Contacts of the helix formed by residues 291 - 305 (chain H) in PDB entry 1FPY
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H LEU 2.5 26.5 + - - -
282H PHE* 3.0 10.3 + - - -
283H SER 3.0 21.1 - - - -
284H GLY* 3.3 8.5 - - - +
286H LYS* 4.3 1.8 - - - -
290H LEU* 1.3 75.1 - - - +
292H GLU* 1.3 66.0 + - - +
293H GLN* 3.1 15.8 - - - +
294H ALA* 3.2 10.8 + - - +
295H LEU* 3.0 20.5 + - - +
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Residues in contact with GLU 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H LYS* 4.2 31.2 + - - +
291H SER* 1.3 72.4 - - - +
293H GLN* 1.3 67.1 + - - +
295H LEU* 2.9 23.7 + - - +
296H TYR* 3.3 44.4 + - + +
385H LYS* 4.2 11.4 + - - -
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Residues in contact with GLN 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H ILE* 3.6 19.0 - - + +
274H LEU* 5.4 1.1 - - + -
281H LEU* 3.5 40.4 - - + +
282H PHE* 4.6 7.2 - - + -
291H SER* 3.1 12.7 + - - +
292H GLU* 1.3 79.0 + - - +
294H ALA* 1.3 63.2 + - - +
296H TYR* 3.0 22.8 + - - +
297H TYR* 3.1 10.6 + - - +
382H ILE* 3.7 34.4 - - + +
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Residues in contact with ALA 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H PHE* 3.6 38.5 - - + +
290H LEU* 3.7 25.8 - - + -
291H SER* 3.2 14.3 + - - +
292H GLU 3.2 0.2 + - - -
293H GLN* 1.3 78.2 - - - +
295H LEU* 1.3 58.0 + - - +
297H TYR* 3.0 6.7 + - - +
298H ILE* 2.8 32.0 + - - +
356H ILE* 4.8 3.1 - - + -
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Residues in contact with LEU 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H LYS* 4.0 26.7 - - + -
287H TYR* 4.9 7.2 - - + +
290H LEU* 4.1 19.5 - - + -
291H SER 3.0 25.3 + - - +
292H GLU* 2.9 9.3 + - - +
294H ALA* 1.3 76.9 - - - +
296H TYR* 1.3 58.6 + - + +
298H ILE* 4.0 5.2 - - + -
299H GLY 2.9 21.3 + - - -
334H TYR* 3.5 41.3 - - + +
387H HIS* 5.5 8.1 - - + +
388H PRO* 3.0 29.4 - - + +
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Residues in contact with TYR 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H GLU* 3.3 46.9 + - + +
293H GLN* 3.0 12.6 + - - +
295H LEU* 1.3 74.3 - - + +
297H TYR* 1.3 67.1 + - - +
299H GLY* 3.1 2.1 + - - -
300H GLY 2.9 19.2 + - - -
381H GLY* 3.3 24.6 - - - +
382H ILE* 3.6 16.6 - - + -
385H LYS* 3.3 63.3 - - + +
386H ILE 3.2 19.5 - - - +
387H HIS* 4.3 19.3 - + - -
388H PRO* 4.8 0.4 - - + -
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Residues in contact with TYR 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H VAL* 4.3 6.6 - - + +
272H MET* 3.7 31.9 - - + -
274H LEU* 3.7 27.1 - - + -
282H PHE* 3.7 21.3 - + + -
293H GLN 3.1 10.4 + - - +
294H ALA 3.0 11.4 + - - +
296H TYR* 1.3 74.9 - - - +
298H ILE* 1.3 57.4 + - + +
300H GLY* 2.9 5.7 + - - -
301H VAL* 2.9 46.5 + - + +
356H ILE* 3.7 20.6 - - + -
374H LEU 4.0 3.1 - - - -
375H LEU* 3.2 34.7 + - + +
378H GLY* 3.4 37.1 - - - -
379H LEU 4.4 0.2 - - - -
382H ILE* 4.0 4.4 - - + +
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Residues in contact with ILE 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H LEU* 4.5 8.1 - - + -
294H ALA 2.8 21.0 + - - +
295H LEU* 3.5 11.4 - - - +
297H TYR* 1.3 76.5 - - - +
299H GLY* 1.3 57.6 + - - +
301H VAL* 3.4 7.5 + - - +
