Contacts of the helix formed by residues 349 - 365 (chain B) 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 ASN 349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348B VAL* 1.3 78.6 - - - +
350B ASN* 1.3 65.9 + - - +
351B ALA* 3.4 9.0 + - - +
352B GLU* 3.2 32.6 + - - +
353B LYS* 3.1 17.8 + - - +
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Residues in contact with ASN 350 (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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349B ASN* 1.3 75.2 - - - +
351B ALA* 1.3 59.3 + - - +
353B LYS* 3.5 25.3 + - - +
354B PHE* 2.8 32.4 + - - +
408B GLY* 3.1 33.0 + - - +
409B ILE* 5.2 0.7 - - - +
411B ASP* 4.4 7.1 + - - +
412B PHE* 3.8 21.2 - - + +
415B GLN* 4.3 16.6 - - - +
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Residues in contact with ALA 351 (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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349B ASN* 3.4 9.7 + - - +
350B ASN* 1.3 77.4 - - - +
352B GLU* 1.3 58.4 + - + +
354B PHE* 3.8 5.5 - - - +
355B ASP* 2.8 39.8 + - - +
415B GLN* 5.7 0.4 - - - -
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Residues in contact with GLU 352 (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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345B LYS* 5.4 1.3 + - - -
348B VAL* 3.5 34.8 - - + +
349B ASN* 3.2 27.9 + - - +
351B ALA* 1.3 76.8 - - + +
353B LYS* 1.3 55.8 + - - +
355B ASP* 3.3 9.7 + - - +
356B TYR* 2.8 35.9 + - - +
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Residues in contact with LYS 353 (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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342B SER 5.3 3.2 + - - -
344B ILE 3.8 8.5 + - - +
345B LYS* 3.2 37.6 - - + +
346B GLN* 4.4 7.3 - - - +
347B GLY 4.7 1.2 - - - +
348B VAL* 3.2 21.4 + - + +
349B ASN 3.1 13.0 + - - +
350B ASN* 3.5 28.1 + - - +
352B GLU* 1.3 74.3 - - - +
354B PHE* 1.3 63.6 + - - +
356B TYR* 3.3 8.5 + - - +
357B VAL* 3.0 26.9 + - - +
409B ILE* 3.8 24.5 - - - +
412B PHE* 3.5 26.8 - - + -
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Residues in contact with PHE 354 (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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350B ASN 2.8 21.1 + - - +
351B ALA* 3.8 6.1 - - - +
353B LYS* 1.3 71.5 - - - +
355B ASP* 1.3 68.2 + - - +
357B VAL* 3.3 3.0 + - - +
358B MET* 2.9 66.9 + - + +
372B PHE* 3.4 30.7 - + + -
412B PHE* 3.8 13.9 - + + -
415B GLN* 3.8 39.3 - - + +
416B LEU* 4.3 4.5 - - + -
419B ILE* 3.7 23.8 - - + -
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Residues in contact with ASP 355 (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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351B ALA* 2.8 33.2 + - - +
352B GLU* 3.3 9.9 + - - +
354B PHE* 1.3 82.1 - - - +
356B TYR* 1.3 58.4 + - - +
358B MET* 3.3 7.2 + - - +
359B GLN* 2.9 31.5 + - - +
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Residues in contact with TYR 356 (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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294B ILE* 4.1 14.6 - - + -
298B ASP* 2.5 39.4 + - - -
344B ILE* 4.1 15.0 - - + -
345B LYS* 3.5 46.7 - - + -
352B GLU 2.8 17.7 + - - +
353B LYS 3.4 5.6 - - - +
354B PHE 3.2 0.2 - - - -
355B ASP* 1.3 77.6 - - - +
357B VAL* 1.3 62.2 + - + +
359B GLN* 3.3 29.5 - - - +
360B PHE* 3.3 32.9 + + - +
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Residues in contact with VAL 357 (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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287B VAL* 5.6 2.0 - - + -
291B LYS* 5.2 5.2 - - + -
294B ILE* 3.9 20.4 - - + -
344B ILE* 4.0 30.7 - - + -
353B LYS 3.0 18.4 + - - +
354B PHE 4.0 3.4 - - - +
356B TYR* 1.3 78.4 - - + +
358B MET* 1.3 57.6 + - - +
360B PHE* 3.1 7.3 + - - +
361B LEU* 2.8 45.0 + - + +
412B PHE* 4.1 11.2 - - + -
416B LEU* 3.8 24.7 - - + -
419B ILE* 4.6 1.1 - - + -
