Contacts of the helix formed by residues 291 - 305 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281I LEU 2.5 26.0 + - - -
282I PHE* 3.0 10.1 + - - -
283I SER 3.0 21.5 - - - -
284I GLY* 3.3 7.8 - - - +
286I LYS* 4.3 2.0 - - - +
290I LEU* 1.3 74.1 - - - +
292I GLU* 1.3 65.2 + - - +
293I GLN* 3.1 16.8 - - - +
294I ALA* 3.2 10.4 + - - +
295I LEU* 3.0 20.5 + - - +
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Residues in contact with GLU 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I LYS* 4.2 32.1 + - - +
291I SER* 1.3 72.6 - - - +
293I GLN* 1.3 66.1 + - - +
295I LEU* 2.9 23.6 + - - +
296I TYR* 3.3 45.5 + - + +
385I LYS* 4.2 11.8 + - - +
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Residues in contact with GLN 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I ILE* 3.6 18.8 - - + +
274I LEU* 5.4 1.3 - - + -
281I LEU* 3.5 40.3 - - + +
282I PHE* 4.6 7.0 - - + -
291I SER* 3.1 12.3 - - - +
292I GLU* 1.3 78.2 + - - +
294I ALA* 1.3 63.1 + - - +
296I TYR* 3.0 23.3 + - - +
297I TYR* 3.1 10.7 + - - +
382I ILE* 3.7 34.1 - - + +
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Residues in contact with ALA 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282I PHE* 3.6 38.6 - - + +
290I LEU* 3.7 25.1 - - + -
291I SER* 3.2 14.3 + - - +
292I GLU 3.3 0.2 - - - -
293I GLN* 1.3 77.3 - - - +
295I LEU* 1.3 59.1 + - - +
297I TYR* 2.9 6.7 + - - +
298I ILE* 2.8 32.2 + - - +
356I ILE* 4.8 2.9 - - + -
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Residues in contact with LEU 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I LYS* 4.0 26.0 - - + -
287I TYR* 4.9 7.4 - - + +
290I LEU* 4.1 19.5 - - + -
291I SER 3.0 25.3 + - - +
292I GLU* 2.9 10.5 + - - +
294I ALA* 1.3 76.8 - - - +
296I TYR* 1.3 58.6 + - + +
298I ILE* 4.0 5.6 - - + -
299I GLY 2.9 21.7 + - - -
334I TYR* 3.5 40.8 - - + +
387I HIS* 5.5 7.6 - - + +
388I PRO* 3.0 28.7 - - + +
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Residues in contact with TYR 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292I GLU* 3.3 46.9 + - + +
293I GLN* 3.0 12.8 + - - +
295I LEU* 1.3 75.6 - - + +
297I TYR* 1.3 66.7 + - - +
299I GLY* 3.1 1.9 + - - -
300I GLY 2.9 19.2 + - - -
381I GLY* 3.3 24.8 - - - +
382I ILE* 3.6 16.4 - - + -
385I LYS* 3.3 62.5 + - + +
386I ILE 3.2 18.1 - - - +
387I HIS* 4.3 19.0 - + - -
388I PRO* 4.8 0.7 - - + -
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Residues in contact with TYR 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I VAL* 4.3 7.0 - - + +
272I MET* 3.7 30.9 - - + +
273I SER 6.4 0.2 - - - -
274I LEU* 3.7 26.5 - - + -
282I PHE* 3.7 21.1 - + + -
293I GLN 3.1 10.8 + - - +
294I ALA 2.9 11.6 + - - +
296I TYR* 1.3 75.3 - - - +
298I ILE* 1.3 57.0 + - + +
300I GLY* 2.9 5.9 + - - -
301I VAL* 2.9 47.0 + - + +
356I ILE* 3.7 22.0 - - + -
374I LEU 4.0 2.7 - - - -
375I LEU* 3.2 34.7 + - + +
378I GLY* 3.4 36.8 - - - -
379I LEU 4.4 0.2 - - - -
382I ILE* 4.0 4.4 - - + +
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Residues in contact with ILE 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290I LEU* 4.5 7.9 - - + -
294I ALA 2.8 19.5 + - - +
295I LEU* 3.5 11.4 - - - +
297I TYR* 1.3 78.0 - - - +
299I GLY* 1.3 56.9 + - - +
301I VAL* 3.4 7.7 + - - +
