Contacts of the helix formed by residues 350 - 364 (chain J) in PDB entry 5FUR
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 350 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302J HIS* 3.4 26.5 + - + +
348J THR* 2.7 15.5 + - - +
349J ASN* 1.3 73.4 - - - +
351J ILE* 1.3 65.3 + - + +
353J SER* 3.5 5.4 + - - -
354J ARG* 3.0 36.7 + - - +
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Residues in contact with ILE 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301J VAL* 4.6 7.4 - - + -
302J HIS* 3.7 31.6 - - + +
305J ILE* 3.6 28.3 - - + -
340J ILE* 4.9 7.0 - - + +
341J CYS* 5.1 5.4 - - - -
344J PHE* 5.2 2.2 - - + -
345J SER* 4.9 10.1 - - - +
348J THR* 3.1 35.0 + - + +
349J ASN 3.1 1.6 + - - -
350J ASN* 1.3 78.1 - - + +
352J GLN* 1.3 66.2 + - - +
354J ARG* 3.4 9.7 + - - +
355J ILE* 3.0 45.3 + - + +
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Residues in contact with GLN 352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341J CYS* 3.6 22.5 - - - -
345J SER* 4.2 23.4 - - - +
349J ASN 3.5 8.9 + - - +
351J ILE* 1.3 79.1 - - - +
353J SER* 1.3 64.4 + - - +
355J ILE* 3.8 1.6 - - - +
356J THR* 2.7 53.3 + - - +
383J LEU* 4.3 2.9 - - - +
387J VAL* 3.6 25.9 - - - +
391J LEU* 5.7 0.2 - - - +
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Residues in contact with SER 353 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J ASN 3.8 7.3 + - - -
350J ASN* 3.5 7.4 + - - -
351J ILE 3.4 0.6 - - - -
352J GLN* 1.3 79.8 - - - +
354J ARG* 1.3 62.9 + - - +
356J THR* 3.5 6.2 + - - -
357J LYS* 2.7 65.3 + - - +
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Residues in contact with ARG 354 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302J HIS* 3.3 41.2 + - - +
305J ILE* 4.1 14.9 - - - +
306J PRO* 3.6 44.6 - - - +
309J MET* 4.5 11.5 - - + +
350J ASN* 3.0 31.1 + - - +
351J ILE* 3.6 9.3 - - - +
352J GLN 3.3 0.2 - - - -
353J SER* 1.3 77.1 - - - +
355J ILE* 1.3 56.6 + - + +
357J LYS* 4.2 3.5 - - - +
358J THR* 2.8 34.3 + - - +
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Residues in contact with ILE 355 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305J ILE* 4.0 22.0 - - + -
309J MET* 3.9 20.0 - - - -
337J VAL* 3.9 20.2 - - + +
340J ILE* 5.3 0.4 - - + -
341J CYS* 4.8 13.7 - - + +
351J ILE* 3.0 36.7 + - + +
352J GLN* 3.9 3.4 - - - +
354J ARG* 1.3 74.3 - - + +
356J THR* 1.3 66.1 + - - +
358J THR* 3.1 4.0 + - - -
359J PHE* 2.9 59.1 + - + -
383J LEU* 4.2 12.6 - - + -
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Residues in contact with THR 356 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352J GLN* 2.7 54.6 + - - +
353J SER* 3.4 9.0 + - - -
355J ILE* 1.3 74.9 - - - +
357J LYS* 1.3 59.8 + - - +
360J THR* 2.8 36.4 + - - -
380J LEU* 4.5 6.7 - - + +
383J LEU* 3.9 16.2 - - + -
387J VAL* 4.6 1.6 - - + -
391J LEU* 3.7 27.4 - - + -
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Residues in contact with LYS 357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353J SER* 2.7 48.1 + - - +
354J ARG* 4.2 3.6 - - - +
356J THR* 1.3 76.4 - - - +
358J THR* 1.3 56.6 + - - +