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Residues in contact with MET 358 (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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354B PHE* 2.9 61.2 + - + +
355B ASP* 3.3 7.4 + - - +
357B VAL* 1.3 74.5 - - - +
359B GLN* 1.3 61.3 + - - +
361B LEU* 3.4 4.8 + - - +
362B ASN* 2.9 37.7 + - - +
370B VAL* 3.9 19.1 - - + +
371B GLY* 3.5 29.2 - - - +
372B PHE* 4.3 3.1 - - + -
419B ILE* 3.9 25.4 - - + -
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Residues in contact with GLN 359 (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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355B ASP 2.9 13.7 + - - +
356B TYR* 3.3 37.7 - - - +
358B MET* 1.3 76.5 - - - +
360B PHE* 1.3 68.6 + - + +
362B ASN* 3.3 15.1 + - - +
363B LYS* 3.2 47.7 + - - +
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Residues in contact with PHE 360 (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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294B ILE* 3.8 33.2 - - + -
297B ASN* 3.7 22.7 - - - -
298B ASP* 4.2 0.7 - - - -
356B TYR* 3.6 35.7 - + - +
357B VAL 3.1 9.4 + - - +
359B GLN* 1.3 82.7 - - + +
361B LEU* 1.3 64.5 + - - +
363B LYS* 3.2 10.3 + - + +
364B MET* 3.1 32.9 + - + +
446B VAL* 3.2 36.6 - - + -
447B LEU* 3.4 21.1 - - + -
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Residues in contact with LEU 361 (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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283B LEU* 4.6 4.0 - - + -
287B VAL* 4.5 10.1 - - + -
290B LEU* 4.0 26.2 - - + -
294B ILE* 4.6 6.1 - - + -
357B VAL* 2.8 28.4 + - + +
358B MET* 3.7 6.3 - - - +
360B PHE* 1.3 76.5 - - - +
362B ASN* 1.3 60.0 + - - +
364B MET* 3.5 25.1 + - + +
365B ALA* 3.1 26.2 + - - +
370B VAL* 4.0 15.7 - - + -
419B ILE* 3.8 41.3 - - + -
429B MET* 3.4 11.6 - - + +
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Residues in contact with ASN 362 (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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358B MET* 2.9 26.8 + - - +
359B GLN* 3.3 17.4 - - - +
360B PHE 3.2 0.4 - - - -
361B LEU* 1.3 76.8 - - - +
363B LYS* 1.3 58.6 + - + +
365B ALA 3.4 1.2 + - - -
366B GLY 3.2 2.6 + - - -
367B ASN* 2.7 49.1 + - - +
368B GLU 4.7 1.7 - - - +
370B VAL* 3.3 29.7 + - - +
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Residues in contact with LYS 363 (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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359B GLN* 3.2 44.6 + - - +
360B PHE* 3.2 12.3 + - + +
362B ASN* 1.3 74.2 - - + +
364B MET* 1.3 65.2 + - - +
365B ALA 3.1 1.8 - - - -
366B GLY* 3.1 11.6 + - - +
367B ASN* 4.8 5.6 - - - +
439B CYS* 3.5 17.2 - - - +
442B THR* 4.9 1.6 + - - -
444B GLU* 3.3 35.0 - - + +
445B ARG 5.3 1.3 - - - +
446B VAL* 3.8 24.6 - - + +
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Residues in contact with MET 364 (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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290B LEU* 4.0 26.9 - - - +
294B ILE* 3.9 16.8 - - + -
360B PHE* 3.1 35.2 + - + +
361B LEU* 3.9 22.4 - - + +
362B ASN 3.5 0.2 - - - -
363B LYS* 1.3 75.0 - - - +
365B ALA* 1.3 56.7 + - - +
366B GLY 3.3 0.4 - - - -
428B VAL* 3.0 16.3 - - - +
429B MET* 3.9 18.4 - - + +
432B THR* 2.7 29.8 + - + +
433B LEU* 5.7 0.9 - - - -
439B CYS* 3.8 0.3 - - - -
446B VAL* 3.6 15.7 - - + +
447B LEU* 3.6 32.3 - - + -
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Residues in contact with ALA 365 (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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361B LEU 3.1 17.5 + - - +
362B ASN 4.0 1.8 - - - +
363B LYS 3.1 0.8 - - - -
364B MET* 1.3 74.7 - - - +
366B GLY* 1.3 64.5 + - - +
367B ASN 3.1 0.4 - - - -
368B GLU* 3.0 37.9 + - - +
370B VAL* 4.2 1.1 - - + -
425B SER* 3.6 19.1 - - - +
428B VAL* 3.4 17.8 - - - +
429B MET* 3.7 16.2 - - + -
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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