 14.6 + - - -
128A ASP* 3.9 6.6 + - - -
226B GLU* 5.1 8.3 + - - -
230B LEU* 5.6 14.1 - - + +
291B ILE* 3.2 26.3 + - + +
292B ILE* 3.7 6.3 - - - +
293B ARG 3.2 0.4 - - - -
294B LEU* 1.3 74.4 - - - +
296B ILE* 1.4 68.4 + - + +
298B CYS* 3.2 20.3 + - + +
299B ARG* 3.0 49.7 + - + +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP 5.8 3.4 - - - +
292B ILE* 3.4 28.5 - - + +
293B ARG* 3.0 10.4 + - - +
295B ARG* 1.4 79.2 - - + +
297B TYR* 1.3 56.0 + - - +
299B ARG* 2.9 39.7 + - + +
300B PHE* 3.5 4.2 + - - +
319B PHE* 4.0 30.5 - - + -
327B ILE* 3.6 44.4 - - + -
330B ILE* 6.1 6.1 - - + -
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Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 6.0 2.9 - - + -
253B LEU* 3.5 47.5 + - + +
256B GLU* 4.4 5.8 - - + +
257B ILE* 4.2 36.6 - - + -
260B GLU* 5.5 9.4 - - + -
293B ARG 3.1 11.4 + - - +
294B LEU* 3.2 17.9 + - + +
296B ILE* 1.3 75.0 - - - +
298B CYS* 1.4 60.1 + - - +
300B PHE* 3.3 19.8 + + + +
301B THR* 2.9 33.9 + - - -
319B PHE* 6.3 2.7 - + - -
330B ILE* 4.4 22.7 - - + -
334B LEU* 4.1 23.2 - - + +
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Residues in contact with CYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 4.5 21.8 - - + -
233B SER* 5.7 3.6 - - - -
234B LEU* 4.8 14.4 - - - -
237B LYS* 3.4 26.5 - - - +
294B LEU* 3.2 24.4 + - - -
295B ARG* 3.4 11.4 - - + +
296B ILE 3.2 0.4 - - - -
297B TYR* 1.4 72.6 - - - +
299B ARG* 1.3 64.4 + - + +
301B THR* 3.1 3.8 + - - -
302B GLU* 2.9 31.1 + - + +
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 2.3 45.7 + - - +
129A THR* 3.0 30.4 + - + -
295B ARG* 3.0 54.2 + - - +
296B ILE* 2.9 24.3 + - + +
298B CYS* 1.3 71.6 - - + +
300B PHE* 1.3 63.6 - - - +
302B GLU* 3.3 14.4 + - - +
303B HIS* 3.3 14.4 + - - +
319B PHE* 6.5 0.4 - - + -
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.8 39.5 - - + -
296B ILE 3.5 4.3 + - - +
297B TYR* 3.3 26.8 + + + +
298B CYS 3.2 0.4 - - - -
299B ARG* 1.3 80.6 - - - +
301B THR* 1.4 56.7 - - - +
303B HIS* 4.8 0.7 - - - -
304B LEU* 3.1 29.6 + - + +
312B PHE* 5.0 3.6 - + + -
315B GLU* 3.3 54.6 - - + +
316B LEU* 4.6 11.2 - - + -
319B PHE* 4.2 48.0 - + + -
334B LEU* 5.0 8.1 - - + -
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LYS* 3.9 35.0 + - + +
241B PHE* 4.0 30.1 - - + -
257B ILE* 5.8 1.2 - - - +
297B TYR* 2.9 29.6 + - - -
298B CYS* 3.1 8.2 + - - -
300B PHE* 1.4 74.3 - - - +
302B GLU* 1.4 66.9 + - - +
304B LEU* 3.3 19.7 - - + +
305B GLU* 3.4 6.6 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LYS* 3.6 26.7 + - - -
298B CYS* 2.9 22.6 + - + +
299B ARG* 3.3 8.9 + - - +
301B THR* 1.4 72.7 - - - +
303B HIS* 1.3 61.5 + - - +
305B GLU* 3.2 27.6 + - - +
306B GLU* 2.9 19.2 - - - +
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Residues in contact with HIS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ARG 3.3 9.4 + - - +
300B PHE* 3.7 4.0 - - - +
301B THR 3.3 0.4 - - - -
302B GLU* 1.3 78.6 - - - +
304B LEU* 1.3 61.1 + - - +
305B GLU 3.2 1.0 + - - -
306B GLU* 3.3 15.9 + - + +
307B LEU* 3.3 41.7 - - + +
311B THR* 5.6 0.6 + - - -
315B GLU* 2.9 31.9 + - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE* 3.5 38.8 - - + -
246B ILE* 6.3 0.4 - - + -
250B LYS* 5.0 7.6 - - + -
253B LEU* 3.4 33.7 - - + -
300B PHE* 3.1 20.7 + - + +
301B THR* 3.3 14.4 - - + +
303B HIS* 1.3 76.4 - - - +
305B GLU* 1.4 58.9 + - - +
307B LEU* 2.7 41.8 + - - +
312B PHE* 3.9 28.9 - - + -
315B GLU* 3.9 2.4 + - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR 3.4 4.9 + - - +
302B GLU* 3.2 30.6 + - - +
304B LEU* 1.4 81.2 - - - +
306B GLU* 1.3 78.2 + - - +
307B LEU 4.2 1.7 - - - +
308B SER* 5.5 0.7 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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