Contacts of the helix formed by residues 304 - 313 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300K GLY* 2.8 23.3 + - - +
301K VAL 3.6 1.3 - - - -
303K LYS* 1.3 98.8 - - + +
305K ALA* 1.3 65.3 + - - +
306K LYS 3.4 1.6 - - - -
307K ALA* 2.9 7.7 + - - +
308K ILE* 2.8 21.6 + - + -
377K ALA* 3.4 32.1 - - + -
380K ASP* 3.0 30.3 + - - -
424K ASP* 2.8 37.1 + - - +
427K PHE* 3.5 32.8 - + + -
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Residues in contact with ALA 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K VAL 2.8 15.9 + - - +
302K ILE 3.6 5.8 - - - +
303K LYS 3.3 2.4 - - - +
304K HIS* 1.3 75.0 - - - +
306K LYS* 1.3 55.7 + - + +
308K ILE* 2.8 11.3 + - - +
309K ASN* 2.7 38.6 + - - -
332K LEU* 3.4 42.2 - - + -
360K PHE* 4.8 8.5 - - + -
410K VAL* 4.9 2.9 - - + -
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Residues in contact with LYS 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303K LYS 5.1 0.8 + - - -
304K HIS 3.4 0.8 - - - -
305K ALA* 1.3 78.5 - - + +
307K ALA* 1.3 62.4 + - - +
309K ASN* 3.2 24.0 - - - +
332K LEU* 5.7 0.7 - - + -
409K GLN* 2.9 31.6 + - - +
410K VAL 3.8 8.3 + - - -
411K ALA* 3.8 14.8 - - + +
412K GLY 4.9 0.2 - - - +
416K GLU* 3.3 32.3 + - + +
417K ALA* 3.2 15.9 - - - +
420K ALA* 3.6 20.2 - - + -
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Residues in contact with ALA 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304K HIS 2.9 9.6 + - - +
306K LYS* 1.3 75.2 - - - +
308K ILE* 1.3 67.1 + - - +
310K ALA* 3.1 20.6 + - - +
311K LEU* 3.9 2.9 + - - +
420K ALA* 3.9 5.0 - - - +
421K LEU* 3.7 40.8 - - + +
424K ASP* 4.0 18.6 + - + +
427K PHE* 4.2 16.4 - - + -
428K LEU* 5.9 0.4 - - - -
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Residues in contact with ILE 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K VAL* 3.7 27.1 - - + +
304K HIS* 2.8 22.0 + - + +
305K ALA* 2.8 6.8 + - - +
307K ALA* 1.3 77.2 - - - +
309K ASN* 1.3 62.6 + - - +
311K LEU* 2.8 14.6 + - - +
312K ALA* 2.9 18.2 + - + +
360K PHE* 4.5 10.1 - - + -
370K CYS 4.7 1.3 - - - +
373K ALA* 3.9 28.0 - - + +
374K LEU* 3.3 37.7 - - + -
377K ALA* 3.6 25.8 - - + -
427K PHE* 4.5 4.0 - - + -
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Residues in contact with ASN 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305K ALA 2.7 15.0 + - - +
306K LYS* 3.2 15.7 + - - +
307K ALA 3.1 0.2 - - - -
308K ILE* 1.3 71.1 - - - +
310K ALA* 1.3 59.4 + - - +
311K LEU 2.8 0.3 + - - -
312K ALA 3.0 0.2 + - - -
313K ASN* 2.6 59.1 + - - +
319K TYR* 3.8 9.0 - - - +
322K LEU* 5.1 0.4 - - - +
360K PHE* 3.2 23.4 - - - +
410K VAL* 3.4 14.1 - - - +
411K ALA* 2.6 34.9 + - - +
417K ALA* 3.6 12.1 - - + -
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Residues in contact with ALA 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306K LYS 3.5 1.8 + - - -
307K ALA 3.1 11.2 + - - +
309K ASN* 1.3 76.7 - - - +
311K LEU* 1.3 59.8 + - + +
313K ASN 4.4 2.9 - - - -
314K PRO* 3.8 9.8 - - - +
414K LEU* 5.1 2.0 - - - -
417K ALA* 3.3 32.2 - - - +
418K LEU* 4.0 14.4 - - + +
421K LEU* 3.9 22.0 - - + -
442K TYR* 2.8 23.2 + - - -
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Residues in contact with LEU 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K ALA 4.6 4.9 - - - +
308K ILE 2.8 14.9 + - - +
309K ASN 2.8 0.2 + - - -
310K ALA* 1.3 83.1 - - + +
312K ALA* 1.3 57.7 + - - +
313K ASN 3.4 0.7 - - - -
314K PRO* 3.3 10.3 - - - +
365K ALA* 3.3 17.3 - - - +
366K ASN* 3.7 6.1 + - - +
369K LEU* 3.0 38.4 - - + +
370K CYS* 3.8 15.5 - - - +
373K ALA* 3.6 18.4 - - + -
421K LEU* 4.5 13.5 - - + -
428K LEU* 5.6 3.1 - - + -
434K PHE* 4.1 17.0 - - + -
442K TYR* 3.6 34.9 + - + -
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Residues in contact with ALA 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308K ILE* 2.9 15.0 + - + +
311K LEU* 1.3 75.3 - - - +
313K ASN* 1.3 78.9 + - - +
314K PRO* 3.7 3.1 - - - -
360K PHE* 4.5 3.8 - - + -
361K PRO* 3.5 19.1 - - + -
362K ASP* 2.9 22.7 + - - +
365K ALA* 3.5 11.6 - - - +
370K CYS* 3.1 23.3 - - - -
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Residues in contact with ASN 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309K ASN* 2.6 43.2 + - - +
312K ALA* 1.3 98.9 + - - +
314K PRO* 1.4 61.0 - - - +
315K THR 3.2 9.2 + - - -
318K SER* 3.5 15.7 - - - -
319K TYR* 2.9 35.3 + - + +
321K ARG* 4.1 0.2 + - - -
322K LEU* 3.8 14.5 - - - +
360K PHE* 2.9 28.3 + - - +
362K ASP* 3.3 12.4 - - - +
414K 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