Contacts of the helix formed by residues 370 - 383 (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 TRP 370 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319J LEU* 3.6 37.5 - - + -
323J VAL* 5.0 4.3 - - + -
327J TRP* 5.8 1.1 - - + -
369J PRO* 1.3 69.5 - - - +
371J THR* 1.3 71.1 + - - +
373J ARG* 3.3 1.7 + - - +
374J TYR* 2.9 62.1 + + + +
407J LEU* 3.1 34.8 + - + +
408J ASP 3.5 9.8 + - - +
411J VAL* 2.8 31.2 + - + +
412J LEU* 2.9 42.8 + - - +
415J ILE* 3.2 50.1 - - + -
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Residues in contact with THR 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314J SER 5.1 0.4 - - - +
315J ARG 5.6 4.5 - - - +
317J LEU 4.8 1.3 - - - +
318J CYS* 6.1 0.4 - - - -
319J LEU* 2.9 33.5 - - + +
330J ARG* 2.8 50.0 + - - +
369J PRO* 2.9 21.5 + - + -
370J TRP* 1.3 90.6 - - - +
372J THR* 1.3 60.9 + - + +
374J TYR* 4.0 1.2 - - - +
375J GLY 3.1 19.8 + - - -
411J VAL* 3.9 9.3 - - + +
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Residues in contact with THR 372 (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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313J VAL* 3.3 37.1 - - - +
314J SER 4.2 1.1 - - - +
315J ARG* 4.2 22.0 - - + -
330J ARG* 4.4 3.4 - - - +
362J SER* 4.5 5.1 - - - -
368J THR* 3.2 25.3 - - - -
369J PRO* 2.8 38.3 + - + +
371J THR* 1.3 82.2 - - + +
373J ARG* 1.3 55.2 + - - -
375J GLY* 3.5 1.6 + - - -
376J SER* 3.0 29.6 + - - -
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Residues in contact with ARG 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362J SER 3.8 5.4 - - - +
363J TRP* 2.9 58.1 + - + +
365J ASP 3.6 4.9 + - - -
368J THR* 3.0 44.0 - - - +
369J PRO 3.0 1.6 + - - +
370J TRP 3.7 6.5 - - - +
372J THR* 1.3 72.9 - - - +
374J TYR* 1.3 59.5 + - - +
376J SER* 2.8 24.6 + - - -
377J ILE* 2.9 16.6 + - - +
399J GLU* 4.0 3.6 - - - +
403J ILE* 2.9 50.5 + - - +
407J LEU* 3.0 14.5 + - + +
408J ASP* 3.0 33.1 - - - +
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Residues in contact with TYR 374 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319J LEU* 5.3 0.2 - - + -
327J TRP* 3.1 48.5 - + + +
330J ARG* 5.0 7.4 - - + -
370J TRP* 2.9 45.6 + + + +
371J THR 4.7 1.6 - - - -
373J ARG* 1.3 70.4 - - - +
375J GLY* 1.3 65.1 + - - +
377J ILE* 3.6 8.7 - - - +
378J ALA* 3.0 36.9 + - + +
407J LEU* 4.2 9.3 - - + +
415J ILE* 5.6 2.7 - - + -
418J ILE* 4.8 2.4 + - - +
419J GLY* 3.2 43.4 - - - -
422J HIS* 3.1 31.1 + - + -
423J VAL* 4.0 8.5 - - + -
426J LEU* 6.1 1.6 - - + -
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Residues in contact with GLY 375 (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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312J ILE* 3.5 30.1 - - - +
330J ARG* 4.0 14.6 - - - -
334J ALA* 4.6 1.7 - - - +
371J THR 3.1 16.6 + - - -
372J THR 3.8 3.4 - - - -
373J ARG 3.2 0.4 - - - -
374J TYR* 1.3 76.6 - - - +
376J SER* 1.3 60.6 + - - +
378J ALA* 3.7 5.4 - - - +
379J GLY 3.1 18.2 + - - -
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Residues in contact with SER 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312J ILE* 4.2 2.3 - - - +
313J VAL* 4.6 2.2 - - - +
359J PHE* 3.4 37.4 - - - +
362J SER* 3.4 15.9 - - - -
363J TRP* 3.0 24.1 + - - -
372J THR 3.0 10.3 + - - -
373J ARG 2.8 18.5 + - - -
375J GLY* 1.3 74.6 - - - +
377J ILE* 1.3 54.8 + - - +
379J GLY* 3.4 1.9 + - - -
380J LEU* 3.0 34.2 + - - +
