Contacts of the helix formed by residues 419 - 433 (chain B) in PDB entry 4Y5U
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 ASP 419 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B VAL* 3.8 28.8 - - + +
413B ILE* 4.0 9.8 - - + +
417B ASN* 4.4 0.2 + - - -
418B GLN* 1.3 95.6 - - - +
420B ASN* 1.3 59.6 + - - +
421B ASN 3.3 2.5 - - - -
422B ALA* 3.2 6.7 + - - -
423B LYS* 2.8 54.8 + - + +
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Residues in contact with ASN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B ASN* 5.6 0.4 + - - +
418B GLN 3.9 1.4 + - - -
419B ASP* 1.3 78.0 + - - +
421B ASN* 1.3 73.9 + - - +
423B LYS* 3.5 8.8 + - - +
424B ALA 3.3 7.6 + - - -
503B ASN* 4.4 2.3 - - - +
515B TRP* 3.0 41.8 + - - +
516B GLN* 3.4 46.3 + - - +
519B ASP* 3.9 12.4 + - - +
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Residues in contact with ASN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 4.7 18.5 - - + +
418B GLN 5.0 3.5 + - - +
419B ASP 3.3 0.4 - - - -
420B ASN* 1.3 88.5 + - - +
422B ALA* 1.3 59.3 + - - +
424B ALA* 3.3 4.3 + - - +
425B THR* 2.8 27.2 + - - -
499B TRP* 5.2 0.9 - - - -
503B ASN* 3.3 23.6 + - - +
504B LYS* 4.4 15.0 + - - +
516B GLN* 5.5 3.8 - - - +
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B VAL* 3.7 22.0 - - + +
381B GLU 4.7 3.5 - - - +
411B VAL* 3.9 27.2 - - + +
413B ILE* 4.0 18.8 - - + -
418B GLN 5.1 0.8 + - - +
419B ASP* 3.2 12.0 + - - +
421B ASN* 1.3 80.8 - - - +
423B LYS* 1.3 60.6 + - - +
425B THR* 3.5 7.7 - - - -
426B ILE* 3.3 19.8 + - - +
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Residues in contact with LYS 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B VAL* 4.2 14.4 - - + -
419B ASP* 2.8 48.4 + - - +
420B ASN* 3.7 5.2 - - - +
422B ALA* 1.3 77.1 - - - +
424B ALA* 1.3 59.3 + - - +
426B ILE* 3.7 3.1 + - - +
427B LEU* 3.2 23.2 + - - +
458B LYS* 6.3 3.1 - - - -
462B GLU* 5.2 8.1 + - - -
515B TRP* 3.9 14.3 - - + -
519B ASP* 3.7 30.4 + - - +
523B ASP* 5.0 6.5 + - - -
526B LYS* 5.7 4.8 - - - +
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Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B ASN 3.3 3.2 + - - -
421B ASN 3.6 3.4 - - - +
422B ALA 3.3 0.2 - - - -
423B LYS* 1.3 75.5 - - - +
425B THR* 1.3 59.9 + - - +
427B LEU* 3.5 5.8 - - - +
428B TRP* 3.0 29.6 + - - +
499B TRP* 3.5 10.1 - - + -
502B PHE* 4.1 7.0 - - + -
503B ASN* 3.1 35.4 - - + +
515B TRP* 3.4 25.7 - - + +
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Residues in contact with THR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B GLU* 3.8 29.9 - - - +
383B LYS* 3.9 21.4 + - + +
411B VAL* 4.1 19.5 - - + -
421B ASN 2.8 15.4 + - - -
422B ALA* 3.5 11.2 - - - -
424B ALA* 1.3 73.8 - - - +
426B ILE* 1.3 64.7 + - + +
428B TRP* 3.5 2.6 + - - +
429B ASP* 3.3 23.9 + - - +
499B TRP* 3.7 18.6 - - + -
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Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLY 5.3 3.4 - - - +
213B ASN* 4.9 1.1 - - - +
281B GLN* 3.7 41.5 - - + +
282B VAL* 4.2 6.5 - - + -
383B LYS* 5.6 2.0 - - + -
409B PRO* 3.4 33.9 - - + +
410B LEU 4.3 0.2 - - - -
411B VAL* 4.3 15.3 - - + +
422B ALA 3.3 15.0 + - - +
423B LYS* 4.2 4.7 - - - +
424B ALA 3.5 0.2 - - - -
425B THR* 1.3 79.6 - - + +
