Contacts of the helix formed by residues 291 - 305 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E LEU 2.5 26.5 + - - -
282E PHE* 3.0 10.3 + - - -
283E SER 3.0 21.1 - - - -
284E GLY* 3.3 8.2 - - - +
286E LYS* 4.3 2.0 - - - +
290E LEU* 1.3 74.3 - - - +
292E GLU* 1.3 64.7 + - - +
293E GLN* 3.1 16.0 + - - +
294E ALA* 3.2 10.4 + - - +
295E LEU* 3.0 21.0 + - - +
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Residues in contact with GLU 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E LYS* 4.2 32.4 + - - +
291E SER* 1.3 72.5 - - - +
293E GLN* 1.3 67.9 + - - +
295E LEU* 2.9 23.6 + - - +
296E TYR* 3.3 43.3 + - + +
385E LYS* 4.2 11.4 + - - -
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Residues in contact with GLN 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ILE* 3.6 18.3 - - - +
274E LEU* 5.4 1.6 - - + -
281E LEU* 3.5 40.0 - - + +
282E PHE* 4.6 7.4 - - + -
291E SER* 3.1 12.5 - - - +
292E GLU* 1.3 79.8 + - - +
294E ALA* 1.3 63.8 + - - +
296E TYR* 3.0 22.1 + - - +
297E TYR* 3.1 10.6 + - - +
382E ILE* 3.7 34.1 - - + +
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Residues in contact with ALA 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E PHE* 3.6 38.7 - - + +
290E LEU* 3.7 25.4 - - + -
291E SER* 3.2 15.2 + - - +
292E GLU 3.3 0.2 - - - -
293E GLN* 1.3 77.7 - - - +
295E LEU* 1.3 58.3 + - - +
297E TYR* 3.0 7.0 + - - +
298E ILE* 2.8 31.5 + - - +
356E ILE* 4.8 2.7 - - + -
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Residues in contact with LEU 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E LYS* 4.0 26.5 - - + -
287E TYR* 4.9 7.4 - - + +
290E LEU* 4.1 18.4 - - + -
291E SER 3.0 25.8 + - - +
292E GLU* 2.9 10.2 + - - +
294E ALA* 1.3 77.6 - - - +
296E TYR* 1.3 57.6 + - + +
298E ILE* 3.5 5.1 + - + -
299E GLY 2.9 21.3 + - - -
334E TYR* 3.5 41.7 - - + +
387E HIS* 5.5 7.4 - - + +
388E PRO* 3.0 30.2 - - + +
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Residues in contact with TYR 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E GLU* 3.3 48.1 + - + +
293E GLN* 3.0 13.9 + - - +
295E LEU* 1.3 74.3 - - + +
297E TYR* 1.3 67.7 + - - +
299E GLY* 3.1 2.1 + - - -
300E GLY 2.9 18.7 + - - -
381E GLY* 3.3 24.7 - - - +
382E ILE* 3.6 15.7 - - + -
385E LYS* 3.3 60.2 + - + +
386E ILE 3.3 18.7 - - - +
387E HIS* 4.3 19.7 - + - -
388E PRO* 4.8 0.4 - - + -
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Residues in contact with TYR 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E VAL* 4.3 6.8 - - + +
272E MET* 3.7 31.7 - - + +
273E SER 6.0 0.2 - - - -
274E LEU* 3.7 26.0 - - + -
282E PHE* 3.7 21.1 - + + -
293E GLN 3.1 10.4 + - - +
294E ALA 3.0 12.1 + - - +
296E TYR* 1.3 74.9 - - - +
298E ILE* 1.3 57.0 + - + +
300E GLY* 2.9 5.9 + - - -
301E VAL* 2.9 46.5 + - + +
356E ILE* 3.7 21.5 - - + -
374E LEU 4.0 2.7 - - - -
375E LEU* 3.2 34.9 + - + +
378E GLY* 3.4 35.5 - - - -
379E LEU 4.4 0.4 - - - -
382E ILE* 4.0 5.0 - - + +
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Residues in contact with ILE 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E LEU* 4.5 8.1 - - + -
294E ALA 2.8 21.2 + - - +
295E LEU* 3.5 11.0 - - - +
297E TYR* 1.3 76.5 - - - +
299E GLY* 1.3 56.3 + - - +
