Contacts of the helix formed by residues 366 - 384 (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 ASN 366 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L THR* 4.1 0.8 - - - +
23L ASP 3.3 15.0 + - - -
24L THR 2.8 25.4 + - - +
25L LYS 4.0 5.5 + - - +
26L GLY* 3.4 19.1 - - - -
104L PRO* 3.8 7.7 - - - +
311L LEU 4.0 4.2 + - - +
314L PRO* 4.8 1.6 - - - +
364L ALA 3.6 2.4 + - - -
365L ALA* 1.3 69.5 - - - +
367L PRO* 1.3 70.5 - - - +
368L TYR* 3.0 27.5 + - - +
369L LEU* 3.6 26.6 - - + +
370L CYS* 2.8 24.8 + - - +
442L TYR* 5.6 2.9 + - + +
446L ARG* 5.2 2.6 - - - +
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Residues in contact with PRO 367 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L THR* 5.7 0.2 - - + -
26L GLY 4.7 2.2 - - - +
232L ALA* 3.7 34.8 - - + +
235L ILE* 3.8 22.4 - - + -
236L GLN* 3.7 26.0 - - - +
239L LYS* 4.5 2.9 - - - +
268L MET* 5.2 3.4 - - + -
365L ALA 3.0 11.5 - - - +
366L ASN* 1.3 87.2 - - - +
368L TYR* 1.3 61.1 + - + +
370L CYS* 4.5 1.8 - - + -
371L PHE* 2.9 50.2 + - + -
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Residues in contact with TYR 368 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L THR* 3.4 27.6 + - + -
88L ARG* 3.8 13.9 + - - -
104L PRO* 3.3 33.4 - - + +
105L ARG* 3.9 23.8 + - + -
107L ILE* 6.0 0.2 - - - -
108L ALA* 4.0 21.5 - - + +
229L THR* 4.0 5.4 - - + -
232L ALA* 3.3 25.3 + - + -
233L ASP* 2.6 37.7 + - - -
236L GLN* 4.1 10.8 - - + +
366L ASN* 3.0 13.6 + - - +
367L PRO* 1.3 80.1 - - + +
369L LEU* 1.3 58.9 + - - +
371L PHE* 3.9 1.7 - - - +
372L ALA* 2.9 33.1 + - - +
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Residues in contact with LEU 369 (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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24L THR* 3.8 25.1 - - + +
104L PRO* 3.8 27.6 - - + -
107L ILE* 3.8 25.1 - - + -
311L LEU* 3.5 20.1 - - + +
366L ASN* 3.3 20.2 + - + +
368L TYR* 1.3 80.5 - - - +
370L CYS* 1.3 57.4 + - - +
372L ALA* 3.9 3.8 - - - +
373L ALA* 3.0 30.8 + - - +
434L PHE* 4.2 13.8 - - + -
442L TYR* 3.8 27.6 - - + -
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Residues in contact with CYS 370 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268L MET* 4.9 2.0 - - - -
270L CYS* 5.0 0.4 - - - -
308L ILE* 4.9 1.4 - - - +
311L LEU* 3.7 23.2 - - - +
312L ALA* 3.5 31.2 - - - -
361L PRO* 4.3 8.5 - - - -
365L ALA* 3.9 10.3 - - + -
366L ASN 2.8 23.0 + - - +
367L PRO* 4.0 2.5 - - + +
369L LEU* 1.3 74.9 - - - +
371L PHE* 1.3 73.3 + - + +
373L ALA* 3.3 3.2 + - - +
374L LEU* 3.0 35.5 + - - +
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Residues in contact with PHE 371 (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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108L ALA* 6.2 0.2 - - + -
126L PHE* 3.3 36.6 - + + -
128L PRO* 3.4 31.0 - - + -
228L MET* 3.6 35.8 - - + +
231L LYS* 4.1 6.7 - - + -
232L ALA* 3.8 28.5 - - + -
235L ILE* 4.2 3.4 - - + -
268L MET* 4.3 13.5 - - + -
270L CYS* 4.0 22.2 - - - -
367L PRO* 2.9 31.9 + - + +
368L TYR* 3.9 2.5 - - - +
370L CYS* 1.3 81.1 - - - +
372L ALA* 1.3 63.6 + - - +
