Contacts of the helix formed by residues 333 - 344 (chain D) in PDB entry 5FI2
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 VAL 333 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D LYS* 3.9 2.7 - - - -
313D SER* 5.8 4.9 - - - -
320D LEU 6.1 0.2 - - - +
329D HIS* 4.6 16.2 - - + +
330D ASN* 3.4 39.5 - - - +
331D PRO 3.5 0.3 - - - +
332D MET* 1.3 81.5 - - + +
334D ASN* 1.3 54.5 + - - +
335D ALA* 4.1 8.7 - - + +
336D GLY 2.9 12.5 + - - +
337D ALA* 2.8 31.5 + - - +
462D CYS* 5.6 3.1 - - + +
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Residues in contact with ASN 334 (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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285D SER* 4.4 1.7 + - - -
288D LYS* 3.3 19.3 + - - +
333D VAL* 1.3 73.1 - - - +
335D ALA* 1.3 59.3 + - - +
337D ALA* 3.7 0.3 - - - +
338D ILE* 2.9 37.4 + - + +
386D ARG* 4.0 20.4 - - - +
387D ASN* 4.5 15.3 + - - +
390D ILE* 4.0 15.0 - - + +
413D TYR* 3.2 21.9 + - - +
465D TYR* 6.0 1.6 - - - -
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Residues in contact with ALA 335 (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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321D PHE* 3.6 34.3 - - + +
328D PRO* 3.5 9.2 - - + +
333D VAL* 3.3 6.8 - - + +
334D ASN* 1.3 77.4 - - - +
336D GLY* 1.3 61.1 + - - +
338D ILE* 3.7 0.4 + - - -
339D VAL* 3.3 28.1 + - - +
390D ILE* 3.7 30.2 - - + +
394D LEU* 3.8 6.3 - - + +
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Residues in contact with GLY 336 (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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308D VAL* 3.9 5.1 - - - +
328D PRO* 3.5 14.6 - - - +
330D ASN 3.2 23.3 - - - -
331D PRO* 3.9 7.2 - - - -
333D VAL* 2.9 6.1 + - - +
335D ALA* 1.3 77.5 - - - +
337D ALA* 1.3 59.6 + - - +
339D VAL* 3.2 4.2 + - - +
340D VAL* 2.9 31.0 + - - +
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D LYS* 3.5 38.4 - - + -
291D LYS* 3.8 9.7 - - - +
331D PRO 3.3 12.1 + - - +
333D VAL 2.8 10.5 + - - +
334D ASN 3.7 0.9 - - - +
336D GLY* 1.3 70.8 - - - +
338D ILE* 1.3 55.4 + - - +
340D VAL* 3.7 5.3 - - - +
341D THR* 2.5 39.9 + - - -
413D TYR* 3.7 15.3 - - + -
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Residues in contact with ILE 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D ASN* 2.9 25.7 + - + +
335D ALA 3.8 4.3 - - - +
337D ALA* 1.3 74.1 - - - +
339D VAL* 1.3 63.5 + - - +
341D THR* 3.3 10.5 - - - -
342D SER* 3.3 14.6 + - - -
387D ASN* 3.9 20.4 - - + +
390D ILE* 3.6 24.2 - - + -
391D GLY* 5.1 0.2 - - - -
394D LEU* 3.7 18.4 - - + -
400D PHE* 3.9 13.7 - - + -
409D ILE* 3.7 11.6 - - + +
410D LEU* 3.9 33.4 - - + -
413D TYR* 3.9 19.7 - - + -
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Residues in contact with VAL 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D TYR* 3.4 42.8 - - + +
308D VAL* 4.7 3.4 - - + -
328D PRO* 3.6 18.4 - - + -
335D ALA 3.3 13.2 + - - +
336D GLY* 3.2 8.6 + - - +
338D ILE* 1.3 74.9 - - - +
340D VAL* 1.3 61.1 + - - +
342D SER* 2.4 36.2 + - - +
343D LEU* 3.4 6.3 - - + +
394D LEU* 3.7 21.3 - - + -
399D CYS* 4.1 12.3 - - + +
400D PHE* 4.1 9.2 - - + -
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Residues in contact with VAL 340 (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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288D LYS 5.3 0.2 - - - +
291D LYS* 3.8 34.1 - - + +
292D TYR* 3.8 34.5 - - + +
295D ALA* 4.3 6.1 - - + -
304D VAL* 4.8 2.0 - - + -
308D VAL* 4.3 15.7 - - + -
331D PRO* 4.2 11.7 - - + -
336D GLY 2.9 18.3 + - - +
337D ALA* 3.7 5.8 - - - +
339D VAL* 1.3 74.9 - - - +
341D THR* 1.3 65.2 + - - +
343D LEU* 2.9 30.4 + - + +
344D ILE* 3.6 9.7 + - + +
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Residues in contact with THR 341 (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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291D LYS* 3.4 20.1 + - - +
337D ALA 2.5 22.7 + - - -
338D ILE* 3.3 11.0 - - - -
339D VAL 3.2 0.2 - - - -
340D VAL* 1.3 76.4 - - - +
342D SER* 1.3 59.0 + - - +
343D LEU 3.6 0.3 + - - -
344D ILE* 3.9 15.9 + - - +
353D LYS* 5.4 0.3 + - - -
409D ILE* 4.0 11.8 - - + +
412D PHE* 3.4 39.1 - - + -
413D TYR* 3.7 19.2 - - + +
416D LEU* 3.8 13.9 - - + -
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Residues in contact with SER 342 (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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338D ILE 3.3 4.4 + - - -
339D VAL* 2.4 25.9 + - - +
341D THR* 1.3 78.7 - - - +
343D LEU* 1.3 61.5 + - - +
344D ILE 3.4 1.9 - - - +
346D GLN* 3.4 17.0 - - - +
353D LYS* 5.4 2.2 + - - -
400D PHE* 3.4 25.9 - - - -
401D PRO* 3.3 26.0 - - - +
404D THR* 4.4 5.4 + - - -
409D ILE* 3.8 22.8 - - - +
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Residues in contact with LEU 343 (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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295D ALA* 4.8 3.6 - - + -
299D LEU* 3.4 27.0 - - + +
303D TYR* 4.3 5.8 - - + +
304D VAL* 4.1 43.5 - - + +
307D TYR* 3.8 29.2 - - + -
308D VAL* 5.5 0.2 - - + -
339D VAL* 3.4 14.6 - - + +
340D VAL* 2.9 22.0 + - + +
342D SER* 1.3 80.1 - - - +
344D ILE* 1.3 63.8 + - - +
345D LYS 3.5 2.3 + - - -
346D GLN* 3.2 20.4 + - - +
401D PRO* 3.4 26.9 - - + -
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Residues in contact with ILE 344 (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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291D LYS* 3.5 40.4 - - + +
294D ILE* 4.5 9.0 - - + -
295D ALA* 4.0 17.7 - - + +
298D ASP* 5.1 2.7 - - - +
299D LEU* 5.1 2.5 - - - -
340D VAL* 3.6 15.9 - - + +
341D THR* 3.9 15.2 + - - +
342D SER 3.4 2.0 - - - +
343D LEU* 1.3 75.7 - - - +
345D LYS* 1.3 82.2 + - + +
346D GLN* 3.2 1.2 + - - -
353D LYS* 3.7 15.6 - - - +
356D TYR* 4.3 13.0 - - + -
357D VAL* 4.2 26.0 - - + -
412D PHE* 4.8 8.7 - - + -
416D LEU* 5.6 1.8 - - + -
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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