427B LEU* 1.3 64.3 + - - +
428B TRP 3.4 0.2 + - - -
429B ASP* 3.8 4.7 - - + +
430B ASN* 3.0 42.9 + - - +
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Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ASN* 3.2 32.0 + - - +
423B LYS 3.2 15.2 + - - +
424B ALA* 3.5 6.1 - - - +
426B ILE* 1.3 81.8 - - - +
428B TRP* 1.3 62.5 + - - +
431B ALA* 3.2 11.7 + - + +
432B PHE* 5.5 0.2 - - + -
451B MET* 4.9 5.6 - - + -
454B THR* 3.7 21.1 - - + -
455B LEU* 5.3 3.8 - - + -
458B LYS* 3.5 44.4 - - + +
502B PHE* 4.0 25.8 - - + -
515B TRP* 4.2 14.4 - - + -
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Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B LYS* 6.0 0.7 - - - +
424B ALA 3.0 17.6 + - - +
425B THR* 3.9 4.0 - - - +
426B ILE 3.3 0.4 - - - -
427B LEU* 1.3 75.1 - - - +
429B ASP* 1.3 61.0 + - - +
432B PHE* 3.0 51.5 + + - +
442B VAL* 3.8 16.3 - - + +
443B ALA 2.9 21.8 + - - -
444B GLU* 3.5 25.5 + - - -
446B VAL* 3.8 30.3 - - + -
451B MET* 3.3 26.9 - - + -
497B VAL* 4.2 2.0 - - + -
498B SER 3.6 10.8 - - - -
499B TRP* 3.5 45.3 - + + -
502B PHE* 3.8 14.4 - + + -
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Residues in contact with ASP 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLN* 3.8 5.0 + - - -
383B LYS* 3.0 32.7 + - + +
409B PRO* 3.2 19.9 - - + +
425B THR 3.3 9.2 + - - +
426B ILE* 3.8 6.3 - - + +
428B TRP* 1.3 75.9 - - - +
430B ASN* 1.3 64.8 + - - +
433B SER* 2.9 31.5 + - - -
437B ARG* 2.2 37.5 + - - -
440B PHE* 4.5 2.3 - - - -
442B VAL* 3.4 20.1 - - - +
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Residues in contact with ASN 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ARG* 3.2 17.3 + - - -
209B GLN* 3.5 38.2 + - - +
210B LEU* 3.6 8.7 - - - +
212B GLY* 3.8 8.5 - - - -
213B ASN* 3.1 31.2 + - - +
281B GLN* 3.3 35.4 + - - -
408B LEU* 4.1 2.1 - - - +
409B PRO* 5.5 0.2 - - - +
426B ILE* 3.0 21.7 + - - +
429B ASP* 1.3 81.2 - - - +
431B ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ARG* 2.9 20.7 + - - -
210B LEU* 4.0 9.4 - - - +
213B ASN* 3.7 7.1 - - - +
427B LEU 3.2 18.7 + - - +
430B ASN* 1.3 80.5 - - - +
432B PHE* 1.3 83.3 + - + +
433B SER 3.5 0.7 - - - -
454B THR* 3.3 27.5 + - + +
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Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ARG* 4.7 0.7 - - - -
427B LEU* 4.9 0.4 - - + -
428B TRP* 3.0 59.1 + + - +
431B ALA* 1.3 98.3 - - + +
433B SER* 1.3 65.2 + - - +
434B GLU* 3.9 8.1 + - - +
442B VAL* 3.7 15.0 - - + +
443B ALA* 4.5 9.7 + - + +
446B VAL* 3.4 42.8 - - + -
447B PRO* 5.7 0.4 - - + -
450B LYS* 3.9 29.8 - - + -
451B MET* 3.8 25.4 - - + -
454B THR* 4.3 4.0 - - + -
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Residues in contact with SER 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 3.6 20.0 + - - -
209B GLN* 3.7 19.7 - - - -
429B ASP* 2.9 19.9 + - - -
431B ALA 3.5 1.8 - - - -
432B PHE* 1.3 81.2 - - - +
434B GLU* 1.3 64.8 + - - +
435B MET 4.0 0.7 + - - -
437B ARG* 2.9 40.9 + - - +
441B VAL 4.1 2.8 + - - -
442B VAL* 3.7 7.1 - - - +
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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
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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