Contacts of the helix formed by residues 291 - 305 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281C LEU 2.5 26.4 + - - -
282C PHE* 3.0 10.7 + - - -
283C SER 3.0 21.5 - - - -
284C GLY* 3.3 9.4 - - - +
286C LYS* 4.3 2.0 - - - +
290C LEU* 1.3 74.0 - - - +
292C GLU* 1.3 65.6 + - - +
293C GLN* 3.1 15.2 - - - +
294C ALA* 3.2 11.0 + - - +
295C LEU* 3.0 19.5 + - - +
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Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C LYS* 4.2 31.6 + - - +
291C SER* 1.3 72.9 - - - +
293C GLN* 1.3 67.8 + - - +
295C LEU* 2.9 23.9 + - - +
296C TYR* 3.3 42.7 + - + +
385C LYS* 4.2 11.8 + - - -
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Residues in contact with GLN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ILE* 3.6 18.5 - - - +
274C LEU* 5.4 1.1 - - + -
281C LEU* 3.5 39.2 - - + +
282C PHE* 4.6 7.4 - - + -
291C SER* 3.1 12.5 - - - +
292C GLU* 1.3 79.0 + - - +
294C ALA* 1.3 63.8 + - - +
296C TYR* 3.0 22.7 + - - +
297C TYR* 3.1 10.8 + - - +
382C ILE* 3.7 35.3 - - + +
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PHE* 3.6 40.5 - - + +
290C LEU* 3.7 25.8 - - + -
291C SER* 3.2 14.7 + - - +
292C GLU 3.3 0.2 - - - -
293C GLN* 1.3 79.7 - - - +
295C LEU* 1.3 58.0 + - - +
297C TYR* 2.9 7.0 + - - +
298C ILE* 2.8 32.2 + - - +
356C ILE* 4.8 2.5 - - + -
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C LYS* 4.0 26.0 - - + -
287C TYR* 4.9 7.2 - - + +
290C LEU* 4.1 19.7 - - + -
291C SER 3.0 26.0 + - - +
292C GLU* 2.9 9.6 + - - +
294C ALA* 1.3 76.0 - - - +
296C TYR* 1.3 58.9 + - + +
298C ILE* 3.5 5.6 + - + -
299C GLY 2.9 21.5 + - - -
334C TYR* 3.5 42.2 - - + +
387C HIS* 5.5 7.6 - - + +
388C PRO* 3.0 28.7 - - + +
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Residues in contact with TYR 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C GLU* 3.3 47.1 + - + +
293C GLN* 3.0 13.2 + - - +
295C LEU* 1.3 75.0 - - + +
297C TYR* 1.3 66.3 + - - +
299C GLY* 3.1 2.1 + - - -
300C GLY 2.9 19.1 + - - -
381C GLY* 3.3 24.1 - - - +
382C ILE* 3.6 15.5 - - + -
385C LYS* 3.3 60.9 + - + +
386C ILE 3.3 18.6 - - - +
387C HIS* 4.3 19.3 - + - -
388C PRO* 4.8 0.4 - - + -
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Residues in contact with TYR 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C VAL* 4.3 6.8 - - + +
126C PHE* 4.6 0.2 - - - -
272C MET* 3.7 32.5 - - + +
273C SER 6.0 0.2 - - - -
274C LEU* 3.7 26.2 - - + -
282C PHE* 3.7 22.7 - + + -
293C GLN 3.1 11.0 + - - +
294C ALA 2.9 11.6 + - - +
296C TYR* 1.3 74.3 - - - +
298C ILE* 1.3 57.8 + - - +
300C GLY* 2.9 6.1 + - - -
301C VAL* 2.9 45.8 + - + +
356C ILE* 3.7 22.4 - - + -
374C LEU 4.0 2.7 - - - -
375C LEU* 3.2 34.8 + - + +
378C GLY* 3.4 38.0 - - - -
379C LEU 4.4 0.4 - - - -
382C ILE* 4.0 4.9 - - + +
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Residues in contact with ILE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LEU* 4.5 8.3 - - + -
294C ALA 2.8 21.3 + - - +
295C LEU* 3.5 11.2 - - - +
296C TYR 3.2 0.2 - - - -
297C TYR* 1.3 75.5 - - - +
299C GLY* 1.3 57.4 + - - +
301C VAL* 3.4 8.2 + - - +
