Contacts of the helix formed by residues 406 - 438 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405Y CYS* 3.8 28.9 - - - +
407Y LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 407 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406Y ARG* 3.8 29.2 - - - +
408Y ASP* 3.8 27.4 - - - +
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Residues in contact with ASP 408 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407Y LEU* 3.8 27.6 - - - +
409Y CYS* 3.8 28.9 - - - +
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Residues in contact with CYS 409 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408Y ASP* 3.8 25.8 - - - +
410Y TYR* 3.8 29.4 - - - +
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Residues in contact with TYR 410 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409Y CYS* 3.8 28.9 - - - +
411Y GLU* 3.8 26.9 - - - +
413Y LEU* 4.5 17.0 - - - +
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Residues in contact with GLU 411 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410Y TYR* 3.8 27.6 - - - +
412Y GLY* 3.8 28.7 - - - +
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Residues in contact with GLY 412 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411Y GLU* 3.8 29.6 - - - +
413Y LEU* 3.8 25.6 - - - +
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Residues in contact with LEU 413 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410Y TYR* 4.5 17.7 - - - +
412Y GLY* 3.8 28.9 - - - +
414Y ILE* 3.8 26.7 - - - +
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Residues in contact with ILE 414 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413Y LEU* 3.8 28.7 - - - +
415Y GLU* 3.8 26.2 - - - +
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Residues in contact with GLU 415 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414Y ILE* 3.8 28.9 - - - +
416Y CYS* 3.8 25.6 - - - +
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Residues in contact with CYS 416 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415Y GLU* 3.8 27.1 - - - +
417Y TYR* 3.8 29.2 - - - +
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Residues in contact with TYR 417 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416Y CYS* 3.8 28.9 - - - +
418Y LEU* 3.8 25.4 - - - +
420Y SER* 4.4 16.4 - - - +
422Y SER* 4.5 18.6 - - - +
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Residues in contact with LEU 418 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417Y TYR* 3.8 26.5 - - - +
419Y ALA* 3.8 29.6 - - - +
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Residues in contact with ALA 419 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418Y LEU* 3.8 29.8 - - - +
420Y SER* 3.8 25.1 - - - +
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Residues in contact with SER 420 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417Y TYR* 4.4 15.7 - - - +
419Y ALA* 3.8 28.7 - - - +
421Y ASN* 3.8 26.7 - - - +
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Residues in contact with ASN 421 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420Y SER* 3.8 27.6 - - - +
422Y SER* 3.8 29.8 - - - +
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Residues in contact with SER 422 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417Y TYR* 4.5 17.7 - - - +
421Y ASN* 3.8 29.4 - - - +
423Y ILE* 3.8 27.8 - - - +
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Residues in contact with ILE 423 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422Y SER* 3.8 29.4 - - - +
424Y ARG* 3.8 28.7 - - - +
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Residues in contact with ARG 424 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423Y ILE* 3.8 28.9 - - - +
425Y GLU* 3.8 26.7 - - - +
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Residues in contact with GLU 425 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424Y ARG* 3.8 24.5 - - - +
426Y ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 426 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425Y GLU* 3.8 29.2 - - - +
427Y MET* 3.8 26.7 - - - +
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Residues in contact with MET 427 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426Y ALA* 3.8 26.0 - - - +
428Y VAL* 3.8 28.7 - - - +
430Y ALA* 4.6 14.6 - - - +
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Residues in contact with VAL 428 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427Y MET* 3.8 25.6 - - - +
429Y MET* 3.8 28.5 - - - +
431Y ASN* 4.5 16.2 - - - +
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Residues in contact with MET 429 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428Y VAL* 3.8 25.1 - - - +
430Y ALA* 3.8 29.2 - - - +
432Y ASN* 4.4 17.5 - - - +
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Residues in contact with ALA 430 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427Y MET* 4.6 14.6 - - - +
429Y MET* 3.8 28.7 - - - +
431Y ASN* 3.8 25.4 - - - +
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Residues in contact with ASN 431 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428Y VAL* 4.5 16.2 - - - +
430Y ALA* 3.8 28.5 - - - +
432Y ASN* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with ASN 432 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429Y MET* 4.4 16.6 - - - +
431Y ASN* 3.8 26.2 - - - +
433Y VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 433 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432Y ASN* 3.8 29.4 - - - +
434Y TYR* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with TYR 434 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433Y VAL* 3.8 26.9 - - - +
435Y LYS* 3.8 28.9 - - - +
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Residues in contact with LYS 435 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434Y TYR* 3.8 27.4 - - - +
436Y THR* 3.8 29.2 - - - +
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Residues in contact with THR 436 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435Y LYS* 3.8 29.2 - - - +
437Y LEU* 3.8 27.4 - - - +
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Residues in contact with LEU 437 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436Y THR* 3.8 26.9 - - - +
438Y GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 438 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437Y LEU* 3.8 29.2 - - - +
439Y ALA* 3.8 29.4 - - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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