302H ILE* 2.9 55.7 + - + +
334H TYR* 3.9 28.0 - - + -
343H ILE* 4.2 11.0 - - + -
345H ILE* 3.7 29.2 - - + -
356H ILE* 3.8 22.0 - - + -
388H PRO* 3.9 9.6 - - + -
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Residues in contact with GLY 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295H LEU 2.9 13.0 + - - -
296H TYR 3.1 4.2 + - - -
298H ILE* 1.3 76.2 - - - +
300H GLY* 1.3 56.5 + - - +
302H ILE* 3.4 5.2 + - - +
303H LYS* 2.8 29.5 + - - +
386H ILE* 3.7 25.8 - - - +
387H HIS 4.6 0.4 - - - -
388H PRO* 3.9 15.5 - - - +
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Residues in contact with GLY 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296H TYR 2.9 10.9 + - - -
297H TYR 2.9 1.3 + - - -
299H GLY* 1.3 73.8 - - - +
301H VAL* 1.3 65.2 + - - +
303H LYS* 2.8 16.3 + - - +
304H HIS* 2.8 21.9 + - - -
377H ALA 3.1 24.7 - - - -
381H GLY* 3.7 14.2 - - - -
386H ILE* 4.8 2.2 - - - -
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Residues in contact with VAL 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H MET* 5.4 0.2 - - + -
297H TYR* 2.9 44.7 + - + +
298H ILE* 3.6 8.3 - - - +
300H GLY* 1.3 73.3 - - - +
302H ILE* 1.3 60.7 + - + +
304H HIS 3.6 0.9 - - - -
305H ALA* 2.8 30.1 + - - +
308H ILE* 3.7 18.7 - - + +
332H LEU* 6.4 0.2 - - + -
343H ILE* 5.1 8.3 - - + -
356H ILE* 5.1 0.9 - - + -
358H VAL* 4.3 34.1 - - + -
360H PHE* 4.5 7.4 - - + -
374H LEU* 4.3 16.2 - - + +
377H ALA* 3.7 2.3 + - + -
378H GLY* 4.5 1.3 - - - -
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Residues in contact with ILE 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298H ILE* 2.9 44.6 + - + +
299H GLY* 3.7 5.2 - - - +
301H VAL* 1.3 76.9 - - - +
303H LYS* 1.3 63.5 + - - +
305H ALA* 3.6 11.8 - - - +
332H LEU* 3.6 49.0 - - + +
333H ALA* 4.3 6.7 - - - -
334H TYR* 4.7 1.6 - - + -
343H ILE* 4.0 17.5 - - + -
388H PRO* 4.6 16.6 - - + +
408H PRO* 4.4 14.1 - - + +
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Residues in contact with LYS 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H GLY 2.8 14.4 + - - +
300H GLY* 2.8 11.0 + - - +
302H ILE* 1.3 79.9 - - - +
304H HIS* 1.3 80.1 + - + +
305H ALA 3.3 0.9 + - - -
306H LYS 5.1 1.0 + - - -
380H ASP* 5.2 1.6 + - - -
384H ASN* 5.8 1.6 + - - -
386H ILE* 3.6 33.1 - - + +
424H ASP* 4.2 4.8 - - - +
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Residues in contact with HIS 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300H GLY* 2.8 23.9 + - - +
301H VAL 3.6 1.1 - - - -
303H LYS* 1.3 97.9 - - + +
305H ALA* 1.3 65.4 + - - +
306H LYS 3.4 2.2 - - - -
307H ALA* 2.9 7.0 + - - +
308H ILE* 2.8 21.0 + - + -
377H ALA* 3.4 32.3 - - + -
380H ASP* 3.0 30.6 + - - -
424H ASP* 2.8 37.8 + - - +
427H PHE* 3.5 32.3 - + + -
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Residues in contact with ALA 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301H VAL 2.8 16.7 + - - +
302H ILE 3.6 5.8 - - - +
303H LYS 3.3 2.4 + - - +
304H HIS* 1.3 73.1 - - - +
306H LYS* 1.3 53.5 + - + +
308H ILE* 2.8 10.6 + - - +
309H ASN* 2.7 39.7 + - - +
332H LEU* 3.4 43.3 - - + -
360H PHE* 4.8 7.9 - - + -
410H VAL* 4.9 2.9 - - + -
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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