302C ILE* 2.9 55.9 + - + +
334C TYR* 3.9 26.9 - - + -
343C ILE* 4.2 10.1 - - + -
345C ILE* 3.7 29.8 - - + -
356C ILE* 3.8 22.4 - - + -
388C PRO* 3.9 9.4 - - + -
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Residues in contact with GLY 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU 2.9 13.0 + - - -
296C TYR 3.1 4.0 + - - -
298C ILE* 1.3 76.4 - - - +
300C GLY* 1.3 57.3 + - - +
302C ILE* 3.4 4.8 + - - +
303C LYS* 2.8 29.3 + - - +
386C ILE* 3.7 27.3 - - - +
387C HIS 4.8 0.2 - - - -
388C PRO* 4.0 15.0 - - - -
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Residues in contact with GLY 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C TYR 2.9 11.1 + - - -
297C TYR 2.9 1.1 + - - -
299C GLY* 1.3 73.2 - - - +
301C VAL* 1.3 66.2 + - - +
303C LYS* 2.8 16.5 + - - +
304C HIS* 2.8 21.4 + - - -
377C ALA 3.1 25.4 - - - -
381C GLY* 3.7 12.9 - - - -
386C ILE* 4.8 2.2 - - - -
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C MET* 5.4 0.2 - - + -
297C TYR* 2.9 44.8 + - + +
298C ILE* 3.6 8.7 - - - +
300C GLY* 1.3 73.8 - - - +
302C ILE* 1.3 59.1 + - + +
304C HIS 3.4 1.0 + - - -
305C ALA* 2.8 30.3 + - - +
308C ILE* 3.7 19.1 - - + +
332C LEU* 6.4 0.2 - - + -
343C ILE* 5.1 8.5 - - + -
356C ILE* 5.1 1.1 - - + -
358C VAL* 4.3 33.2 - - + -
360C PHE* 4.5 8.3 - - + -
374C LEU* 4.3 15.9 - - + +
377C ALA* 3.7 2.6 + - + -
378C GLY* 4.5 1.1 - - - -
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Residues in contact with ILE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C ILE* 2.9 45.0 + - + +
299C GLY* 3.7 5.4 - - - +
301C VAL* 1.3 76.8 - - - +
303C LYS* 1.3 63.2 + - - +
305C ALA* 3.6 12.0 - - - +
332C LEU* 3.6 48.6 - - + +
333C ALA* 4.3 6.7 - - - -
334C TYR* 4.7 1.6 - - + -
343C ILE* 4.0 17.0 - - + -
388C PRO* 4.6 17.0 - - + +
408C PRO* 4.4 13.5 - - + +
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Residues in contact with LYS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C GLY 2.8 14.1 + - - +
300C GLY* 2.8 11.0 + - - +
302C ILE* 1.3 80.0 - - - +
304C HIS* 1.3 79.0 + - + +
305C ALA* 3.6 0.5 + - - +
306C LYS 5.1 1.0 + - - -
380C ASP* 5.2 1.4 + - - -
384C ASN* 5.8 1.8 + - - -
386C ILE* 3.6 33.3 - - + +
424C ASP* 4.2 5.3 - - - +
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Residues in contact with HIS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C GLY* 2.8 22.8 + - - +
301C VAL 3.6 1.3 - - - -
303C LYS* 1.3 97.2 - - + +
305C ALA* 1.3 65.2 + - - +
306C LYS 3.4 1.8 - - - -
307C ALA* 2.9 7.1 + - - +
308C ILE* 2.8 20.9 + - + -
377C ALA* 3.4 32.3 - - + -
380C ASP* 3.0 31.3 + - - -
424C ASP* 2.8 37.8 + - - +
427C PHE* 3.5 32.7 - + + -
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Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C VAL 2.8 17.1 + - - +
302C ILE 3.6 5.8 - - - +
303C LYS 3.3 3.0 + - - +
304C HIS* 1.3 73.4 - - - +
306C LYS* 1.3 54.4 + - + +
308C ILE* 2.8 11.4 + - - +
309C ASN* 2.7 38.1 + - - -
332C LEU* 3.4 41.3 - - + -
360C PHE* 4.8 8.5 - - + -
410C VAL* 4.9 3.6 - - + -
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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