Contacts of the helix formed by residues 304 - 313 (chain L) in PDB entry 1F1H
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 HIS 304 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300L GLY* 3.0 22.9 + - - +
301L VAL 3.6 1.8 - - - -
303L LYS* 1.3 102.2 + - + +
305L ALA* 1.3 65.1 + - - +
306L LYS 3.4 2.5 - - - -
307L ALA* 3.1 5.5 + - - +
308L ILE* 2.9 22.1 + - - +
377L ALA* 4.0 14.1 - - + -
380L ASP* 2.9 29.9 + - - -
386L ILE* 5.1 0.2 - - - +
424L ASP* 2.7 39.8 + - - +
427L PHE* 3.6 43.8 - + + +
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Residues in contact with ALA 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301L VAL* 2.8 18.0 + - + +
302L ILE 3.6 1.8 + - - +
303L LYS 3.4 2.8 + - - -
304L HIS* 1.3 74.1 - - - +
306L LYS* 1.3 59.1 + - - +
308L ILE* 2.8 11.5 + - - +
309L ASN* 2.8 35.1 + - - +
332L LEU* 3.6 42.4 - - + -
360L PHE* 4.6 11.8 - - + -
410L VAL* 5.1 0.9 - - + -
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Residues in contact with LYS 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303L LYS 5.2 0.8 + - - -
304L HIS 3.4 0.8 + - - -
305L ALA* 1.3 77.3 - - + +
307L ALA* 1.3 61.4 + - - +
309L ASN* 3.2 24.0 - - - +
332L LEU* 5.5 2.5 - - + -
409L GLN* 3.2 30.2 + - - +
410L VAL 4.0 6.9 + - - -
411L ALA* 3.9 16.2 - - + +
416L GLU* 3.1 30.5 + - + +
417L ALA* 3.5 16.1 - - - -
420L ALA* 3.5 18.6 - - + -
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Residues in contact with ALA 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304L HIS* 3.1 10.2 + - - +
306L LYS* 1.3 75.8 - - - +
308L ILE* 1.3 66.1 + - - +
310L ALA* 3.1 19.4 + - - +
311L LEU* 3.8 10.2 - - - +
417L ALA 4.3 0.2 - - - -
420L ALA* 3.6 6.0 - - - +
421L LEU* 3.8 34.4 - - + +
424L ASP* 3.8 19.0 + - + +
427L PHE* 4.0 16.8 - - + -
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Residues in contact with ILE 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301L VAL* 3.9 21.8 - - + +
304L HIS 2.9 18.2 + - - +
305L ALA* 2.8 9.0 + - - +
307L ALA* 1.3 76.5 - - - +
309L ASN* 1.3 56.9 + - - +
311L LEU* 2.8 27.4 + - + +
312L ALA* 2.8 19.1 + - + +
360L PHE* 4.1 13.0 - - + -
370L CYS 4.9 1.1 - - - +
373L ALA* 4.1 20.0 - - + +
374L LEU* 3.5 36.6 - - + -
377L ALA* 3.6 27.8 - - + -
427L PHE* 4.4 7.4 - - + -
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Residues in contact with ASN 309 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305L ALA 2.8 11.5 + - - +
306L LYS* 3.2 18.4 - - - +
308L ILE* 1.3 77.8 - - - +
310L ALA* 1.3 58.0 + - - +
313L ASN* 2.7 59.0 + - - +
319L TYR* 3.7 17.7 - - - +
322L LEU* 4.7 1.4 - - - +
360L PHE* 3.4 21.0 - - - -
410L VAL* 3.4 13.9 - - - +
411L ALA* 2.7 32.8 + - + +
417L ALA* 3.8 4.0 - - + -
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Residues in contact with ALA 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306L LYS 3.7 0.2 + - - -
307L ALA 3.1 14.2 + - - +
309L ASN* 1.3 78.5 - - - +
311L LEU* 1.3 52.1 + - + +
313L ASN 4.7 1.6 - - - -
314L PRO* 3.7 9.7 - - - +
414L LEU* 5.0 1.7 - - - +
417L ALA* 3.5 33.2 - - + +
418L LEU* 4.1 12.6 - - + +
421L LEU* 3.8 23.8 - - + -
442L TYR* 2.6 30.1 + - - -
446L ARG* 5.3 0.2 - - - +
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Residues in contact with LEU 311 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307L ALA 3.8 16.2 - - - +
308L ILE* 2.8 7.2 + - - +
310L ALA* 1.3 81.8 - - + +
312L ALA* 1.3 57.9 + - - +
313L ASN 3.4 1.5 + - - -
314L PRO* 3.8 4.1 - - - +
365L ALA* 3.2 22.7 - - - +
366L ASN* 4.0 4.2 + - - +
369L LEU* 3.5 32.1 - - + +
370L CYS* 3.7 21.9 - - - +
373L ALA* 3.7 23.8 - - + -
421L LEU* 4.3 18.4 - - + -
428L LEU* 4.9 4.9 - - + -
434L PHE* 4.9 11.0 - - + -
442L TYR* 3.7 27.7 + - + -
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Residues in contact with ALA 312 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308L ILE* 2.8 18.5 + - + +
311L LEU* 1.3 73.0 - - - +
313L ASN* 1.3 67.7 + - - +
314L PRO* 3.4 3.8 - - - +
360L PHE* 4.1 5.6 - - + -
361L PRO* 3.4 31.4 - - + -
362L ASP* 3.0 28.4 + - - +
365L ALA* 3.5 8.4 - - - +
370L CYS* 3.5 19.0 - - - -
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Residues in contact with ASN 313 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309L ASN* 2.7 39.7 + - - +
312L ALA* 1.3 81.5 - - - +
314L PRO* 1.3 59.4 - - - +
315L THR 3.3 4.4 + - - -
318L SER* 3.6 17.7 - - - -
319L TYR* 2.8 38.3 + - + +
321L ARG* 4.1 0.2 + - - -
322L LEU* 3.3 18.6 - - + +
360L PHE* 2.7 36.0 + - - +
362L ASP* 3.3 11.8 - - - +
414L LEU* 4.0 1.6 - - - +
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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