374L LEU* 3.2 2.4 + - + -
375L LEU 3.1 17.0 + - - -
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Residues in contact with ALA 372 (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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107L ILE* 4.5 3.8 - - + -
108L ALA* 4.4 8.5 - - - -
111L ALA* 4.2 17.5 - - + -
228L MET* 3.7 15.4 - - + -
368L TYR 2.9 19.5 + - - +
369L LEU 3.9 3.1 - - - +
371L PHE* 1.3 75.9 - - - +
373L ALA* 1.3 59.1 + - - +
375L LEU* 3.1 4.8 + - - +
376L MET* 2.9 33.9 + - - +
434L PHE* 4.2 18.2 - - + -
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Residues in contact with ALA 373 (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* 4.1 14.0 - - + +
311L LEU* 3.7 27.1 - - + -
369L LEU 3.0 21.0 + - - +
370L CYS 3.6 4.0 - - - +
371L PHE 3.3 0.2 - - - -
372L ALA* 1.3 76.0 - - - +
374L LEU* 1.3 63.3 + - - +
377L ALA* 3.2 25.1 + - - +
427L PHE* 3.7 4.9 - - + -
428L LEU* 3.9 20.2 - - + -
434L PHE* 4.6 2.4 - - + -
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Residues in contact with LEU 374 (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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126L PHE* 4.1 11.9 - - + -
270L CYS* 4.5 10.3 - - + -
272L MET* 3.9 25.6 - - + -
297L TYR* 3.8 5.9 + - - -
301L VAL* 4.2 22.1 - - + +
308L ILE* 3.5 31.9 - - + -
358L VAL* 4.4 12.3 - - + -
360L PHE* 4.7 1.1 - - + -
361L PRO* 4.5 11.7 - - + -
370L CYS* 3.0 37.5 + - - +
371L PHE* 3.2 8.5 + - - +
373L ALA* 1.3 78.5 - - - +
375L LEU* 1.3 62.8 + - - +
377L ALA* 3.3 3.1 + - - +
378L GLY* 3.0 17.8 + - - -
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Residues in contact with LEU 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L ALA* 3.7 31.9 - - + +
115L LEU* 4.4 5.4 - - + -
124L VAL* 3.7 42.2 - - + -
126L PHE* 4.6 1.1 - - + -
228L MET* 4.2 10.5 - - - -
274L LEU* 4.4 3.6 - - + -
297L TYR* 3.3 21.0 + - + +
371L PHE 3.1 9.6 + - - +
372L ALA 3.3 9.4 - - - +
374L LEU* 1.3 76.1 - - - +
376L MET* 1.3 55.8 + - - +
378L GLY* 2.8 4.0 + - - -
379L LEU* 2.8 59.6 + - + +
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Residues in contact with MET 376 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L ALA* 4.1 15.9 - - + +
114L TYR* 4.1 21.3 - - + -
372L ALA 2.9 26.1 + - - +
373L ALA 4.1 0.2 - - - +
375L LEU* 1.3 73.6 - - - +
377L ALA* 1.3 58.8 + - - +
379L LEU* 3.9 9.4 - - - +
380L ASP* 3.1 26.7 + - - +
427L PHE* 3.5 29.0 - - - +
428L LEU* 3.7 25.6 - - + +
430L ALA* 3.2 33.7 - - + +
433L VAL* 3.5 26.9 - - + -
434L PHE* 4.8 0.7 - - + -
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Residues in contact with ALA 377 (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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300L GLY* 3.2 26.5 - - - +
301L VAL* 4.2 1.1 - - - -
304L HIS* 4.0 4.0 - - + -
308L ILE* 3.6 20.0 - - + -
373L ALA 3.2 18.3 + - - +
374L LEU 3.5 4.9 - - - +
375L LEU 3.1 0.6 - - - -
376L MET* 1.3 73.8 - - - +
378L GLY* 1.3 66.5 + - - +
380L ASP* 3.3 4.0 + - - +
381L GLY 3.1 15.9 + - - -
427L PHE* 3.5 22.8 - - + -
