Contacts of the helix formed by residues 415 - 429 (chain B) in PDB entry 1F1J
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 SER 415 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413B ASP 3.8 2.2 + - - -
414B CYS* 1.3 77.3 - - - +
416B CYS* 1.3 63.2 + - - +
417B ALA* 3.4 7.0 + - - +
418B LYS* 2.8 28.0 + - - +
419B MET* 3.2 21.0 + - - +
452B GLY* 4.2 2.5 - - - -
453B LYS* 4.0 23.1 - - - +
454B ASP* 3.9 20.4 - - - -
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Residues in contact with CYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B SER* 1.3 72.9 - - - +
417B ALA* 1.3 64.7 + - - +
419B MET* 3.6 10.0 + - - +
420B GLN* 3.3 28.3 + - - +
452B GLY* 3.8 7.4 - - - -
454B ASP* 3.6 11.7 - - + +
455B GLY* 3.6 19.3 - - - -
456B VAL 3.5 31.4 - - - +
457B THR* 3.7 24.9 - - + +
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B SER* 3.3 6.8 + - - +
416B CYS* 1.3 78.2 - - - +
418B LYS* 1.3 59.3 + - - +
420B GLN* 3.5 6.5 + - - +
421B ASP* 3.0 30.5 + - - +
454B ASP* 4.9 3.9 + - - +
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 4.3 28.0 - - - -
414B CYS* 3.9 20.4 - - + -
415B SER* 2.8 29.4 + - - +
416B CYS 3.2 0.2 - - - -
417B ALA* 1.3 74.9 - - - +
419B MET* 1.3 67.7 + - - +
420B GLN 3.0 0.7 + - - -
421B ASP* 3.1 11.3 + - + +
422B LEU* 2.9 38.3 + - + +
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Residues in contact with MET 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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373B ILE* 4.0 26.2 - - + -
375B ASN* 3.6 22.0 - - - -
414B CYS* 3.6 14.8 - - + -
415B SER 3.2 14.0 + - - +
416B CYS* 3.9 3.6 - - - +
417B ALA 3.5 0.2 - - - -
418B LYS* 1.3 75.2 - - - +
420B GLN* 1.3 61.6 + - - +
422B LEU* 4.1 4.2 - - - +
423B LEU* 3.2 30.8 + - - +
441B LEU* 5.4 3.1 - - - -
443B SER* 6.0 0.4 - - - -
450B ILE* 4.3 11.9 - - + -
451B TYR 3.8 4.3 - - - +
452B GLY* 3.4 29.2 - - - +
457B THR* 3.5 28.9 - - + -
462B LEU* 4.1 13.5 - - + -
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Residues in contact with GLN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B CYS 3.3 16.4 + - - +
417B ALA* 3.7 7.0 - - - +
418B LYS 3.1 0.8 - - - -
419B MET* 1.3 77.0 - - - +
421B ASP* 1.3 60.0 + - - +
423B LEU* 3.4 1.4 + - - -
424B LYS* 2.9 30.4 + - - +
457B THR* 3.2 24.4 + - - +
461B ASP* 3.5 26.5 + - - +
462B LEU* 3.6 15.1 - - + +
465B HIS* 3.0 34.2 + - - -
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Residues in contact with ASP 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ALA 3.0 18.6 + - - +
418B LYS* 3.8 12.5 + - + +
420B GLN* 1.3 72.9 - - - +
422B LEU* 1.3 58.8 + - - +
424B LYS* 3.2 18.0 + - - +
425B LYS* 2.8 73.8 + - - +
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Residues in contact with LEU 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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371B ILE* 3.7 27.8 - - + +
373B ILE* 4.0 18.8 - - + -
411B TYR* 3.6 49.1 + - + +
414B CYS* 4.3 9.6 - - - -
418B LYS* 2.9 31.0 + - + +
419B MET* 4.2 1.8 - - - +
421B ASP* 1.3 78.2 + - - +
423B LEU* 1.3 77.4 + - + +
425B LYS* 3.6 6.6 + - - +
426B ALA* 3.1 25.1 + - - +
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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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371B ILE* 4.5 9.4 - - + -
373B ILE* 4.7 9.0 - - + -
419B MET 3.2 20.5 + - - +
420B GLN 3.9 2.5 - - - +
421B ASP 3.2 0.4 - - - -
422B LEU* 1.3 93.3 - - + +
424B LYS* 1.3 63.3 + - - +
426B ALA* 3.5 0.8 + - - +
427B SER* 3.3 18.4 + - - -
437B PHE* 4.7 0.4 - - + -
439B CYS* 4.0 28.3 - - + -
441B LEU* 5.0 1.3 - - + -
462B LEU* 3.6 39.9 - - + +
465B HIS* 4.1 9.1 - - + +
466B PHE* 3.3 38.1 - - + -
481B PHE* 5.2 2.9 - - + -
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Residues in contact with LYS 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 GLN 2.9 18.8 + - - +
421B ASP* 3.6 22.1 + - - +
423B LEU* 1.3 74.8 - - - +
425B LYS* 1.3 67.1 + - - +
427B SER* 2.5 24.6 + - - +
428B GLU* 3.1 39.7 + - + +
465B HIS* 3.9 27.9 - - + +
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Residues in contact with LYS 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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421B ASP* 2.8 52.9 + - - +
422B LEU* 3.9 6.5 - - - +
424B LYS* 1.3 83.6 - - - +
426B ALA* 1.3 61.0 + - - +
427B SER 3.1 1.6 - - - -
428B GLU* 2.8 34.8 + - - +
429B GLU* 3.1 19.3 + - - +
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LYS* 5.5 1.8 - - + -
371B ILE* 3.5 31.6 - - + -
422B LEU 3.1 13.9 + - - +
423B LEU* 3.5 5.8 + - - +
425B LYS* 1.3 76.0 - - - +
427B SER* 1.3 54.3 + - - +
429B GLU* 3.4 23.1 + - - +
431B HIS* 2.7 32.5 + - + +
437B PHE* 4.4 4.9 - - + -
466B PHE* 4.2 13.0 - - + -
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU 3.3 9.2 + - - -
424B LYS* 2.5 24.1 + - - +
426B ALA* 1.3 77.7 - - - +
428B GLU* 1.3 61.4 + - - +
429B GLU 3.2 7.8 + - - +
431B HIS* 4.5 0.2 - - - -
465B HIS* 3.4 32.8 + - - +
466B PHE* 3.7 19.5 - - - -
470B ARG 4.3 4.2 + - - +
471B SER* 3.3 29.6 + - - -
473B THR* 5.2 0.2 + - - -
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Residues in contact with GLU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LYS* 3.1 40.5 - - + +
425B LYS* 2.8 26.3 + - + +
427B SER* 1.3 78.6 - - - +
429B GLU* 1.3 64.9 + - - +
470B ARG 5.9 2.2 - - - +
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Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LYS* 4.8 16.8 + - - +
425B LYS* 3.4 13.0 - - + +
426B ALA* 3.4 28.7 + - - +
427B SER 3.2 4.8 - - - +
428B GLU* 1.3 84.4 - - - +
430B ASP* 1.3 62.1 + - - +
431B HIS* 3.6 16.1 + - - +
473B THR* 3.6 14.2 + - - +
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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