Contacts of the helix formed by residues 304 - 313 (chain J) 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 HIS 304 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300J GLY* 2.8 24.4 + - - +
301J VAL 3.6 1.1 - - - -
303J LYS* 1.3 99.1 - - + +
305J ALA* 1.3 64.7 + - - +
306J LYS 3.4 2.2 - - - -
307J ALA* 2.9 7.4 + - - +
308J ILE* 2.8 21.7 + - + -
377J ALA* 3.4 31.4 - - + -
380J ASP* 3.0 30.8 + - - -
424J ASP* 2.8 37.2 + - - +
427J PHE* 3.5 33.2 - + + -
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Residues in contact with ALA 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301J VAL 2.8 16.5 + - - +
302J ILE 3.6 5.4 - - - +
303J LYS 3.3 2.0 + - - -
304J HIS* 1.3 74.1 - - - +
306J LYS* 1.3 54.0 + - + +
308J ILE* 2.8 11.3 + - - +
309J ASN* 2.7 38.9 + - - -
332J LEU* 3.4 42.8 - - + -
360J PHE* 4.8 8.3 - - + -
410J VAL* 4.9 2.9 - - + -
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Residues in contact with LYS 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303J LYS 5.1 0.8 + - - -
304J HIS 3.4 0.8 - - - -
305J ALA* 1.3 77.5 - - + +
307J ALA* 1.3 61.8 + - - +
309J ASN* 3.2 24.0 - - - +
332J LEU* 5.7 0.4 - - + -
409J GLN* 2.9 32.0 + - - +
410J VAL 3.8 7.7 + - - -
411J ALA* 3.8 14.4 - - + +
412J GLY 4.9 0.2 - - - +
416J GLU* 3.3 32.2 + - + +
417J ALA* 3.2 15.8 - - - +
420J ALA* 3.6 20.4 - - + -
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Residues in contact with ALA 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304J HIS 2.9 9.8 + - - +
306J LYS* 1.3 74.8 - - - +
308J ILE* 1.3 68.3 + - - +
310J ALA* 3.1 20.3 + - - +
311J LEU* 3.9 3.1 + - - +
420J ALA* 3.9 5.9 - - + +
421J LEU* 3.7 40.4 - - + +
424J ASP* 4.0 17.9 + - + +
427J PHE* 4.2 16.2 - - + -
428J LEU* 5.9 0.7 - - - -
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Residues in contact with ILE 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301J VAL* 3.7 27.6 - - + +
304J HIS* 2.8 20.2 + - + +
305J ALA* 2.8 7.7 + - - +
307J ALA* 1.3 77.8 - - - +
309J ASN* 1.3 63.2 + - - +
311J LEU* 2.8 14.6 + - - +
312J ALA* 2.9 17.5 + - + +
360J PHE* 4.5 9.9 - - + -
370J CYS 4.7 0.7 - - - +
373J ALA* 3.9 28.5 - - + +
374J LEU* 3.3 37.7 - - + -
377J ALA* 3.6 25.6 - - + -
427J PHE* 4.5 3.8 - - + -
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Residues in contact with ASN 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305J ALA 2.7 14.4 + - - -
306J LYS* 3.2 16.4 + - - +
307J ALA 3.1 0.2 - - - -
308J ILE* 1.3 72.0 - - - +
310J ALA* 1.3 60.8 + - - +
311J LEU 2.8 0.5 + - - -
312J ALA 3.0 0.3 + - - -
313J ASN* 2.6 57.2 + - - +
319J TYR* 3.8 10.1 - - - +
322J LEU* 5.1 0.6 - - - +
360J PHE* 3.2 24.0 - - - +
410J VAL* 3.4 13.5 - - - +
411J ALA* 2.6 35.0 + - - +
417J ALA* 3.6 12.1 - - + -
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Residues in contact with ALA 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306J LYS 3.5 1.6 + - - -
307J ALA 3.1 10.6 + - - +
309J ASN* 1.3 77.4 - - - +
311J LEU* 1.3 60.3 + - + +
313J ASN 4.4 2.9 - - - -
314J PRO* 3.8 9.8 - - - +
414J LEU* 5.1 1.8 - - - -
417J ALA* 3.3 34.4 - - - +
418J LEU* 4.0 14.6 - - + +
421J LEU* 3.9 22.0 - - + -
442J TYR* 2.8 23.6 + - - -
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Residues in contact with LEU 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307J ALA 4.6 4.7 - - - +
308J ILE 2.8 15.9 + - - +
310J ALA* 1.3 82.9 - - + +
312J ALA* 1.3 58.1 + - - +
313J ASN 3.4 0.9 - - - -
314J PRO* 3.3 9.9 - - - +
365J ALA* 3.3 17.5 - - - +
366J ASN* 3.7 5.9 + - - +
369J LEU* 3.0 38.6 - - + +
370J CYS* 3.8 15.4 + - - +
373J ALA* 3.6 18.2 - - + -
421J LEU* 4.5 12.8 - - + -
428J LEU* 5.6 3.6 - - + -
434J PHE* 4.1 16.8 - - + -
442J TYR* 3.6 34.2 + - + -
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Residues in contact with ALA 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308J ILE* 2.9 15.2 + - + +
311J LEU* 1.3 76.0 - - - +
313J ASN* 1.3 78.0 + - - +
314J PRO* 3.7 3.8 - - - -
360J PHE* 4.5 4.0 - - + -
361J PRO* 3.5 18.8 - - + -
362J ASP* 2.9 22.9 + - - +
365J ALA* 3.5 10.1 - - - +
370J CYS* 3.1 24.5 - - - -
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Residues in contact with ASN 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J ASN* 2.6 44.0 + - - +
312J ALA* 1.3 99.7 + - - +
314J PRO* 1.4 60.0 - - - +
315J THR 3.2 9.3 + - - -
318J SER* 3.5 15.9 - - - -
319J TYR* 2.9 34.5 + - + +
321J ARG* 4.1 0.2 + - - -
322J LEU* 3.8 14.8 - - + +
360J PHE* 2.9 27.9 + - - +
362J ASP* 3.3 13.2 - - - +
414J LEU* 3.6 2.3 - - - +
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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