302I ILE* 2.9 55.5 + - + +
334I TYR* 3.9 27.4 - - + -
343I ILE* 4.2 11.7 - - + -
345I ILE* 3.7 29.8 - - + -
356I ILE* 3.8 22.0 - - + -
388I PRO* 3.9 10.3 - - + -
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Residues in contact with GLY 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295I LEU 2.9 12.2 + - - -
296I TYR 3.1 4.0 + - - -
298I ILE* 1.3 77.6 - - - +
300I GLY* 1.3 56.6 + - - +
302I ILE* 3.4 5.2 + - - +
303I LYS* 2.8 29.5 + - - +
386I ILE* 3.7 27.0 - - - +
387I HIS 4.8 0.4 - - - -
388I PRO* 3.9 15.2 - - - +
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Residues in contact with GLY 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296I TYR 2.9 10.9 + - - -
297I TYR 2.9 1.5 + - - -
299I GLY* 1.3 74.1 - - - +
301I VAL* 1.3 65.4 + - - +
303I LYS* 2.8 16.0 + - - +
304I HIS* 2.8 22.0 + - - -
377I ALA 3.1 24.5 - - - -
381I GLY* 3.7 14.0 - - - -
386I ILE* 4.8 2.0 - - - -
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Residues in contact with VAL 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I MET* 5.4 0.4 - - + -
297I TYR* 2.9 44.6 + - + +
298I ILE* 3.6 8.7 - - - +
300I GLY* 1.3 72.9 - - - +
302I ILE* 1.3 59.3 + - + +
304I HIS 3.4 0.9 + - - -
305I ALA* 2.8 30.1 + - - +
308I ILE* 3.7 19.5 - - + +
343I ILE* 5.1 8.1 - - + -
356I ILE* 5.1 0.9 - - + -
358I VAL* 4.3 34.1 - - + -
360I PHE* 4.5 8.1 - - + -
374I LEU* 4.3 16.4 - - + +
377I ALA* 3.7 2.1 + - + -
378I GLY* 4.5 1.6 - - - -
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Residues in contact with ILE 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298I ILE* 2.9 45.4 + - + +
299I GLY* 3.6 5.4 - - - +
301I VAL* 1.3 76.2 - - - +
303I LYS* 1.3 64.5 + - - +
305I ALA* 3.6 11.3 - - - +
332I LEU* 3.6 49.1 - - + +
333I ALA* 4.3 7.0 - - - -
334I TYR* 4.7 1.8 - - + -
343I ILE* 4.0 17.3 - - + -
388I PRO* 4.6 17.0 - - + +
408I PRO* 4.4 13.6 - - + +
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Residues in contact with LYS 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299I GLY 2.8 14.4 + - - +
300I GLY* 2.8 11.2 + - - +
302I ILE* 1.3 81.3 - - - +
304I HIS* 1.3 80.9 + - + +
305I ALA 3.3 0.9 + - - -
306I LYS 5.1 0.9 + - - -
380I ASP* 4.8 2.0 + - - +
384I ASN* 5.8 1.8 + - - +
386I ILE* 3.6 33.0 - - + +
424I ASP* 4.2 4.7 - - - +
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Residues in contact with HIS 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300I GLY* 2.8 23.1 + - - +
301I VAL 3.6 1.1 - - - -
303I LYS* 1.3 97.9 - - + +
305I ALA* 1.3 65.5 + - - +
306I LYS 3.4 2.0 - - - -
307I ALA* 2.9 7.5 + - - +
308I ILE* 2.8 21.5 + - + -
377I ALA* 3.4 32.5 - - + -
380I ASP* 3.0 30.4 + - - -
424I ASP* 2.8 38.5 + - - +
427I PHE* 3.5 32.8 - + + -
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Residues in contact with ALA 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301I VAL 2.8 16.9 + - - +
302I ILE 3.6 5.6 - - - +
303I LYS 3.3 2.0 - - - +
304I HIS* 1.3 73.3 - - - +
306I LYS* 1.3 53.7 + - + +
308I ILE* 2.8 10.4 + - - +
309I ASN* 2.7 39.5 + - - +
332I LEU* 3.4 43.1 - - + -
360I PHE* 4.8 8.1 - - + -
410I 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
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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