Contacts of the helix formed by residues 413 - 424 (chain B) in PDB entry 5I4V
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 VAL 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336B VAL* 5.3 2.5 - - + -
339B ILE* 5.5 11.7 - - + -
408B ALA* 2.9 20.3 + - + +
411B ALA* 4.2 11.2 - - + +
412B GLY* 1.3 78.2 - - - +
414B GLY* 1.3 64.2 + - - +
415B ALA 3.4 1.8 - - - -
416B ILE* 3.3 17.0 - - + +
417B PHE* 3.2 20.3 + - + +
506B HIS* 3.4 37.0 - - + +
510B PHE* 4.4 19.5 - - + -
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Residues in contact with GLY 414 (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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408B ALA 3.3 7.2 + - - -
409B HIS* 3.6 39.7 - - - +
412B GLY 3.6 2.2 - - - -
413B VAL* 1.3 76.2 - - - +
415B ALA* 1.3 65.9 + - - +
417B PHE* 3.1 6.2 + - - +
418B ASP* 2.9 27.4 + - - -
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Residues in contact with ALA 415 (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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409B HIS* 4.5 1.7 + - - -
413B VAL 3.4 0.8 - - - -
414B GLY* 1.3 75.1 - - - +
416B ILE* 1.3 63.1 + - - +
418B ASP* 3.2 9.5 + - - +
419B ARG* 3.1 30.1 + - + +
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Residues in contact with ILE 416 (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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413B VAL* 3.3 26.9 - - + +
415B ALA* 1.3 75.3 - - - +
417B PHE* 1.3 67.6 + - - +
419B ARG* 3.3 19.3 + - - +
420B VAL* 3.1 24.5 + - + +
499B ILE* 3.9 25.8 - - + +
502B LYS* 3.7 37.5 - - + -
503B CYS* 3.7 22.7 - - - +
506B HIS* 3.9 21.5 - - + +
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Residues in contact with PHE 417 (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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394B GLY* 3.8 11.2 - - - -
395B ILE* 4.1 31.0 - - + -
403B VAL* 3.8 31.6 - - + -
404B HIS 4.1 1.8 - - - -
405B ARG* 3.7 30.5 - - + -
408B ALA* 3.7 20.6 - - + -
409B HIS* 5.5 0.7 - + - -
413B VAL* 3.2 15.7 + - + +
414B GLY 3.3 9.0 - - - +
416B ILE* 1.3 83.8 - - - +
418B ASP* 1.3 65.1 + - - +
420B VAL* 3.2 17.2 + - + +
421B LEU* 3.2 40.9 + - + +
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Residues in contact with ASP 418 (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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405B ARG* 3.4 39.2 + - - +
409B HIS* 3.2 25.4 + - - -
414B GLY 2.9 12.9 + - - +
415B ALA* 3.2 9.7 + - - +
417B PHE* 1.3 77.6 - - - +
419B ARG* 1.3 57.8 + - + +
421B LEU* 3.4 8.0 + - - +
422B THR* 2.9 37.5 + - - +
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Residues in contact with ARG 419 (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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382A ASP* 4.7 18.3 + - - +
384A PRO* 6.0 8.5 - - - +
415B ALA* 3.1 20.8 + - - +
416B ILE* 3.6 15.3 - - - +
417B PHE 3.2 0.4 - - - -
418B ASP* 1.3 73.6 - - + +
420B VAL* 1.3 60.6 + - - +
422B THR* 4.6 4.0 - - - -
423B GLU* 2.9 42.6 + - + +
495B ALA 4.9 0.4 + - - -
498B SER* 3.7 28.5 + - - -
499B ILE* 3.7 29.8 - - + +
502B LYS* 4.0 28.9 - - - +
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Residues in contact with VAL 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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381B ILE* 4.9 4.5 - - + -
384B PHE* 4.2 18.8 - - + -
385B SER* 3.7 21.8 - - - +
395B ILE* 4.7 3.6 - - + -
416B ILE* 3.1 19.6 + - + +
417B PHE* 3.5 11.0 - - + +
419B ARG* 1.3 77.4 - - - +
421B LEU* 1.3 62.5 + - + +
424B LEU* 2.9 28.8 + - + +
425B VAL* 3.1 17.2 + - + -
499B ILE* 3.9 29.6 - - + -
503B CYS* 5.0 5.2 - - - -
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Residues in contact with LEU 421 (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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393B ASP* 4.1 11.9 - - - +
394B GLY 4.1 19.1 - - - +
395B ILE* 3.9 27.6 - - + -
405B ARG* 4.2 9.6 - - + -
417B PHE* 3.2 42.1 + - + +
418B ASP* 3.4 11.4 + - - +
420B VAL* 1.3 78.0 - - + +
422B THR* 1.3 64.1 + - - +
425B VAL* 3.9 14.8 - - + +
426B SER* 2.8 35.5 + - - +
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Residues in contact with THR 422 (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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389A PRO* 5.7 9.0 - - + -
418B ASP* 2.9 21.9 + - - +
419B ARG* 4.1 3.4 - - - -
421B LEU* 1.3 77.8 - - - +
423B GLU* 1.3 78.6 + - - +
426B SER* 3.4 16.5 - - - -
427B LYS* 3.0 28.5 + - - +
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Residues in contact with GLU 423 (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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381A ALA* 4.3 6.6 - - - +
382A ASP* 3.7 39.0 + - + +
389A PRO* 5.3 4.2 - - - +
393A GLU* 4.7 3.9 - - - +
419B ARG* 2.9 26.5 + - + +
422B THR* 1.3 95.6 - - + +
424B LEU* 1.3 62.2 + - - +
427B LYS* 3.2 16.4 + - - +
492B ARG* 2.7 49.8 + - - +
495B ALA* 4.4 6.1 - - + -
499B ILE* 4.1 15.3 - - + -
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 3.7 23.1 - - + -
382B ALA* 5.7 1.1 - - - -
385B SER* 3.5 27.1 - - - +
420B VAL* 2.9 17.8 + - + +
423B GLU* 1.3 88.5 - - + +
425B VAL* 1.3 66.4 + - - +
426B SER 3.3 1.1 - - - -
427B LYS* 3.2 2.0 + - - +
428B MET* 2.8 40.4 + - + +
492B ARG* 4.6 17.5 - - + +
495B ALA* 5.1 0.7 - - + -
496B LEU* 4.0 31.0 - - + +
499B ILE* 4.1 20.6 - - + -
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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