Contacts of the helix formed by residues 271 - 277 (chain D) in PDB entry 5D0A
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 LEU 271 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D GLU* 3.8 39.0 - - + +
92D ARG 3.6 9.4 - - - +
93D ARG* 3.6 43.8 - - + +
266D GLU* 4.8 4.4 + - - +
269D LYS 4.0 0.6 + - - -
270D PRO* 1.3 74.7 - - - +
272D LEU* 1.3 66.6 + - - +
274D PRO* 3.6 30.8 - - + +
275D LEU* 3.6 14.9 + - - +
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Residues in contact with LEU 272 (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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92D ARG* 3.0 31.8 + - + +
93D ARG 4.0 5.6 - - - +
94D GLY* 3.3 29.8 - - - +
237D LEU* 4.0 22.2 - - + -
270D PRO 4.5 0.4 - - - +
271D LEU* 1.3 71.4 - - - +
273D LYS* 1.3 62.1 + - + +
275D LEU* 2.8 29.5 + - - +
276D LEU* 3.6 6.2 + - - +
304D ALA* 4.1 12.1 - - + +
307D ALA* 3.8 23.3 - - + -
308D LEU* 3.7 35.2 - - + -
311D PHE* 3.9 10.3 - - + -
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Residues in contact with LYS 273 (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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90D THR* 4.2 15.7 + - - -
91D GLU* 4.9 6.0 + - - -
92D ARG* 4.9 3.1 + - + +
271D LEU* 4.9 0.2 - - - +
272D LEU* 1.3 75.0 - - + +
274D PRO* 1.3 69.0 - - + +
276D LEU* 3.1 30.2 + - + +
277D ALA* 4.1 3.8 + - - +
308D LEU* 4.3 9.4 - - + -
313D ASP* 3.9 19.7 - - - +
315D SER* 2.7 36.0 + - - +
316D ALA* 4.1 18.6 - - + -
319D GLU* 5.2 5.0 - - + +
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Residues in contact with PRO 274 (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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271D LEU* 3.6 36.8 - - + +
272D LEU 3.6 3.4 - - - -
273D LYS* 1.3 94.5 - - + +
275D LEU* 1.3 61.6 + - + +
277D ALA* 3.4 13.7 + - + +
278D ILE* 3.4 13.7 + - - +
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Residues in contact with LEU 275 (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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237D LEU* 3.7 29.4 - - + -
270D PRO* 4.0 10.3 - - + -
271D LEU 3.6 16.8 - - - +
272D LEU* 2.8 12.9 + - - +
274D PRO* 1.3 74.8 - - + +
276D LEU* 1.3 61.1 + - - +
277D ALA 3.1 2.8 + - - -
278D ILE* 3.5 19.9 - - + +
283D PHE* 5.6 2.0 - - + -
287D PHE* 3.8 31.2 - - + -
300D ILE* 4.2 17.9 - - + -
301D GLN* 2.8 33.8 + - + +
304D ALA* 4.1 17.9 - - + -
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Residues in contact with LEU 276 (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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272D LEU 4.0 6.7 - - - +
273D LYS* 3.1 19.2 + - + +
275D LEU* 1.3 78.5 - - - +
277D ALA* 1.3 55.6 - - - +
301D GLN* 3.5 17.8 + - + +
304D ALA* 4.6 3.4 - - + -
305D ILE* 3.6 35.9 - - + +
308D LEU* 3.5 31.6 - - + -
316D ALA* 4.7 3.8 - - + -
319D GLU* 3.6 32.5 - - + +
320D LEU* 4.0 11.4 - - + -
323D LEU* 3.7 35.2 - - + +
327D ASP* 5.6 0.2 - - - +
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Residues in contact with ALA 277 (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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273D LYS 4.1 3.6 + - - +
274D PRO* 3.4 8.9 + - + +
275D LEU 3.1 0.4 - - - -
276D LEU* 1.3 79.8 - - - +
278D ILE* 1.3 63.6 + - - +
279D SER* 3.4 2.9 + - - -
282D GLU* 5.3 0.7 - - - +
301D GLN* 4.7 0.2 - - - -
319D GLU* 4.1 14.8 - - - +
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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