Contacts of the helix formed by residues 417 - 429 (chain B) in PDB entry 4FGU
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 PRO 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B LEU* 5.8 0.9 - - + -
415B PRO 4.6 1.6 - - - +
416B TYR* 1.4 88.5 - - + +
418B LEU* 1.3 64.1 + - + +
419B HIS* 3.1 29.4 - - + +
420B ARG* 3.0 51.7 + - + +
421B ILE* 3.2 15.8 + - + +
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Residues in contact with LEU 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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377B SER* 3.9 23.3 - - - +
378B CYS* 4.1 30.5 - - + +
382B ALA* 5.5 8.1 - - + -
383B LEU* 3.1 26.3 - - + +
416B TYR 3.3 4.8 + - - +
417B PRO* 1.3 71.3 - - + +
419B HIS* 1.3 62.4 + - + +
421B ILE* 4.2 11.2 - - - -
422B LYS* 3.2 11.5 + - + +
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Residues in contact with HIS 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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417B PRO* 3.1 28.5 - - + +
418B LEU* 1.3 81.9 + - + +
420B ARG* 1.3 79.0 + - + +
421B ILE 3.3 0.7 - - - -
422B LYS* 3.2 17.8 - - + +
423B LEU* 2.9 29.5 + - + +
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Residues in contact with ARG 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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356B LEU* 4.2 17.0 - - + +
416B TYR* 5.8 2.2 - - - -
417B PRO* 3.0 39.5 + - + +
419B HIS* 1.3 102.4 - - + +
421B ILE* 1.3 57.4 + - - +
423B LEU* 3.4 21.6 - - + +
424B SER* 2.8 32.7 + - - -
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Residues in contact with ILE 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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352B ILE* 5.4 2.2 - - + -
356B LEU* 4.3 19.1 - - + -
383B LEU* 4.0 15.0 - - + -
408B LEU* 5.4 3.1 - - + +
411B LEU* 3.9 39.0 - - + +
412B CYS* 3.8 29.2 - - - -
416B TYR* 3.9 13.2 - - + +
417B PRO 3.2 16.8 + - - +
418B LEU 4.2 4.7 - - - +
419B HIS 3.3 0.2 - - - -
420B ARG* 1.3 75.8 - - - +
422B LYS* 1.3 62.8 + - - +
424B SER* 3.4 6.3 + - - -
425B MET* 3.2 42.9 + - + +
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Residues in contact with LYS 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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382B ALA* 4.4 17.5 + - + +
383B LEU* 3.3 15.7 - - + -
386B PHE* 3.7 45.3 - - + -
418B LEU* 3.2 22.4 - - + +
419B HIS* 3.2 17.2 + - + +
421B ILE* 1.3 76.4 - - - +
423B LEU* 1.3 60.6 + - - +
425B MET* 3.5 4.1 + - - +
426B ASP* 3.1 32.4 + - - +
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Residues in contact with LEU 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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419B HIS* 2.9 17.8 + - + +
420B ARG* 3.4 27.1 - - + +
422B LYS* 1.3 76.0 - - - +
424B SER* 1.3 63.7 + - - +
426B ASP* 3.4 12.3 + - + +
427B HIS* 3.2 22.2 + - - +
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Residues in contact with SER 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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352B ILE* 3.3 38.4 + - - +
355B LEU* 3.9 14.1 - - - +
356B LEU* 4.4 13.1 - - - +
420B ARG 2.8 17.0 + - - -
421B ILE* 3.8 8.3 - - - -
422B LYS 3.3 0.4 - - - -
423B LEU* 1.3 72.9 - - - +
425B MET* 1.3 65.1 + - - +
427B HIS* 3.5 6.7 + - - +
428B VAL* 3.3 25.1 + - - +
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Residues in contact with MET 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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352B ILE* 3.6 25.4 - - + -
383B LEU* 4.6 12.1 - - + +
386B PHE* 4.3 24.5 - - + +
387B ARG* 3.6 36.6 - - - +
390B CYS* 3.7 17.7 - - - -
408B LEU* 3.7 19.1 - - + -
421B ILE* 3.2 31.6 + - + +
422B LYS* 3.7 7.2 - - - +
423B LEU 3.3 0.2 - - - -
424B SER* 1.3 75.1 - - - +
426B ASP* 1.3 60.8 - - - +
428B VAL 2.9 1.7 + - - -
429B CYS* 2.6 37.9 + - - +
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Residues in contact with ASP 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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386B PHE* 3.3 31.6 - - - -
390B CYS* 5.7 0.7 - - - -
422B LYS* 3.1 16.9 + - - +
423B LEU* 3.6 14.1 - - + +
424B SER 3.4 0.2 - - - -
425B MET* 1.3 77.5 - - - +
427B HIS* 1.3 57.7 + - - +
430B LEU* 3.6 25.6 - - + +
431B GLY 3.1 24.4 + - - -
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Residues in contact with HIS 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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355B LEU* 3.4 34.0 - - + +
423B LEU 3.2 15.2 + - - +
424B SER* 3.8 6.3 - - - +
425B MET 3.2 0.6 - - - -
426B ASP* 1.3 76.2 - - - +
428B VAL* 1.3 61.0 + - - +
431B GLY* 3.3 22.9 - - - -
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Residues in contact with VAL 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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348B SER* 3.7 38.1 - - - +
351B LYS* 3.9 31.4 - - + +
352B ILE* 3.6 19.1 - - + -
355B LEU* 4.5 10.5 - - + -
424B SER 3.3 12.1 + - - +
425B MET 2.9 3.2 + - - -
427B HIS* 1.3 83.1 - - - +
429B CYS* 1.3 69.2 + - - +
430B LEU 3.5 0.2 - - - -
431B GLY* 3.4 6.9 + - - -
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Residues in contact with CYS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 6.0 2.7 - - - -
352B ILE* 4.8 5.8 - - - -
387B ARG* 4.5 3.8 - - - -
390B CYS* 2.0 59.5 - - + +
391B PHE* 4.8 11.9 - - + -
425B MET* 2.6 23.7 + - - +
428B VAL* 1.3 78.2 - - - +
430B LEU* 1.3 67.1 + - + +
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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