Contacts of the helix formed by residues 291 - 304 (chain A) 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 SER 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A LEU 2.6 28.9 + - - -
282A PHE* 2.9 10.3 + - - -
283A SER 3.4 18.2 - - - -
284A GLY* 3.5 9.1 - - - +
285A ASP 4.9 0.2 - - - +
286A LYS* 4.0 3.1 - - - -
290A LEU* 1.3 78.1 - - - +
292A GLU* 1.3 61.0 + - - +
293A GLN* 3.2 6.2 + - - +
294A ALA* 3.1 22.4 + - - +
295A LEU* 3.5 13.3 + - - +
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LYS* 3.8 36.1 + - + +
291A SER* 1.3 73.5 - - - +
293A GLN* 1.3 67.1 + - + +
295A LEU* 3.2 11.8 + - + +
296A TYR* 3.1 55.5 + - + +
385A LYS* 5.0 6.1 + - - +
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE* 3.7 20.3 + - - +
274A LEU* 5.1 2.1 - - - +
281A LEU* 3.0 45.3 - - - +
282A PHE* 4.8 4.7 - - + -
291A SER* 3.1 11.9 - - - +
292A GLU* 1.3 84.7 - - + +
294A ALA* 1.3 60.9 + - - +
296A TYR* 3.4 5.9 + - - +
297A TYR* 3.1 18.9 + - - +
382A ILE* 3.5 31.2 - - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PHE* 3.7 37.8 - - + +
290A LEU* 3.7 22.4 - - + -
291A SER* 3.1 18.7 + - - +
292A GLU 3.2 0.2 - - - -
293A GLN* 1.3 76.7 - - - +
295A LEU* 1.3 57.7 + - - +
297A TYR* 3.1 10.6 - - - +
298A ILE* 2.9 32.0 + - - +
356A ILE* 5.0 2.2 - - + -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LYS* 4.0 30.5 - - + -
287A TYR* 4.9 6.5 - - + +
290A LEU* 3.8 26.9 - - + -
291A SER 3.6 9.2 - - - +
292A GLU* 3.2 12.0 + - + +
294A ALA* 1.3 77.9 - - - +
296A TYR* 1.3 59.4 + - + +
298A ILE* 3.2 6.6 + - + +
299A GLY 2.8 22.3 + - - -
334A TYR* 4.0 29.4 - - + +
387A HIS* 4.6 16.2 - - + +
388A PRO* 3.2 25.7 - - + +
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU* 3.1 44.9 + - + +
293A GLN* 3.8 8.7 - - - +
294A ALA 3.3 0.2 - - - -
295A LEU* 1.3 76.7 - - + +
297A TYR* 1.3 64.8 + - - +
299A GLY* 3.3 0.9 + - - -
300A GLY 3.0 18.4 + - - -
381A GLY* 3.1 29.2 - - - +
382A ILE* 3.7 13.0 - - + -
385A LYS* 3.5 60.8 + - + +
386A ILE 3.4 19.0 - - - +
387A HIS* 4.2 23.0 - + + -
388A PRO* 4.6 0.2 - - + -
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Residues in contact with TYR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 4.7 4.9 - - - +
126A PHE* 4.8 0.2 - - - -
272A MET* 3.6 31.4 - - + +
273A SER 6.1 0.7 - - - -
274A LEU* 3.8 26.5 - - + -
282A PHE* 3.6 24.5 - + + -
293A GLN 3.1 12.7 + - - +
294A ALA 3.1 12.1 + - - +
296A TYR* 1.3 76.8 - - - +
298A ILE* 1.3 61.8 + - - +
300A GLY 3.1 10.0 + - - -
301A VAL* 3.1 22.7 + - + +
356A ILE* 3.8 20.9 - - + -
374A LEU 4.2 1.3 - - - -
375A LEU* 3.3 35.2 - - + +
378A GLY* 3.5 42.4 - - - -
379A LEU* 4.5 0.7 - - + -
382A ILE* 4.0 4.9 - - + +
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU* 4.4 9.2 - - + -