301E VAL* 3.4 7.7 + - - +
302E ILE* 2.9 56.0 + - + +
334E TYR* 3.9 26.9 - - + -
343E ILE* 4.2 10.8 - - + -
345E ILE* 3.7 29.4 - - + -
356E ILE* 3.8 21.5 - - + -
388E PRO* 3.9 10.5 - - + -
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Residues in contact with GLY 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E LEU 2.9 11.8 + - - -
296E TYR 3.1 4.2 + - - -
298E ILE* 1.3 76.5 - - - +
300E GLY* 1.3 57.0 + - - +
302E ILE* 3.4 5.4 + - - +
303E LYS* 2.8 29.1 + - - +
386E ILE* 3.7 27.6 - - - +
387E HIS 4.8 0.2 - - - -
388E PRO* 4.0 14.8 - - - -
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Residues in contact with GLY 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E TYR 2.9 10.5 + - - -
297E TYR 2.9 2.0 + - - -
299E GLY* 1.3 73.7 - - - +
301E VAL* 1.3 65.6 + - - +
303E LYS* 2.8 15.9 + - - +
304E HIS* 2.8 22.5 + - - -
377E ALA 3.1 24.7 - - - -
381E GLY* 3.7 14.4 - - - -
386E ILE* 4.8 2.2 - - - -
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Residues in contact with VAL 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E MET* 5.4 0.2 - - + -
297E TYR* 2.9 44.8 + - + +
298E ILE* 3.6 8.3 - - - +
300E GLY* 1.3 74.0 - - - +
302E ILE* 1.3 59.3 + - + +
304E HIS 3.4 0.7 + - - -
305E ALA* 2.8 30.0 + - - +
308E ILE* 3.7 19.1 - - + +
332E LEU* 6.4 0.2 - - + -
343E ILE* 5.1 8.7 - - + -
356E ILE* 5.1 1.1 - - + -
358E VAL* 4.3 33.4 - - + -
360E PHE* 4.5 8.1 - - + -
374E LEU* 4.3 15.9 - - + +
377E ALA* 3.7 2.8 + - + -
378E GLY* 4.5 1.1 - - - -
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Residues in contact with ILE 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E ILE* 2.9 45.7 + - + +
299E GLY* 3.7 4.9 - - - +
301E VAL* 1.3 76.1 - - - +
303E LYS* 1.3 64.5 + - - +
305E ALA* 3.6 11.4 - - - +
332E LEU* 3.6 50.5 - - + +
333E ALA* 4.3 7.2 - - - -
334E TYR* 4.7 1.8 - - + -
343E ILE* 4.0 17.3 - - + -
388E PRO* 4.6 17.0 - - + +
408E PRO* 4.4 13.2 - - + +
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Residues in contact with LYS 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E GLY 2.8 15.7 + - - +
300E GLY* 2.8 10.3 + - - +
302E ILE* 1.3 79.9 - - - +
304E HIS* 1.3 80.9 + - + +
305E ALA 3.6 0.7 + - - -
306E LYS 5.1 0.7 + - - -
380E ASP* 5.2 1.4 + - - -
384E ASN* 5.8 2.0 + - - +
386E ILE* 3.6 33.6 - - + +
424E ASP* 4.2 4.5 - - - +
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Residues in contact with HIS 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E GLY* 2.8 23.2 + - - +
301E VAL 3.6 1.3 - - - -
303E LYS* 1.3 99.2 - - + +
305E ALA* 1.3 64.7 + - - +
306E LYS 3.4 2.0 - - - -
307E ALA* 2.9 7.4 + - - +
308E ILE* 2.8 20.6 + - + -
377E ALA* 3.4 31.9 - - + -
380E ASP* 3.0 30.0 + - - -
424E ASP* 2.8 38.2 + - - +
427E PHE* 3.5 33.6 - + + -
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Residues in contact with ALA 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301E VAL 2.8 17.2 + - - +
302E ILE 3.6 5.6 - - - +
303E LYS 3.3 2.0 + - - -
304E HIS* 1.3 74.6 - - - +
306E LYS* 1.3 54.0 + - + +
308E ILE* 2.8 11.3 + - - +
309E ASN* 2.7 38.7 + - - -
332E LEU* 3.4 41.5 - - + -
360E PHE* 4.8 8.3 - - + -
410E 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