Contacts of the helix formed by residues 385 - 407 (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 HIS 385 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K GLY* 1.3 71.5 - - - -
386K ASP* 1.3 69.2 + - - +
388K ILE* 3.1 19.8 + - + +
389K LYS* 2.7 31.4 + - - +
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Residues in contact with ASP 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384K GLY* 3.2 2.0 - - - -
385K HIS* 1.3 86.4 + - - +
387K VAL* 1.3 51.7 + - - +
389K LYS* 4.1 5.6 - - - +
390K THR* 2.8 42.0 + - + +
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Residues in contact with VAL 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352K GLN* 4.0 23.6 - - - +
356K THR* 4.3 9.2 - - + -
380K LEU* 3.7 45.5 - - + +
383K LEU* 4.3 17.0 - - + -
384K GLY* 3.3 11.3 + - - +
386K ASP* 1.3 73.7 - - - +
388K ILE* 1.3 65.2 + - - +
390K THR* 3.7 5.8 - - - +
391K LEU* 3.0 30.9 + - + +
392K ILE* 3.5 4.1 + - + +
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Residues in contact with ILE 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377K ILE* 6.1 0.2 - - + -
380K LEU 4.6 0.7 - - - +
381K ALA* 3.7 43.7 - - + +
384K GLY 2.9 12.4 + - - +
385K HIS* 3.1 24.4 + - + +
387K VAL* 1.3 74.6 - - - +
389K LYS* 1.3 59.8 + - + +
392K ILE* 3.0 36.5 + - + -
393K LEU* 2.7 37.8 + - + +
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Residues in contact with LYS 389 (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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385K HIS 2.7 19.4 + - - +
386K ASP* 4.1 7.9 - - - +
387K VAL 3.4 0.2 - - - -
388K ILE* 1.3 79.5 - - + +
390K THR* 1.3 61.0 + - + +
393K LEU* 3.0 31.2 - - + +
394K PRO* 2.9 23.9 - - - +
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Residues in contact with THR 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386K ASP* 2.8 23.1 + - + +
387K VAL* 3.6 7.4 + - - +
389K LYS* 1.3 79.3 - - + +
391K LEU* 1.3 71.3 + - - +
394K PRO* 3.2 18.0 - - - +
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Residues in contact with LEU 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356K THR* 4.3 16.8 - - + -
360K THR* 3.1 39.0 - - + +
380K LEU* 4.0 14.8 - - + -
387K VAL* 3.0 22.1 + - + +
390K THR* 1.3 85.4 - - - +
392K ILE* 1.3 73.1 + - + +
393K LEU 3.6 0.2 - - - -
394K PRO* 3.7 3.0 - - - +
395K ARG* 3.2 34.8 + - - +
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Residues in contact with ILE 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360K THR* 6.5 0.4 - - + -
363K TRP* 3.3 39.9 - - + +
377K ILE* 4.0 17.0 - - + -
380K LEU* 4.0 33.0 - - + -
387K VAL 3.5 2.7 + - - +
388K ILE* 3.0 42.0 + - + +
391K LEU* 1.3 84.7 - - + +
393K LEU* 1.3 58.7 + - - +
395K ARG* 4.6 2.0 - - + +
396K LEU* 2.8 34.2 + - + +
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Residues in contact with LEU 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388K ILE* 2.7 18.2 + - + +
389K LYS* 3.0 44.3 + - + +
392K ILE* 1.3 72.4 - - - +
394K PRO* 1.4 61.7 - - + +
396K LEU* 3.0 37.4 + - + +
397K GLN* 4.1 3.8 + - - +
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Residues in contact with PRO 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389K LYS 2.9 25.6 - - - +
390K THR* 3.2 21.8 - - - +
391K LEU 3.7 3.4 - - - +
393K LEU* 1.4 81.6 - - + +
395K ARG* 1.3 63.0 + - + +
397K GLN* 4.3 3.8 + - - +
398K GLN* 3.0 25.9 + - - +
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Residues in contact with ARG 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360K THR* 5.6 4.9 - - + -
363K TRP* 4.7 10.1 - - + +
364K VAL* 3.9 31.7 - - + +
391K LEU 3.2 22.8 + - - +
392K ILE* 4.4 2.9 - - + +
394K PRO* 1.3 78.6 - - + +
396K LEU* 1.3 64.0 + - - +
398K GLN* 2.8 47.8 + - - +
399K GLU* 2.6 68.9 + - - +
402K ARG* 4.3 11.1 - - - +
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Residues in contact with LEU 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363K TRP* 5.9 6.7 - - + +
392K ILE* 2.8 30.2 + - + +
393K LEU* 3.0 29.0 + - + +
395K ARG* 1.3 70.7 - - - +
397K GLN* 1.3 80.4 + - + +
