Contacts of the helix formed by residues 288 - 298 (chain D) 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 CYS 288 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C LYS* 4.4 13.2 - - - -
56C GLU 3.6 21.1 - - - -
57C ASN 5.6 0.2 - - - -
58C CYS* 3.7 23.1 - - - -
286D HIS* 6.1 0.2 - - - -
287D LYS* 1.3 76.3 - - - +
289D HIS* 1.3 56.0 + - - +
290D SER* 3.3 20.4 - - - +
291D SER* 3.0 15.9 + - - +
292D TYR* 2.8 32.3 + - - +
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Residues in contact with HIS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D CYS* 1.3 67.7 - - - +
290D SER* 1.4 55.2 + - - +
292D TYR* 3.1 20.5 + + + +
293D ASP* 2.7 34.7 + - - +
323D ILE* 6.1 2.2 - - - +
327D GLU* 3.6 37.9 + - + +
328D PRO* 3.4 23.7 + - + +
331D ILE* 3.5 32.5 - - + +
332D SER* 3.6 13.7 + - - -
335D MET* 3.5 26.7 - - + +
372D VAL* 5.1 5.2 - - + +
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Residues in contact with SER 290 (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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1C MET* 5.5 4.3 - - - +
131C ASP* 4.2 20.8 + - - -
288D CYS* 3.4 16.0 - - - +
289D HIS* 1.4 75.6 - - - +
291D SER* 1.4 65.3 + - - -
293D ASP* 3.2 8.2 + - - +
294D VAL* 2.9 30.1 + - - +
331D ILE* 5.6 1.6 - - - +
335D MET* 4.6 4.9 - - - -
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Residues in contact with SER 291 (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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56C GLU 5.4 0.5 + - - -
129C SER* 5.6 8.1 + - - +
287D LYS* 3.4 19.4 - - - +
288D CYS* 3.0 34.9 + - - +
290D SER* 1.4 79.7 + - - +
292D TYR* 1.3 60.7 + - - +
294D VAL* 3.3 6.7 + - - +
295D MET* 3.1 34.5 + - - +
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Residues in contact with TYR 292 (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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273D THR* 4.7 7.6 - - - -
287D LYS* 4.1 25.1 - - + +
288D CYS 2.8 13.4 + - - +
289D HIS* 3.2 27.1 - + + +
291D SER* 1.3 73.9 - - - +
293D ASP* 1.3 66.2 - - - +
295D MET* 3.3 11.8 + - - +
296D LEU* 3.5 39.4 + - + +
323D ILE* 3.4 33.1 - - + +
335D MET* 4.6 5.6 - - + -
372D VAL* 3.8 28.9 - - + -
373D SER* 3.0 36.8 + - - -
374D GLY* 3.4 12.6 - - - -
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Residues in contact with ASP 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D HIS 2.7 16.7 + - - +
290D SER* 3.2 7.8 + - - +
292D TYR* 1.3 81.1 - - - +
294D VAL* 1.3 61.9 + - + +
295D MET 3.5 0.2 + - - -
296D LEU* 3.7 23.0 - - - +
297D ASP* 2.9 16.6 - - - +
335D MET* 3.6 42.7 - - + +
336D THR* 5.0 1.0 + - - -
339D GLN* 3.0 40.0 + - - +
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Residues in contact with VAL 294 (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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125C LYS 5.4 0.4 - - - +
128C ASP* 3.9 35.7 - - + +
129C SER* 4.5 13.7 - - - +
131C ASP* 6.2 0.2 - - - +
290D SER* 2.9 22.1 + - - +
291D SER* 3.3 8.5 + - - +
293D ASP* 1.3 79.3 - - + +
295D MET* 1.3 66.3 + - + +
297D ASP* 3.2 21.2 + - - +
298D LEU* 3.4 25.6 - - + +
339D GLN* 5.7 0.2 - - - +
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Residues in contact with MET 295 (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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125C LYS* 5.8 12.8 - - - +
129C SER* 6.1 0.4 - - - +
273D THR* 3.6 35.5 - - + +
274D PRO* 5.4 5.2 - - - -
287D LYS* 3.9 42.6 - - + -
291D SER* 3.1 24.0 + - - +
292D TYR* 3.3 4.2 + - - +
293D ASP 3.3 0.8 - - - -
294D VAL* 1.3 81.5 - - + +
296D LEU* 1.3 54.5 + - - +
298D LEU* 3.2 31.5 + - - +
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Residues in contact with LEU 296 (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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271D SER* 6.0 1.2 - - - -
273D THR* 4.0 8.7 + - - +
292D TYR* 3.6 54.5 - - + +
293D ASP* 3.7 18.8 - - - +
295D MET* 1.3 71.2 - - - +
297D ASP* 1.4 64.8 + - - +
298D LEU 4.0 4.5 - - - +
299D LEU* 4.8 1.9 - - - +
319D TYR* 2.8 22.4 + - - +
321D THR* 4.0 28.9 - - + -
323D ILE* 4.9 3.8 - - + -
335D MET* 6.3 0.2 - - + -
374D GLY* 4.2 20.2 - - - +
375D MET 4.5 5.6 - - - +
376D MET* 5.0 7.8 - - + +
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Residues in contact with ASP 297 (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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293D ASP 2.9 21.8 - - - +
294D VAL* 3.2 14.9 + - - +
296D LEU* 1.4 76.5 - - - +
298D LEU* 1.4 63.8 + - + +
299D LEU* 3.7 13.0 - - - +
319D TYR* 4.3 7.4 + - - -
339D GLN* 3.0 33.2 + - - +
344D PHE* 3.2 39.0 - - + +
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Residues in contact with LEU 298 (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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125C LYS* 5.2 18.8 - - + -
128C ASP* 4.6 20.2 - - + +
271D SER* 4.2 7.8 + - - -
273D THR* 5.0 0.9 - - - +
294D VAL* 3.4 38.6 - - + +
295D MET* 3.2 20.2 + - - +
296D LEU 4.0 4.3 - - - +
297D ASP* 1.4 82.0 - - + +
299D LEU* 1.3 58.9 + - - +
300D ASP* 3.3 37.7 + - + +
301D PRO* 4.2 7.7 - - + +
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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
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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