360J THR* 4.2 3.3 - - - -
361J LYS* 3.0 32.1 + - - +
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Residues in contact with THR 358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J MET* 4.3 27.5 - - + +
313J VAL* 5.0 12.3 - - + -
354J ARG* 2.8 20.1 + - - +
355J ILE 3.1 5.7 + - - -
357J LYS* 1.3 76.2 - - - +
359J PHE* 1.3 59.3 + - + +
361J LYS* 3.8 5.3 - - - +
362J SER* 2.8 35.8 + - - +
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Residues in contact with PHE 359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J MET* 4.1 15.7 - - + -
312J ILE* 3.4 44.9 - - + -
313J VAL* 3.9 20.4 - - + -
337J VAL* 3.6 16.4 - - + -
355J ILE* 2.9 40.7 + - + +
358J THR* 1.3 76.1 - - - +
360J THR* 1.3 64.3 + - - +
362J SER 3.2 1.6 + - - -
363J TRP* 2.9 23.0 + - - +
376J SER* 3.4 20.0 + - - +
379J GLY* 4.3 12.8 - - - -
380J LEU* 3.6 38.1 - - + -
383J LEU* 4.5 3.4 - - + -
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Residues in contact with THR 360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356J THR 2.8 27.4 + - - -
357J LYS* 4.2 3.8 - - - -
359J PHE* 1.3 70.8 - - - +
361J LYS* 1.3 62.7 + - - +
363J TRP* 3.4 2.6 + - + +
364J VAL* 3.1 45.2 + - + +
380J LEU* 3.8 13.3 - - + +
391J LEU* 3.8 30.1 - - + +
395J ARG* 5.0 10.3 - - + +
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Residues in contact with LYS 361 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J LYS 3.0 20.4 + - - +
358J THR* 3.8 6.5 - - - +
360J THR* 1.3 75.5 - - - +
362J SER* 1.3 62.3 + - - +
364J VAL* 3.8 2.3 - - - -
365J ASP* 2.7 70.4 + - - +
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Residues in contact with SER 362 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313J VAL* 3.4 28.5 - - - +
358J THR* 2.8 20.7 + - - +
359J PHE 3.5 1.6 - - - -
361J LYS* 1.3 75.2 - - - +
363J TRP* 1.3 64.5 + - - +
365J ASP* 3.0 11.3 + - - -
368J THR* 3.0 31.7 + - - -
372J THR* 4.5 5.8 - - - -
373J ARG* 3.8 2.4 - - - +
376J SER* 3.4 23.1 - - - -
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Residues in contact with TRP 363 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359J PHE 2.9 16.9 + - - +
360J THR* 3.9 2.9 - - + +
362J SER* 1.3 69.9 - - - +
364J VAL* 1.3 70.8 + - + +
365J ASP 3.5 0.2 - - - -
373J ARG* 2.9 61.1 + - + +
376J SER* 3.0 19.5 + - - +
377J ILE* 3.5 43.3 - - + -
380J LEU* 4.4 7.2 - - + -
392J ILE* 3.7 27.4 + - + +
395J ARG* 4.4 10.5 - - + +
396J LEU* 5.7 6.7 - - + +
399J GLU* 3.8 29.6 - - + +
400J GLY 5.7 0.4 - - - -
403J ILE* 3.7 1.7 - - - +
407J LEU* 3.9 22.4 - - + -
423J VAL* 4.2 16.6 - - + -
427J LEU* 5.8 4.0 - - + -
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Residues in contact with VAL 364 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360J THR* 3.1 31.2 + - + +
361J LYS* 3.8 2.7 - - - +
363J TRP* 1.3 88.2 - - + +
365J ASP* 1.3 62.4 + - - +
366J GLU 3.2 4.1 + - - -
395J ARG* 3.8 33.9 - - - +
399J GLU* 3.8 12.3 - - - +
402J ARG* 3.1 32.4 + - - +
403J ILE* 3.3 6.2 - - - +
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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