Contacts of the helix formed by residues 416 - 442 (chain N) 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 ILE 416 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415N VAL* 3.8 26.2 - - - +
417N LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 417 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416N ILE* 3.8 29.4 - - - +
418N GLU* 3.8 28.5 - - - +
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Residues in contact with GLU 418 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417N LEU* 3.8 24.9 - - - +
419N VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 419 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418N GLU* 3.8 26.2 - - - +
420N ALA* 3.8 28.7 - - - +
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Residues in contact with ALA 420 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419N VAL* 3.8 29.4 - - - +
421N CYS* 3.8 29.2 - - - +
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Residues in contact with CYS 421 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420N ALA* 3.8 28.9 - - - +
422N GLU* 3.8 27.8 - - - +
424N ILE* 4.5 16.6 - - - +
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Residues in contact with GLU 422 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421N CYS* 3.8 29.4 - - - +
423N PRO* 3.8 26.5 - - - -
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Residues in contact with PRO 423 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422N GLU* 3.8 24.5 - - - -
424N ILE* 3.8 29.2 - - - -
426N ARG* 4.5 16.6 - - - -
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Residues in contact with ILE 424 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421N CYS* 4.5 17.3 - - - +
423N PRO* 3.8 29.6 - - - -
425N ARG* 3.8 25.4 - - - +
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Residues in contact with ARG 425 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424N ILE* 3.8 24.2 - - - +
426N ARG* 3.8 28.9 - - - +
428N LEU* 4.6 14.8 - - - +
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Residues in contact with ARG 426 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423N PRO* 4.5 17.7 - - - -
425N ARG* 3.8 28.9 - - - +
427N TYR* 3.8 26.9 - - - +
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Residues in contact with TYR 427 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426N ARG* 3.8 25.1 - - - +
428N LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 428 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425N ARG* 4.6 16.8 - - - +
427N TYR* 3.8 27.1 - - - +
429N ARG* 3.8 29.8 - - - +
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Residues in contact with ARG 429 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428N LEU* 3.8 29.2 - - - +
430N THR* 3.8 24.5 - - - +
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Residues in contact with THR 430 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429N ARG* 3.8 29.4 - - - +
431N ARG* 3.8 28.5 - - - +
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Residues in contact with ARG 431 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430N THR* 3.8 28.9 - - - +
432N GLU* 3.8 27.1 - - - +
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Residues in contact with GLU 432 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431N ARG* 3.8 28.7 - - - +
433N ASP* 3.8 28.9 - - - +
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Residues in contact with ASP 433 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432N GLU* 3.8 24.0 - - - +
434N THR* 3.8 29.4 - - - +
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Residues in contact with THR 434 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433N ASP* 3.8 28.3 - - - +
435N VAL* 3.8 30.1 - - - +
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Residues in contact with VAL 435 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434N THR* 3.8 25.1 - - - +
436N ARG* 3.8 28.9 - - - +
438N ILE* 4.4 19.5 - - - +
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Residues in contact with ARG 436 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435N VAL* 3.8 25.4 - - - +
437N GLN* 3.8 29.6 - - - +
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Residues in contact with GLN 437 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436N ARG* 3.8 29.8 - - - +
438N ILE* 3.8 26.5 - - - +
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Residues in contact with ILE 438 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435N VAL* 4.4 18.8 - - - +
437N GLN* 3.8 28.7 - - - +
439N VAL* 3.8 25.8 - - - +
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Residues in contact with VAL 439 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438N ILE* 3.8 27.6 - - - +
440N ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 440 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439N VAL* 3.8 25.8 - - - +
441N GLY* 3.8 29.2 - - - +
443N THR* 4.3 19.3 - - - +
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Residues in contact with GLY 441 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440N ALA* 3.8 24.9 - - - +
442N LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 442 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441N GLY* 3.8 29.6 - - - +
443N THR* 3.8 24.7 - - - +
453N ALA* 4.3 24.0 - - - +
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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