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Residues in contact with GLY 378 (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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297L TYR* 3.5 52.6 - - - -
301L VAL* 4.5 0.6 - - - +
374L LEU 3.0 8.0 + - - -
375L LEU 2.8 7.3 + - - -
377L ALA* 1.3 77.4 - - - +
379L LEU* 1.3 55.5 + - - +
381L GLY* 3.0 14.9 + - - -
382L ILE* 3.0 12.8 + - - +
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Residues in contact with LEU 379 (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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114L TYR* 3.7 38.1 - - + -
115L LEU* 3.4 38.4 - - + -
118L THR* 5.0 2.7 - - - +
120L ILE* 4.2 18.8 - - + +
274L LEU* 4.3 13.7 - - + -
297L TYR* 4.8 0.2 - - + -
375L LEU* 2.8 39.4 + - + +
376L MET* 3.9 8.7 - - - +
378L GLY* 1.3 72.3 - - - +
380L ASP* 1.3 61.5 + - - +
381L GLY 3.0 1.8 - - - -
382L ILE* 3.2 4.8 + - + +
383L LYS* 2.8 38.1 + - + +
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Residues in contact with ASP 380 (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* 4.4 5.0 + - - -
304L HIS* 2.9 30.2 + - - +
376L MET 3.1 18.6 + - - +
377L ALA 3.6 5.6 - - - +
378L GLY 3.3 0.2 - - - -
379L LEU* 1.3 76.5 - - - +
381L GLY* 1.3 59.3 + - - +
382L ILE 3.3 0.2 - - - -
383L LYS* 4.0 22.1 + - - +
384L ASN* 3.4 32.2 + - - +
386L ILE* 3.6 10.2 - - - +
427L PHE* 4.0 16.6 - - + +
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Residues in contact with GLY 381 (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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296L TYR* 3.1 26.7 - - - +
300L GLY* 3.7 6.5 - - - -
377L ALA 3.1 5.3 + - - -
378L GLY 3.0 5.7 + - - -
380L ASP* 1.3 80.8 - - - +
382L ILE* 1.3 55.4 - - - +
385L LYS 3.0 5.7 + - - -
386L ILE* 2.8 42.1 + - - -
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Residues in contact with ILE 382 (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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120L ILE* 3.5 38.8 - - + -
274L LEU* 4.1 7.9 - - + -
293L GLN* 3.5 48.2 - - + +
296L TYR* 3.7 13.0 - - + -
297L TYR* 4.0 16.8 - - + +
378L GLY 3.0 15.1 + - - +
379L LEU* 3.6 9.9 - - + +
381L GLY* 1.3 73.8 - - - +
383L LYS* 1.3 69.5 + - - +
384L ASN 3.0 2.7 + - - -
385L LYS* 3.0 30.4 + - - +
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Residues in contact with LYS 383 (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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114L TYR* 3.3 27.7 + - + +
118L THR* 5.0 8.5 - - + -
120L ILE* 4.2 15.9 - - + -
376L MET 5.8 0.2 + - - -
379L LEU* 2.8 21.7 + - + +
380L ASP* 4.0 26.4 + - - +
382L ILE* 1.3 75.9 - - - +
384L ASN* 1.3 73.2 + - - +
385L LYS* 3.9 7.0 + - - +
430L ALA* 4.8 8.1 - - - +
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Residues in contact with ASN 384 (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* 5.6 4.0 + - - +
380L ASP* 3.4 28.5 + - - +
381L GLY 3.5 0.2 - - - -
382L ILE 3.0 0.8 - - - -
383L LYS* 1.3 104.0 + - - +
385L LYS* 1.3 70.5 + - - +
386L ILE* 2.9 16.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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