399K GLU* 3.7 2.9 - - - +
400K GLY* 2.9 25.5 + - - +
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Residues in contact with GLN 397 (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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393K LEU 4.1 4.4 + - - +
394K PRO 4.3 2.8 + - - +
395K ARG 3.5 0.4 - - - -
396K LEU* 1.3 96.4 - - + +
398K GLN* 1.3 65.9 + - + +
400K GLY* 4.0 0.8 - - - -
401K GLU* 3.1 23.7 + - - +
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Residues in contact with GLN 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394K PRO* 3.0 27.1 + - - +
395K ARG* 2.8 52.5 + - - +
397K GLN* 1.3 80.4 - - + +
399K GLU* 1.3 60.3 + - - +
401K GLU* 3.4 1.8 + - - +
402K ARG* 2.9 42.7 + - - +
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Residues in contact with GLU 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363K TRP* 3.6 50.0 - - + +
364K VAL* 4.3 6.1 - - + -
395K ARG* 2.6 58.4 + - - +
396K LEU* 4.1 1.6 - - - +
398K GLN* 1.3 72.6 - - - +
400K GLY* 1.3 54.8 + - - +
402K ARG* 2.6 31.8 + - - -
403K ILE* 2.7 57.8 + - + +
404K ARG 2.8 0.7 + - - -
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Residues in contact with GLY 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363K TRP* 5.4 0.8 - - - -
396K LEU* 2.9 20.8 + - - +
397K GLN* 4.1 1.3 - - - -
399K GLU* 1.3 73.0 - - - +
401K GLU* 1.3 65.3 + - - +
404K ARG* 2.7 40.5 + - - +
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Residues in contact with GLU 401 (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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397K GLN 3.1 17.2 + - - +
398K GLN* 4.3 2.0 - - - +
400K GLY* 1.3 80.5 - - - +
402K ARG* 1.4 71.8 + - + +
403K ILE 3.1 0.3 + - - -
404K ARG* 2.7 46.7 + - - +
405K SER 4.1 0.3 + - - -
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Residues in contact with ARG 402 (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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364K VAL* 3.5 20.6 + - - +
366K GLU* 2.5 44.6 + - - +
395K ARG* 4.3 11.9 - - - +
398K GLN* 2.9 24.0 + - - +
399K GLU* 2.6 34.1 + - - -
401K GLU* 1.4 77.9 - - + +
403K ILE* 1.3 70.0 + - + +
405K SER* 3.5 15.6 + - - -
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Residues in contact with ILE 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363K TRP* 3.7 10.7 - - - +
364K VAL 3.5 11.0 - - - +
366K GLU* 3.4 44.2 - - + +
373K ARG* 3.2 45.6 + - - +
399K GLU* 2.7 40.3 + - + +
402K ARG* 1.3 89.9 - - + +
404K ARG* 1.4 63.9 + - - +
405K SER* 3.4 6.1 - - - +
407K LEU* 4.7 0.9 - - - +
408K ASP* 3.6 23.8 - - - +
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Residues in contact with ARG 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399K GLU 2.8 11.4 + - - -
400K GLY* 2.7 47.3 + - - +
401K GLU* 2.7 44.5 + - - +
403K ILE* 1.4 75.1 - - - +
405K SER* 1.3 59.6 + - - +
406K VAL* 2.9 22.2 - - + +
407K LEU 2.6 31.1 + - - +
408K ASP 3.1 0.9 + - - -
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Residues in contact with SER 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401K GLU 4.1 0.4 + - - -
402K ARG 3.5 18.0 + - - -
403K ILE* 3.1 10.2 - - - +
404K ARG* 1.3 73.3 - - - +
406K VAL* 1.3 52.6 + - - +
408K ASP* 2.6 52.5 + - - -
409K GLY* 2.8 20.7 + - - -
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Residues in contact with VAL 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370K TRP* 5.0 2.3 - - - -
404K ARG* 2.8 25.3 + - + +
405K SER* 1.3 65.8 - - - +
407K LEU* 1.3 59.9 + - - +
408K ASP 3.9 0.2 - - - +
409K GLY* 2.8 28.0 - - - -
410K PRO* 4.4 5.3 - - + +
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Residues in contact with LEU 407 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363K TRP* 4.1 21.5 - - + -
370K TRP* 3.3 45.8 - - + +
373K ARG* 2.9 17.9 + - + +
374K TYR* 3.3 55.9 - - + +
377K ILE* 5.3 0.9 - - + -
403K ILE 4.8 1.1 - - - +
404K ARG* 2.6 9.4 + - - +
406K VAL* 1.3 69.1 - - - +
408K ASP* 1.3 64.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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