Contacts of the helix formed by residues 274 - 287 (chain A) in PDB entry 3PU8
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 ALA 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A EDO 3.7 9.2 - - - +
272A ARG* 2.7 9.8 + - + +
273A PRO* 1.3 73.2 - - - +
275A SER* 1.3 69.4 + - - +
276A ALA* 3.2 2.9 - - + +
277A ASN* 2.8 28.2 + - - +
278A ILE* 3.1 9.9 + - - +
419B GLU* 3.6 44.2 - - + +
420B ASP* 3.6 5.8 - - - -
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Residues in contact with SER 275 (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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273A PRO 3.6 0.8 + - - -
274A ALA* 1.3 72.1 - - - +
276A ALA* 1.3 62.6 + - - +
278A ILE* 3.3 2.0 + - - -
279A SER* 3.2 20.8 + - - -
347A ARG* 3.5 14.7 + - - +
455A SO4 3.3 24.2 + - - -
228B LEU* 3.8 21.4 - - - +
420B ASP* 2.8 29.7 + - - -
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Residues in contact with ALA 276 (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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274A ALA* 3.2 3.0 - - + +
275A SER* 1.3 78.1 - - - +
277A ASN* 1.3 60.9 + - - +
279A SER* 3.4 8.5 + - - -
280A LEU* 2.9 33.5 + - - +
227B LEU* 4.3 3.0 - - + +
228B LEU* 4.2 11.9 - - + +
420B ASP 5.0 1.4 + - - -
422B LEU 3.6 23.3 - - - +
424B GLU* 3.7 31.9 - - + +
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Residues in contact with ASN 277 (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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271A ILE* 3.6 12.4 - - + +
272A ARG 3.0 26.0 + - - +
274A ALA* 2.8 21.4 + - - +
276A ALA* 1.3 72.2 - - - +
278A ILE* 1.3 58.4 + - - +
280A LEU* 3.3 11.6 + - - +
281A TYR* 2.8 30.1 + - - +
295A PHE* 3.8 3.3 - - - -
299A VAL* 3.5 29.6 - - + +
300A ASP 5.0 1.8 + - - +
301A LYS 5.4 2.2 + - - +
320A ILE* 4.0 10.3 - - + -
419B GLU* 3.7 20.0 + - - -
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Residues in contact with ILE 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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250A ILE* 4.8 14.6 - - + -
273A PRO* 3.5 27.4 - - + +
274A ALA 3.1 9.2 + - - +
275A SER 3.6 5.6 - - - +
277A ASN* 1.3 76.4 - - - +
279A SER* 1.3 57.0 + - - +
281A TYR* 3.2 7.6 + - + +
282A GLU* 2.9 27.9 + - + +
318A GLY 5.3 0.2 - - - +
320A ILE* 4.4 6.1 - - + -
344A MET* 3.7 15.0 - - - -
347A ARG* 3.6 29.6 - - + +
348A ALA* 6.2 0.7 - - - -
351A VAL* 4.0 15.5 - - + -
455A SO4 3.5 31.2 - - - +
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Residues in contact with SER 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 SER* 3.2 8.5 + - - -
276A ALA* 3.7 7.6 - - - -
278A ILE* 1.3 78.9 - - - +
280A LEU* 1.3 60.7 + - - +
282A GLU* 3.3 9.2 + - - +
283A ARG* 3.1 30.2 + - - +
347A ARG* 3.3 17.9 + - - +
227B LEU* 4.0 35.1 + - - +
228B LEU* 6.1 0.3 - - - +
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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 ALA 2.9 22.9 + - - +
277A ASN* 3.6 16.8 - - - +
279A SER* 1.3 74.6 - - - +
281A TYR* 1.3 58.8 + - - +
283A ARG* 3.3 10.3 + - + +
284A TRP* 2.9 30.3 + - - +
295A PHE* 3.6 12.5 - - + -
298A GLN* 3.6 37.5 - - + +
299A VAL* 4.6 1.8 - - + -
227B LEU* 3.7 20.4 - - + -
424B GLU* 3.9 17.9 - - + -
425B HIS* 4.0 25.6 - - + +
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Residues in contact with TYR 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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248A PHE 3.9 8.3 - - - -
249A HIS* 3.4 25.4 - - - +
250A ILE* 3.2 48.5 + - + +
277A ASN 2.8 17.5 + - - +
278A ILE* 3.2 7.4 + - + +
280A LEU* 1.3 77.6 - - - +
282A GLU* 1.3 60.1 + - - +
284A TRP* 3.2 18.4 + + - +
285A ARG* 2.8 46.2 + - + +
295A PHE* 3.5 15.4 - + + -
320A ILE* 4.0 24.0 - - + -
351A VAL* 4.5 17.0 - - + -
355A LEU* 4.6 8.2 - - + +
357A LEU* 5.6 2.1 - - - +
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Residues in contact with GLU 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 ILE 2.9 15.6 + - - +
279A SER* 3.7 7.1 - - - +
281A TYR* 1.3 81.8 - - - +
283A ARG* 1.3 65.3 + - + +
285A ARG* 3.4 0.8 + - - -
286A SER* 3.1 25.2 + - - +
347A ARG* 4.4 3.8 + - - -
351A VAL* 3.5 27.3 - - + +
354A ARG* 2.8 57.8 + - - +
355A LEU* 3.7 14.0 - - + +
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Residues in contact with ARG 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 SER* 3.1 17.8 + - - +
280A LEU* 3.8 8.8 - - + +
282A GLU* 1.3 76.9 - - + +
284A TRP* 1.3 66.5 + - - +
286A SER* 3.1 17.2 + - - -
287A ALA* 3.5 9.7 + - - +
227B LEU* 3.9 35.6 - - - +
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Residues in contact with TRP 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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247A ASP* 3.6 33.7 - - + -
248A PHE* 3.3 35.9 - - + -
280A LEU 2.9 17.4 + - - +
281A TYR* 3.6 24.0 - + - +
283A ARG* 1.3 74.6 - - - +
285A ARG* 1.3 86.4 + - - +
287A ALA* 3.1 16.1 + - - +
290A HIS* 3.2 48.5 + + + +
293A MET* 3.1 46.6 + - + +
295A PHE* 3.7 28.4 - + + +
298A GLN* 4.0 17.0 + - - +
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Residues in contact with ARG 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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248A PHE 4.9 2.6 + - - -
249A HIS* 6.0 2.4 - - - +
281A TYR* 2.8 34.6 + - + +
282A GLU 4.0 3.8 - - - +
284A TRP* 1.3 99.0 - - + +
286A SER* 1.3 60.3 + - - +
287A ALA 3.5 0.5 + - - +
290A HIS* 3.0 46.7 + - - -
355A LEU* 3.9 27.3 - - + +
357A LEU* 3.9 37.2 - - + +
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Residues in contact with SER 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 GLU* 3.1 15.3 + - - +
283A ARG* 3.1 18.2 + - - -
285A ARG* 1.3 78.6 - - - +
287A ALA* 1.3 63.1 + - - +
288A SER* 3.4 3.1 + - - -
355A LEU* 3.8 15.2 - - - +
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Residues in contact with ALA 287 (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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283A ARG 3.5 7.4 + - - +
284A TRP* 3.1 13.0 + - - +
285A ARG 3.9 0.2 - - - +
286A SER* 1.3 80.1 + - - +
288A SER* 1.3 65.8 + - - +
289A ASN* 3.0 17.3 + - - +
290A HIS* 3.0 25.6 + - - +
293A MET* 3.8 15.0 - - + -
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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