Contacts of the helix formed by residues 314 - 321 (chain D) in PDB entry 5DO7
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 TYR 314 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C HIS* 5.0 4.9 - - + +
104D ILE* 3.2 45.9 - - + +
272D PRO* 5.0 1.3 - - + -
277D PHE* 3.6 47.1 - + + +
283D VAL* 4.1 6.7 - - + +
285D LEU* 2.8 48.4 - - + +
300D MET* 3.1 35.5 - - + +
301D VAL* 6.2 1.8 - - + -
309D TYR* 4.2 22.0 - + + -
313D ARG* 1.3 70.1 - - - +
315D SER* 1.3 65.5 + - - +
316D ASN 3.2 1.6 - - - -
317D PRO* 3.2 12.6 - - + +
318D ALA* 4.6 2.4 + - + +
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Residues in contact with SER 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ARG* 3.6 6.8 + - - -
254C SER* 3.7 2.2 + - - -
255C GLU* 2.7 28.2 + - - +
271D GLN* 5.5 2.8 - - - +
272D PRO* 4.7 12.5 - - - +
313D ARG* 2.6 51.3 + - - +
314D TYR* 1.3 78.6 - - - +
316D ASN* 1.3 66.9 + - - +
317D PRO 3.3 0.7 - - - -
318D ALA* 3.4 18.4 + - - +
319D ASP* 4.0 1.2 + - - +
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Residues in contact with ASN 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C SER* 4.4 4.0 + - - +
255C GLU* 4.2 12.8 - - + +
309D TYR* 4.5 2.6 - - - -
310D PRO* 3.7 33.2 - - + +
312D PRO* 5.1 5.8 - - + +
313D ARG 3.2 17.6 + - - +
314D TYR 3.2 0.4 - - - -
315D SER* 1.3 79.7 - - - +
317D PRO* 1.3 89.8 - - + +
319D ASP* 3.0 33.1 + - - +
320D PHE* 3.3 7.5 + - - +
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Residues in contact with PRO 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LEU* 4.5 9.2 - - + -
304D PHE* 4.8 0.4 - - + -
309D TYR* 2.5 44.2 - - + +
313D ARG 4.0 2.0 - - - +
314D TYR* 3.2 21.8 - - + +
316D ASN* 1.3 99.3 - - + +
318D ALA* 1.3 65.8 + - - +
320D PHE* 2.8 10.7 + - + -
321D TYR* 2.8 46.8 + - + -
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Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C CYS* 5.4 10.9 - - - -
104D ILE* 4.5 6.7 - - + +
105D GLY 5.6 0.4 - - - -
106D SER* 5.1 10.6 - - - +
270D HIS 6.1 1.3 - - - +
285D LEU* 3.6 34.3 - - + +
287D THR* 3.4 20.3 + - - +
314D TYR* 4.6 4.4 + - + +
315D SER* 3.4 12.9 + - - +
316D ASN 3.3 0.2 + - - -
317D PRO* 1.3 78.1 - - - +
319D ASP* 1.3 59.5 + - - +
322D VAL* 3.5 10.0 + - - +
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Residues in contact with ASP 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C CYS* 4.5 18.8 - - + -
229C ASN* 5.2 1.5 + - - +
253C ARG* 4.9 1.6 - - - +
255C GLU* 2.9 43.2 - - - +
315D SER 4.0 0.8 + - - -
316D ASN* 3.0 17.0 + - - +
318D ALA* 1.3 74.0 - - - +
320D PHE* 1.3 90.9 + - - +
321D TYR 3.1 1.6 - - - -
322D VAL* 2.8 35.3 + - + +
324D LEU* 5.9 0.5 - - - +
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Residues in contact with PHE 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D ILE* 3.7 39.5 - - + -
308D GLY 6.0 0.2 - - - -
309D TYR* 6.2 1.8 - + - -
316D ASN* 3.3 8.4 + - - +
317D PRO* 2.8 24.1 + - + +
319D ASP* 1.3 84.6 + - - +
321D TYR* 1.3 74.2 + + + +
322D VAL 3.6 6.1 + - - +
333D GLU* 4.7 5.7 - - - +
336D LEU* 4.3 2.9 - - - +
339D ARG* 3.9 26.6 + - - -
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Residues in contact with TYR 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LEU* 5.0 0.7 - - + -
287D THR* 2.9 33.2 + - - +
292D ILE* 3.5 35.5 - - + +
304D PHE* 3.2 39.0 - + - -
307D ILE* 3.7 17.2 - - + +
309D TYR* 6.0 0.2 - + - -
317D PRO* 2.8 37.6 + - + +
318D ALA* 5.2 0.2 - - - -
320D PHE* 1.3 89.9 - + - +
322D VAL* 1.3 58.0 + - - -
323D ASP* 4.0 2.4 - - - +
336D LEU* 3.6 19.2 - - + +
339D ARG* 2.8 53.0 + - + -
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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