Contacts of the helix formed by residues 304 - 313 (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 HIS 304 (chain C).
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Specific contacts
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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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Residues in contact with LYS 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C LYS 5.1 0.8 + - - -
304C HIS 3.2 1.0 + - - -
305C ALA* 1.3 78.1 - - + +
307C ALA* 1.3 61.7 + - - +
309C ASN* 3.2 23.8 - - - +
310C ALA 3.6 0.2 + - - -
332C LEU* 5.7 0.4 - - + -
409C GLN* 2.9 31.4 + - - +
410C VAL 3.8 7.7 + - - -
411C ALA* 3.8 15.0 - - + +
416C GLU* 3.3 32.0 + - + +
417C ALA* 3.2 15.6 - - - +
420C ALA* 3.6 20.6 - - + -
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Residues in contact with ALA 307 (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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304C HIS 2.9 10.4 + - - +
306C LYS* 1.3 75.4 - - - +
308C ILE* 1.3 67.1 + - - +
310C ALA* 3.1 20.8 + - - +
311C LEU* 3.9 2.9 + - - +
420C ALA* 3.9 5.0 - - - +
421C LEU* 3.7 41.2 - - + +
424C ASP* 4.0 17.9 - - + +
427C PHE* 4.2 17.0 - - + -
428C LEU* 5.9 0.7 - - - -
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Residues in contact with ILE 308 (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* 3.7 27.6 - - + +
304C HIS* 2.8 21.7 + - + +
305C ALA* 2.8 7.0 + - - +
307C ALA* 1.3 76.9 - - - +
309C ASN* 1.3 62.8 + - - +
311C LEU* 2.8 14.6 + - - +
312C ALA* 2.9 17.6 + - + -
360C PHE* 4.5 10.3 - - + -
370C CYS 4.7 1.3 - - - +
373C ALA* 3.9 26.7 - - + +
374C LEU* 3.3 37.0 - - + -
377C ALA* 3.6 26.2 - - + -
427C PHE* 4.5 4.0 - - + -
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Residues in contact with ASN 309 (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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305C ALA 2.7 15.5 + - - +
306C LYS* 3.2 15.5 - - - +
308C ILE* 1.3 70.2 - - - +
310C ALA* 1.3 59.9 + - - +
311C LEU 2.8 0.5 + - - -
312C ALA 3.0 0.2 + - - -
313C ASN* 2.6 58.1 + - - +
319C TYR* 3.8 9.6 - - - +
322C LEU* 5.1 1.2 - - - +
360C PHE* 3.2 23.4 - - - -
410C VAL* 3.4 14.3 - - - +
411C ALA* 2.6 34.5 + - - +
417C ALA* 3.6 11.7 - - + -
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Residues in contact with ALA 310 (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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306C LYS 3.6 1.6 + - - -
307C ALA 3.1 11.0 + - - +
309C ASN* 1.3 77.8 - - - +
311C LEU* 1.3 58.9 + - + +
313C ASN 4.4 3.8 - - - -
314C PRO* 3.8 9.4 - - - +
414C LEU* 5.1 1.8 - - - -
417C ALA* 3.3 32.0 - - - +
418C LEU* 4.0 14.0 - - + +
421C LEU* 3.9 22.2 - - + -
442C TYR* 2.8 24.0 + - + -
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Residues in contact with LEU 311 (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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307C ALA 4.6 4.9 - - - +
308C ILE 2.8 15.5 + - - +
310C ALA* 1.3 83.1 - - + +
312C ALA* 1.3 56.7 + - - +
313C ASN 3.4 0.9 - - - -
314C PRO* 3.3 10.6 - - - +
365C ALA* 3.3 17.2 - - - +
366C ASN* 3.7 6.1 + - - +
369C LEU* 3.0 39.3 - - + +
370C CYS* 3.8 14.6 + - - +
373C ALA* 3.6 18.6 - - + -
421C LEU* 4.5 12.3 - - + -
428C LEU* 5.6 3.4 - - + -
434C PHE* 4.1 16.8 - - + -
442C TYR* 3.6 33.8 + - + -
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Residues in contact with ALA 312 (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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308C ILE* 2.9 15.6 + - + +
311C LEU* 1.3 75.9 - - - +
313C ASN* 1.3 76.9 + - - +
314C PRO* 3.7 3.8 - - - -
360C PHE* 4.5 3.6 - - + -
361C PRO* 3.5 18.2 - - + -
362C ASP* 2.9 23.0 + - - +
365C ALA* 3.5 10.5 - - - +
370C CYS* 3.1 24.2 - - - -
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Residues in contact with ASN 313 (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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309C ASN* 2.6 42.3 + - - +
312C ALA* 1.3 99.9 + - - +
314C PRO* 1.4 60.9 - - - +
315C THR 3.2 9.6 + - - -
318C SER* 3.5 16.6 - - - -
319C TYR* 2.9 34.3 + - + +
321C ARG* 4.1 0.2 + - - -
322C LEU* 3.8 14.2 - - - +
360C PHE* 2.9 28.0 - - - +
362C ASP* 3.3 11.8 - - - +
414C LEU* 3.6 2.4 - - - +
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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