294A ALA 2.9 19.5 + - - +
295A LEU* 3.3 12.6 - - + +
297A TYR* 1.3 74.3 - - - +
299A GLY* 1.3 66.0 + - - +
301A VAL* 3.0 10.1 + - - +
302A ILE* 2.9 37.1 + - + +
334A TYR* 4.1 24.9 - - + -
343A ILE* 4.0 14.8 - - + -
345A ILE* 4.0 26.5 - - + -
356A ILE* 4.0 23.1 - - + -
388A PRO* 3.8 14.6 - - + -
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Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A LEU 2.8 11.8 + - - -
296A TYR 3.3 0.4 + - - -
298A ILE* 1.3 76.4 - - - +
300A GLY* 1.3 57.0 + - - +
302A ILE* 3.3 5.5 + - - +
303A LYS* 2.9 29.5 + - - +
386A ILE* 3.6 31.7 - - - +
388A PRO* 3.9 15.3 - - - -
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Residues in contact with GLY 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A TYR 3.0 11.1 + - - -
297A TYR 3.1 3.1 + - - -
299A GLY* 1.3 76.6 - - - +
301A VAL* 1.3 55.5 + - - +
303A LYS* 3.2 1.7 + - - -
304A HIS* 3.0 36.8 + - - +
377A ALA 3.2 25.4 - - - -
381A GLY* 3.7 12.7 - - - -
386A ILE* 4.4 7.4 - - - -
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TYR* 3.1 35.3 + - + +
298A ILE* 3.0 10.4 + - - +
300A GLY* 1.3 76.3 - - - +
302A ILE* 1.3 58.3 + - - +
304A HIS 3.6 0.3 - - - -
305A ALA* 2.8 29.6 + - - +
308A ILE* 3.9 17.6 - - + +
343A ILE* 4.3 17.7 - - + -
356A ILE* 5.2 1.1 - - + -
358A VAL* 4.4 18.4 - - + -
360A PHE* 4.5 8.1 - - + -
374A LEU* 4.2 28.3 - - + +
377A ALA* 4.2 1.1 - - + -
378A GLY 4.5 0.9 - - - +
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Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ILE* 2.9 40.1 + - + +
299A GLY* 3.7 5.2 - - - +
301A VAL* 1.3 78.6 - - + +
303A LYS* 1.3 64.9 + - - +
305A ALA* 3.6 14.2 + - - +
332A LEU* 3.6 53.9 - - + +
333A ALA* 4.1 11.7 - - - -
334A TYR* 4.7 1.1 - - + -
343A ILE* 4.2 9.9 - - + -
388A PRO* 4.6 16.4 - - + +
408A PRO* 4.9 7.1 - - + +
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A GLY 2.9 17.6 + - - +
300A GLY* 3.6 6.3 - - - +
302A ILE* 1.3 80.3 - - - +
304A HIS* 1.3 78.6 + - + +
305A ALA 3.7 0.3 + - - -
306A LYS 5.2 0.7 + - - -
380A ASP* 4.4 6.9 + - - -
384A ASN* 5.6 3.6 + - - +
386A ILE* 3.6 33.4 - - + +
424A ASP* 4.1 3.7 - - - +
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Residues in contact with HIS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A GLY* 3.0 24.0 + - - +
301A VAL 3.6 1.8 - - - -
303A LYS* 1.3 100.7 + - + +
305A ALA* 1.3 65.1 + - - +
306A LYS 3.4 2.5 - - - -
307A ALA* 3.1 6.2 + - - +
308A ILE* 2.9 22.1 + - - +
377A ALA* 4.0 13.9 - - + -
380A ASP* 2.9 29.4 + - - -
424A ASP* 2.7 39.2 + - - +
427A PHE* 3.6 44.2 - + + +
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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