Contacts of the helix formed by residues 370 - 383 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319K LEU* 3.8 26.5 - - + -
323K VAL* 3.4 38.6 - - + +
327K TRP* 4.5 6.3 - - + -
330K ARG* 5.1 0.7 - - - -
368K THR 3.6 1.0 + - - -
369K PRO* 1.3 68.4 - - - +
371K THR* 1.3 88.0 - - - +
373K ARG* 3.2 1.5 + - - -
374K TYR* 2.9 64.2 + + + +
406K VAL 5.0 2.7 - - - -
407K LEU* 3.3 46.8 + - + +
408K ASP 3.6 18.4 + - - +
410K PRO* 5.4 10.3 - - + -
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Residues in contact with THR 371 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314K SER 5.6 0.2 - - - +
315K ARG* 6.1 1.3 - - - -
319K LEU* 2.8 31.7 - - + +
330K ARG* 2.7 55.9 + - - +
369K PRO* 2.8 21.9 + - + +
370K TRP* 1.3 93.8 - - - +
372K THR* 1.3 66.7 + - + +
375K GLY* 3.3 10.7 + - - -
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Residues in contact with THR 372 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313K VAL* 3.5 39.0 - - + +
314K SER 5.0 0.2 - - - -
315K ARG* 4.3 20.4 - - + +
330K ARG* 5.2 0.2 - - - +
362K SER* 4.3 5.0 - - - -
368K THR* 3.3 25.6 + - - -
369K PRO* 2.7 35.4 + - + +
371K THR* 1.3 81.2 - - + +
373K ARG* 1.3 57.2 + - - -
375K GLY* 3.5 1.7 + - - -
376K SER* 2.9 30.4 + - - -
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Residues in contact with ARG 373 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362K SER 3.6 6.5 - - - +
363K TRP* 2.9 49.0 + - + +
365K ASP 3.4 14.4 + - - -
368K THR* 3.0 39.9 - - - +
369K PRO 3.1 1.8 + - - +
370K TRP 3.6 6.1 - - - +
372K THR* 1.3 71.2 + - - +
374K TYR* 1.3 57.3 + - - +
376K SER* 2.6 38.1 + - - -
377K ILE* 2.9 12.5 + - - +
399K GLU* 4.4 0.6 - - - +
403K ILE* 3.2 42.6 + - - +
407K LEU* 2.9 17.5 + - + +
408K ASP* 2.9 43.3 - - - +
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Residues in contact with TYR 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327K TRP* 2.5 62.2 + + + -
330K ARG* 5.2 5.6 - - + -
370K TRP* 2.9 38.0 + + + +
371K THR 4.9 0.4 - - - -
373K ARG* 1.3 70.8 - - - +
375K GLY* 1.3 65.2 + - - +
377K ILE* 3.7 12.3 - - + +
378K ALA* 3.1 32.4 + - + +
407K LEU* 3.3 31.9 - - + +
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Residues in contact with GLY 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312K ILE* 3.5 30.9 - - - +
330K ARG* 4.4 13.2 - - - -
334K ALA* 4.5 1.6 - - - +
371K THR 3.3 14.1 + - - -
372K THR 3.8 3.6 - - - -
373K ARG 3.1 1.4 - - - -
374K TYR* 1.3 80.7 - - - +
376K SER* 1.3 61.1 + - - +
378K ALA* 3.7 4.9 - - - +
379K GLY 3.2 17.5 + - - -
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Residues in contact with SER 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312K ILE* 4.4 0.8 - - - +
313K VAL* 4.4 2.2 - - - -
359K PHE* 3.4 38.9 + - - +
362K SER* 3.6 10.5 - - - -
363K TRP* 3.1 23.6 + - - -
372K THR 2.9 13.9 + - - -
373K ARG 2.6 24.1 + - - -
375K GLY* 1.3 72.6 - - - +
377K ILE* 1.3 54.5 + - - -
379K GLY* 3.3 2.3 + - - -
380K LEU* 2.9 33.5 + - - +
