Contacts of the helix formed by residues 274 - 286 (chain A) in PDB entry 1P84
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 ASN 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A GLU* 3.5 26.4 - - - +
272A SER* 3.0 3.3 + - - -
273A PRO* 1.3 90.1 + - - +
275A TYR* 1.3 64.1 + - - +
276A PHE 3.0 5.0 + - - -
277A VAL* 3.2 26.4 + - + +
278A ALA* 3.1 22.3 + - - +
417A ASP* 5.4 2.0 + - - +
421A TRP* 3.8 21.6 - - + +
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Residues in contact with TYR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 4.5 10.0 - - - +
269A PRO 4.2 2.0 - - - +
270A VAL* 4.1 24.1 - - + +
271A ASN 4.7 2.2 - - - +
272A SER* 3.1 24.7 + - - +
273A PRO 3.6 0.6 - - - -
274A ASN* 1.3 77.9 - - - +
276A PHE* 1.3 94.2 + + + +
278A ALA* 4.0 2.4 - - - +
279A LYS* 3.4 54.9 + - + +
319A SER* 4.9 0.9 + - - -
321A SER* 3.7 35.2 - - - -
374A LEU* 5.8 3.4 - - + +
378A TYR* 5.0 7.8 + - - -
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PRO 5.2 0.8 + - - +
274A ASN* 3.0 0.8 - - - +
275A TYR* 1.3 106.6 - + + +
277A VAL* 1.3 60.8 + - + +
278A ALA 3.1 1.3 - - - -
279A LYS* 3.2 6.3 + - + +
280A LEU* 2.8 32.1 + - - +
370A LEU* 4.4 6.4 - - + +
374A LEU* 3.9 24.5 - - + -
401A LEU* 4.1 15.0 - - + -
406A ALA* 4.1 20.6 - - + -
409A LYS* 4.1 34.3 - - + -
410A ILE* 3.8 21.5 - - + -
413A ILE* 4.1 15.6 - - + +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PRO 4.8 2.9 - - - +
274A ASN* 3.2 33.4 + - + +
276A PHE* 1.3 75.1 - - + +
278A ALA* 1.3 53.6 + - - +
280A LEU* 3.1 5.7 + - - +
281A ALA* 2.8 33.1 + - - +
413A ILE* 4.1 21.0 - - + +
417A ASP* 4.0 15.3 - - + +
418A VAL* 3.9 30.1 - - + +
421A TRP* 3.8 26.7 - - + -
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLU* 4.0 11.7 - - + +
274A ASN 3.1 13.9 + - - +
275A TYR 4.0 3.4 - - - +
277A VAL* 1.3 79.2 - - - +
279A LYS* 1.3 62.6 + - - +
281A ALA 3.0 11.3 + - - -
282A ALA* 3.1 10.7 + - - +
319A SER* 3.4 18.8 - - - +
328A TRP* 3.2 9.5 + - + -
421A TRP* 3.5 36.9 - - + +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR* 3.4 54.2 + - + +
276A PHE* 3.2 10.2 + - + +
278A ALA* 1.3 79.6 - - - +
280A LEU* 1.3 60.5 + - - +
282A ALA* 3.7 5.1 + - + +
283A GLN* 3.5 19.8 + - - +
319A SER* 3.6 36.5 + - - +
321A SER* 5.2 1.1 - - - +
370A LEU* 4.1 20.7 - - + +
373A GLN* 5.2 13.1 + - - +
374A LEU* 5.2 15.8 - - + +
377A LEU* 6.2 2.0 - - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A PHE 2.8 16.6 + - - +
277A VAL 3.4 4.0 - - - +
279A LYS* 1.3 75.6 - - - +
281A ALA* 1.3 62.7 + - - +
283A GLN* 2.9 23.8 + - - +
284A ILE* 3.2 18.3 + - + +
363A VAL* 4.3 12.3 - - + +
366A ALA* 3.8 15.0 - - + -
367A LYS* 3.7 39.0 - - + +
370A LEU* 4.1 11.8 - - + +
410A ILE* 4.5 5.2 - - + -
413A ILE* 3.9 24.7 - - + -
418A VAL* 3.9 27.1 - - + -
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL 2.8 13.6 + - - +
278A ALA 3.0 8.7 + - - +
280A LEU* 1.3 77.9 - - - +
282A ALA* 1.3 58.6 + - - +
284A ILE* 3.5 26.4 - - - +
285A PHE* 3.6 14.9 - - - -
328A TRP* 3.7 5.6 - - - +
354A LEU* 3.9 11.8 - - + +
418A VAL* 4.9 6.5 - - + -
421A TRP* 3.5 31.6 - - + -
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ALA 3.1 7.6 + - - +
279A LYS 3.9 9.4 - - - +
280A LEU 3.1 0.4 - - - -
281A ALA* 1.3 74.6 - - - +
283A GLN* 1.3 53.5 + - - +
285A PHE 3.4 1.7 + - - -
286A GLY* 2.8 31.2 + - - -
317A HIS* 3.5 13.5 - - + +
318A PHE* 4.0 33.0 - - - +
319A SER* 4.4 2.7 - - - +
328A TRP* 3.6 21.9 - - + +
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LYS 3.5 9.5 + - - +
280A LEU* 2.9 15.1 + - - +
282A ALA* 1.3 78.9 - - - +
284A ILE* 1.3 63.1 + - - +
286A GLY* 3.1 18.0 + - - +
365A ARG* 3.3 17.3 + - - -
366A ALA* 3.8 27.1 - - + +
369A LEU* 3.5 32.9 - - + +
370A LEU* 3.9 7.8 - - + +
373A GLN* 3.1 38.3 - - - +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LEU* 3.2 21.6 + - + +
281A ALA* 3.5 16.8 - - - +
282A ALA 3.2 0.4 - - - -
283A GLN* 1.3 77.4 - - - +
285A PHE* 1.3 80.5 + - + +
299A GLY 5.0 1.0 - - - +
300A ILE* 3.8 14.9 - - - +
354A LEU* 3.8 24.0 - - + -
358A VAL* 4.0 15.0 - - + -
362A GLU* 4.1 34.5 - - + +
363A VAL* 4.8 2.2 - - + -
365A ARG* 3.8 13.5 + - - +
366A ALA* 3.9 17.0 - - + -
418A VAL* 4.8 4.5 - - + -
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Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ALA 3.6 12.3 - - - -
282A ALA 3.4 1.8 + - - -
283A GLN 3.2 0.2 - - - -
284A ILE* 1.3 89.5 - - + +
286A GLY* 1.3 65.7 + - - +
300A ILE* 3.4 32.4 - - + +
302A LEU* 5.1 5.4 - - + -
315A PHE* 3.4 12.8 - - + -
317A HIS* 3.2 33.0 - + + +
328A TRP* 4.1 4.3 - + - -
350A GLN* 3.7 50.3 - - + -
351A TRP* 3.6 23.6 - + - -
353A ARG* 5.2 3.6 - - - -
354A LEU* 3.6 40.6 - - + -
362A GLU* 5.8 0.4 - - - -
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ALA 2.8 17.1 + - - -
283A GLN* 3.1 19.9 + - - -
285A PHE* 1.3 78.3 - - - +
287A SER* 1.3 59.8 + - - -
298A GLN* 5.8 0.2 - - - -
300A ILE* 4.9 2.5 - - - -
315A PHE* 3.8 0.3 - - - -
316A ASN* 3.6 0.3 - - - -
317A HIS* 2.9 36.6 + - - -
365A ARG* 5.2 1.6 - - - -
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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