Contacts of the helix formed by residues 270 - 281 (chain A) in PDB entry 4ORA
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A SER* 3.5 13.2 - - - +
248A PHE* 3.4 12.4 - - - -
251A GLU* 3.2 29.3 - - + +
253A SER 3.9 8.1 + - - -
254A GLN 4.2 1.8 - - - -
255A GLU 2.3 31.4 + - - +
256A HIS* 3.3 9.1 + - - +
269A TYR* 1.3 76.5 - - - +
271A TYR* 1.3 67.3 + - - +
272A PRO* 3.2 15.5 - - - +
273A ALA* 3.0 20.6 + - - +
274A VAL* 3.1 9.9 + - - +
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Residues in contact with TYR 271 (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* 3.4 19.6 - + + -
249A GLY* 3.6 11.2 - - - +
251A GLU* 3.0 17.4 + - - +
270A ASN* 1.3 76.4 - - - +
272A PRO* 1.3 74.3 - - + +
274A VAL* 3.1 3.1 + - - +
275A CYS* 2.9 47.4 + - - -
301A ARG* 3.4 58.4 + - + -
302A LYS 3.3 4.2 + - - -
303A SER* 3.2 24.1 - - - -
304A GLN* 3.8 7.7 + - + +
310A SER* 3.7 28.0 - - - -
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Residues in contact with PRO 272 (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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251A GLU* 3.8 11.9 - - + +
254A GLN* 4.7 12.6 - - + +
256A HIS* 3.9 21.3 - - + +
270A ASN* 3.2 20.6 - - - +
271A TYR* 1.3 98.2 - - + +
273A ALA* 1.3 62.3 + - - +
274A VAL 3.2 0.3 + - - -
275A CYS* 3.2 7.4 + - + +
276A GLU* 2.9 26.0 + - - +
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Residues in contact with ALA 273 (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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211A LEU* 3.9 5.2 - - + +
256A HIS* 3.5 45.2 + - + +
257A PHE* 4.2 16.6 - - + -
269A TYR* 4.3 4.9 - - + -
270A ASN* 3.0 16.7 + - - +
272A PRO* 1.3 78.1 - - - +
274A VAL* 1.3 59.5 + - - +
276A GLU* 3.8 2.9 + - - +
277A PHE* 3.2 23.4 + - - +
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Residues in contact with VAL 274 (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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211A LEU* 3.8 21.8 - - + -
248A PHE* 3.8 21.1 - - + -
269A TYR* 3.8 15.5 - - + -
270A ASN 3.1 10.9 + - - +
271A TYR 3.1 7.5 + - - +
273A ALA* 1.3 74.4 - - - +
275A CYS* 1.3 56.4 + - - +
277A PHE* 3.1 2.0 + - - +
278A LEU* 2.7 62.2 + - + +
286A ILE* 4.2 11.2 - - + -
310A SER* 3.9 24.2 - - - +
311A LEU* 4.9 2.5 - - + -
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Residues in contact with CYS 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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271A TYR* 2.9 62.6 + - - +
272A PRO* 3.7 6.5 - - + +
274A VAL* 1.3 76.0 - - - +
276A GLU* 1.3 63.2 + - - +
278A LEU* 3.2 7.3 + - - +
279A GLN* 2.9 46.0 + - - +
303A SER* 4.6 10.8 - - - -
310A SER* 5.4 2.5 - - - -
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Residues in contact with GLU 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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216A HIS* 4.9 13.0 - - - -
256A HIS* 3.1 27.7 + - + -
272A PRO 2.9 16.3 + - - +
273A ALA 3.8 4.9 - - - +
275A CYS* 1.3 77.5 - - - +
277A PHE* 1.3 58.2 + - - +
279A GLN* 3.2 7.2 + - - -
280A ASN* 2.9 57.7 + - - +
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Residues in contact with PHE 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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205A LEU* 3.9 29.8 - - + -
211A LEU* 4.0 28.9 - - + -
215A ILE* 3.5 36.1 - - + -
216A HIS* 3.6 24.9 - - - -
217A THR 4.2 3.1 - - - -
218A LEU* 4.2 12.6 - - + -
221A ILE* 5.0 0.4 - - + -
273A ALA 3.2 14.8 + - - +
274A VAL 3.1 4.1 + - - +
276A GLU* 1.3 81.5 - - + +
278A LEU* 1.3 65.3 + - + +
280A ASN* 4.8 2.0 - - - +
281A ASN* 2.9 42.2 + - - +
283A LEU* 4.0 15.5 - - + -
286A ILE* 4.3 9.2 - - + -
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Residues in contact with LEU 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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274A VAL* 2.7 40.9 + - + +
275A CYS* 3.7 6.7 - - - +
277A PHE* 1.3 74.7 - - + +
279A GLN* 1.3 59.3 + - + +
282A ASN* 3.1 7.6 + - - -
283A LEU* 2.9 49.0 + - + +
284A LEU 3.9 18.2 - - - +
285A SER* 3.8 16.8 - - - +
286A ILE* 3.6 30.5 - - + -
303A SER* 5.1 8.5 - - - +
310A SER* 3.9 18.8 - - - +
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Residues in contact with GLN 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 CYS* 2.9 38.5 + - - +
276A GLU* 3.9 5.7 + - - +
278A LEU* 1.3 76.0 - - + +
280A ASN* 1.3 62.5 + - - +
281A ASN 3.0 9.3 + - - -
282A ASN* 3.4 10.7 + - - +
303A SER* 5.9 3.0 - - - -
305A THR* 3.7 25.6 + - + +
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Residues in contact with ASN 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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216A HIS* 4.6 10.2 + - - +
217A THR* 5.1 5.7 - - + +
276A GLU* 2.9 46.2 + - - +
277A PHE* 4.8 1.4 - - - +
279A GLN* 1.3 78.0 - - - +
281A ASN* 1.3 73.3 + - - +
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Residues in contact with ASN 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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216A HIS 3.1 22.6 + - - -
217A THR* 3.3 11.7 - - - +
218A LEU* 3.3 34.5 + - + +
277A PHE* 2.9 40.0 + - - +
279A GLN 3.0 1.0 - - - -
280A ASN* 1.3 87.3 - - - +
282A ASN* 1.3 72.7 + - - +
283A LEU* 3.4 22.8 - - + +
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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