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Residues in contact with ILE 377 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363K TRP* 3.4 61.7 - - + +
373K ARG 2.9 15.4 + - - +
374K TYR* 3.7 14.4 - - + +
376K SER* 1.3 69.6 + - - +
378K ALA* 1.3 61.7 + - - +
380K LEU* 4.2 4.9 - - - -
381K ALA* 2.9 42.9 + - + +
392K ILE* 4.0 21.1 - - + -
407K LEU* 5.3 0.9 - - + -
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Residues in contact with ALA 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331K ASP* 5.3 12.3 - - - +
334K ALA* 4.8 9.9 - - + -
335K ARG* 5.6 3.4 - - - +
374K TYR* 3.1 28.0 + - + +
375K GLY* 3.7 5.8 - - - +
377K ILE* 1.3 76.5 - - - +
379K GLY* 1.3 61.6 + - - +
381K ALA* 3.5 3.9 + - - +
382K GLU* 3.1 32.9 + - + +
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Residues in contact with GLY 379 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334K ALA* 4.2 20.5 - - - +
338K ALA* 5.5 0.5 - - - +
359K PHE* 4.3 14.4 - - - -
375K GLY 3.2 14.8 + - - -
376K SER 3.7 3.1 - - - -
377K ILE 3.3 0.2 - - - -
378K ALA* 1.3 71.7 - - - +
380K LEU* 1.3 65.2 + - - +
382K GLU* 3.2 5.6 + - - +
383K LEU* 3.0 31.5 + - - +
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Residues in contact with LEU 380 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356K THR* 4.5 4.3 - - - +
359K PHE* 3.7 37.7 - - + +
360K THR* 3.8 23.1 - - + +
363K TRP* 4.3 8.3 - - + -
376K SER 2.9 24.2 + - - +
377K ILE* 3.8 4.7 - - - +
379K GLY* 1.3 69.9 - - - +
381K ALA* 1.3 64.6 + - - +
383K LEU* 3.0 29.9 + - + +
384K GLY 4.2 2.4 + - - +
387K VAL* 3.7 30.1 - - + +
388K ILE* 4.6 2.3 - - - +
391K LEU* 4.0 9.0 - - + -
392K ILE* 4.0 30.3 - - + -
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Residues in contact with ALA 381 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377K ILE* 2.9 32.4 + - + +
378K ALA* 3.7 6.7 - - - +
380K LEU* 1.3 73.1 - - - +
382K GLU* 1.3 63.5 + - + +
383K LEU 3.7 0.3 + - - -
384K GLY 4.4 4.5 + - - +
385K HIS* 6.1 0.2 - - - -
388K ILE* 3.7 34.1 - - + +
392K ILE* 5.0 0.6 - - - +
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Residues in contact with GLU 382 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334K ALA* 5.6 3.4 - - + +
335K ARG* 2.9 48.3 + - + +
338K ALA* 3.9 21.8 - - + +
378K ALA* 3.1 21.1 + - + +
379K GLY* 3.6 4.0 - - - +
381K ALA* 1.3 80.4 - - + +
383K LEU* 1.3 62.7 + - - +
384K GLY 3.5 0.2 - - - -
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Residues in contact with LEU 383 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337K VAL* 4.4 13.9 - - + -
338K ALA* 4.2 20.0 - - + +
341K CYS* 4.0 31.6 - - + +
342K LYS* 5.1 14.6 + - - +
352K GLN* 4.4 6.3 - - - +
355K ILE* 4.6 11.0 - - + -
356K THR* 3.8 29.4 - - + -
359K PHE* 4.7 2.7 - - + -
379K GLY* 3.0 24.8 + - - +
380K LEU* 3.0 18.5 + - + +
382K GLU* 1.3 79.7 - - - +
384K GLY* 1.3 57.2 + - - +
387K VAL* 4.3 18.8 - - + -
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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