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Residues in contact with ILE 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J TRP* 3.5 40.6 - - + -
373J ARG 2.9 12.0 + - - +
374J TYR* 3.6 6.5 - - - +
376J SER* 1.3 72.3 + - - +
378J ALA* 1.3 62.3 + - - +
380J LEU* 3.7 5.1 - - - +
381J ALA* 2.9 39.3 + - + +
392J ILE* 3.6 37.7 - - + -
423J VAL* 3.5 45.5 - - + -
426J LEU* 6.0 1.6 - - + -
427J LEU* 4.5 9.0 - - + +
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Residues in contact with ALA 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327J TRP* 6.5 0.7 - - + -
331J ASP* 5.0 15.5 - - + +
334J ALA* 4.6 7.9 - - + -
335J ARG* 6.0 0.7 - - - +
374J TYR* 3.0 30.5 + - + +
375J GLY* 3.7 6.3 - - - +
377J ILE* 1.3 76.7 - - - +
379J GLY* 1.3 61.8 + - - +
381J ALA* 3.3 6.2 + - - +
382J GLU* 3.1 33.4 + - + +
423J VAL* 5.3 2.0 - - + +
426J LEU* 5.2 13.2 - - + -
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Residues in contact with GLY 379 (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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334J ALA* 3.8 23.9 - - - +
338J ALA* 5.1 0.9 - - - +
359J PHE* 4.3 14.8 - - - -
375J GLY 3.1 12.9 + - - -
376J SER 3.7 3.6 - - - -
377J ILE 3.3 0.2 - - - -
378J ALA* 1.3 76.7 - - - +
380J LEU* 1.3 62.1 + - - +
382J GLU* 3.3 3.3 + - - +
383J LEU* 3.0 30.7 + - - +
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Residues in contact with LEU 380 (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* 4.5 4.0 - - + +
359J PHE* 3.6 20.1 - - + +
360J THR* 3.8 30.3 - - + +
363J TRP* 4.4 5.4 - - + -
376J SER 3.0 23.2 + - - +
377J ILE 3.7 2.9 - - - +
379J GLY* 1.3 72.8 - - - +
381J ALA* 1.3 64.4 + - - +
383J LEU* 3.1 24.7 + - + -
384J GLY 4.3 0.5 + - - -
387J VAL* 3.5 25.2 - - + +
388J ILE* 4.5 1.4 - - - +
391J LEU* 3.9 28.7 - - + -
392J ILE* 3.7 35.0 - - + -
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Residues in contact with ALA 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377J ILE* 2.9 29.1 + - + +
378J ALA* 3.5 8.1 - - - +
379J GLY 3.3 0.2 - - - -
380J LEU* 1.3 72.0 - - - +
382J GLU* 1.3 64.1 + - + +
384J GLY 4.3 5.0 + - - +
385J HIS* 6.0 0.2 - - - -
388J ILE* 3.2 40.6 - - + +
392J ILE* 4.7 0.6 - - - +
426J LEU* 4.6 17.0 - - + -
430J HIS* 3.8 18.7 + - + -
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Residues in contact with GLU 382 (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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334J ALA* 5.3 3.6 - - + +
335J ARG* 2.8 52.6 + - + +
338J ALA* 3.6 23.0 - - + +
342J LYS* 5.9 1.7 - - - +
378J ALA* 3.1 20.2 + - + +
379J GLY* 3.9 4.3 - - - +
381J ALA* 1.3 76.0 - - + +
383J LEU* 1.4 63.7 + - - +
384J GLY* 3.3 3.1 + - - -
426J LEU* 4.1 20.4 - - + +
430J HIS* 4.7 13.5 + - - -
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Residues in contact with LEU 383 (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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337J VAL* 3.9 24.0 - - + -
338J ALA* 4.0 17.9 - - - +
341J CYS* 3.9 31.5 - - + -
342J LYS* 4.6 15.6 + - - +
352J GLN* 4.3 7.9 - - - +
355J ILE* 4.2 13.5 - - + -
356J THR* 3.9 27.4 - - + -
359J PHE* 4.5 2.5 - - + -
379J GLY 3.0 23.8 + - - +
380J LEU* 3.1 16.9 + - + +
382J GLU* 1.4 77.4 - - - +
384J GLY* 1.3 57.9 + - - +
387J VAL* 4.0 17.7 - - + -
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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