Contacts of the helix formed by residues 406 - 438 (chain X) in PDB entry 5KHU
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 ARG 406 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405X CYS* 3.8 29.2 - - - +
407X LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 407 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406X ARG* 3.8 29.6 - - - +
408X ASP* 3.8 28.7 - - - +
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Residues in contact with ASP 408 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407X LEU* 3.8 26.9 - - - +
409X CYS* 3.8 29.2 - - - +
411X GLU* 4.4 17.3 - - - +
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Residues in contact with CYS 409 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408X ASP* 3.8 25.8 - - - +
410X TYR* 3.8 29.6 - - - +
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Residues in contact with TYR 410 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409X CYS* 3.8 29.6 - - - +
411X GLU* 3.8 24.9 - - - +
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Residues in contact with GLU 411 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408X ASP* 4.4 18.8 - - - +
410X TYR* 3.8 27.6 - - - +
412X GLY* 3.8 29.2 - - - +
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Residues in contact with GLY 412 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411X GLU* 3.8 28.9 - - - +
413X LEU* 3.8 26.7 - - - +
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Residues in contact with LEU 413 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412X GLY* 3.8 28.7 - - - +
414X ILE* 3.8 28.7 - - - +
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Residues in contact with ILE 414 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413X LEU* 3.8 26.9 - - - +
415X GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 415 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414X ILE* 3.8 25.4 - - - +
416X CYS* 3.8 28.7 - - - +
418X LEU* 4.6 15.7 - - - +
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Residues in contact with CYS 416 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415X GLU* 3.8 28.9 - - - +
417X TYR* 3.8 25.4 - - - +
419X ALA* 4.4 17.0 - - - +
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Residues in contact with TYR 417 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416X CYS* 3.8 24.5 - - - +
418X LEU* 3.8 29.6 - - - +
420X SER* 4.3 17.5 - - - +
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Residues in contact with LEU 418 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415X GLU* 4.6 15.3 - - - +
417X TYR* 3.8 25.4 - - - +
419X ALA* 3.8 29.8 - - - +
421X ASN* 4.6 15.0 - - - +
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Residues in contact with ALA 419 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416X CYS* 4.4 15.9 - - - +
418X LEU* 3.8 29.4 - - - +
420X SER* 3.8 24.9 - - - +
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Residues in contact with SER 420 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417X TYR* 4.3 18.2 - - - +
419X ALA* 3.8 28.9 - - - +
421X ASN* 3.8 25.1 - - - +
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Residues in contact with ASN 421 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418X LEU* 4.6 14.6 - - - +
420X SER* 3.8 26.7 - - - +
422X SER* 3.8 28.7 - - - +
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Residues in contact with SER 422 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421X ASN* 3.8 28.0 - - - +
423X ILE* 3.8 29.6 - - - +
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Residues in contact with ILE 423 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422X SER* 3.8 29.6 - - - +
424X ARG* 3.8 27.8 - - - +
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Residues in contact with ARG 424 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423X ILE* 3.8 29.4 - - - +
425X GLU* 3.8 28.0 - - - +
427X MET* 4.7 14.6 - - - +
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Residues in contact with GLU 425 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424X ARG* 3.8 25.4 - - - +
426X ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 426 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425X GLU* 3.8 29.2 - - - +
427X MET* 3.8 25.1 - - - +
429X MET* 4.5 17.9 - - - +
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Residues in contact with MET 427 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424X ARG* 4.7 16.6 - - - +
426X ALA* 3.8 26.0 - - - +
428X VAL* 3.8 28.9 - - - +
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Residues in contact with VAL 428 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427X MET* 3.8 24.9 - - - +
429X MET* 3.8 29.8 - - - +
431X ASN* 4.5 16.8 - - - +
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Residues in contact with MET 429 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426X ALA* 4.5 16.2 - - - +
428X VAL* 3.8 29.4 - - - +
430X ALA* 3.8 25.4 - - - +
432X ASN* 4.7 14.6 - - - +
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Residues in contact with ALA 430 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429X MET* 3.8 28.7 - - - +
431X ASN* 3.8 24.9 - - - +
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Residues in contact with ASN 431 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428X VAL* 4.5 16.8 - - - +
430X ALA* 3.8 28.9 - - - +
432X ASN* 3.8 26.0 - - - +
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Residues in contact with ASN 432 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429X MET* 4.7 14.8 - - - +
431X ASN* 3.8 27.4 - - - +
433X VAL* 3.8 28.3 - - - +
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Residues in contact with VAL 433 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432X ASN* 3.8 24.9 - - - +
434X TYR* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with TYR 434 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433X VAL* 3.8 28.9 - - - +
435X LYS* 3.8 26.0 - - - +
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Residues in contact with LYS 435 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434X TYR* 3.8 27.8 - - - +
436X THR* 3.8 29.2 - - - +
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Residues in contact with THR 436 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435X LYS* 3.8 28.9 - - - +
437X LEU* 3.8 26.7 - - - +
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Residues in contact with LEU 437 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436X THR* 3.8 25.8 - - - +
438X GLY* 3.8 28.5 - - - +
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Residues in contact with GLY 438 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437X LEU* 3.8 29.2 - - - +
439X ALA* 3.8 29.2 - - - +
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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
------------------------------------------------------------
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