Contacts of the helix formed by residues 267 - 274 (chain A) in PDB entry 5OY0
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 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLN* 5.2 2.4 + - - -
262A PRO* 2.8 33.0 + - + +
265A THR* 3.1 15.0 - - - +
266A LEU* 1.3 75.4 - - - +
268A TRP* 1.3 62.0 + - - +
269A GLY* 3.1 5.9 + - - -
270A VAL* 3.4 28.0 + - - +
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Residues in contact with TRP 268 (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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262A PRO 3.6 13.7 - - - -
263A PHE* 3.1 41.2 + + - +
266A LEU* 3.3 33.0 + - + +
267A ASN* 1.3 76.6 - - - +
269A GLY* 1.3 57.4 + - - +
271A TYR* 2.9 40.9 + + + +
275A LEU* 5.6 1.7 - - + +
302A VAL* 6.3 4.0 - - + -
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Residues in contact with GLY 269 (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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267A ASN* 3.1 4.0 + - - -
268A TRP* 1.3 77.3 - - - +
270A VAL* 1.3 62.0 + - - +
272A SER* 2.9 28.6 + - - -
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Residues in contact with VAL 270 (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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255A SER* 3.2 26.6 - - - -
258A GLN* 3.3 41.7 - - + +
262A PRO* 4.0 15.5 - - + -
267A ASN* 3.4 34.1 + - - +
268A TRP 3.1 0.6 + - - -
269A GLY* 1.3 75.4 - - - +
271A TYR* 1.3 61.5 + - + +
272A SER* 3.1 7.8 + - - -
273A ASP* 3.9 5.4 - - - +
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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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255A SER* 3.9 13.5 - - - -
256A PHE* 6.0 0.7 - - - -
259A GLY 2.6 29.3 + - - -
260A LEU* 3.4 7.1 - - + +
262A PRO* 3.7 13.6 - - + +
263A PHE* 3.1 52.3 + + + +
268A TRP* 2.9 26.2 + + + +
270A VAL* 1.3 77.0 - - + +
272A SER* 1.3 55.7 + - - -
273A ASP* 3.1 7.4 + - - -
274A PHE* 3.3 35.3 + + + -
275A LEU* 3.0 47.9 + - + +
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Residues in contact with SER 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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268A TRP 5.1 0.4 - - - -
269A GLY* 2.9 20.8 + - - -
270A VAL 3.1 4.6 + - - -
271A TYR* 1.3 75.1 - - - +
273A ASP* 1.3 61.4 + - - +
274A PHE 3.4 0.2 - - - -
275A LEU 3.7 16.6 - - - +
276A THR* 3.8 10.0 - - - +
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Residues in contact with ASP 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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221A MET* 5.2 0.2 - - - +
253A TYR* 3.8 19.1 - - + +
254A PRO* 3.8 20.4 - - + +
255A SER* 2.5 49.5 + - - -
270A VAL 3.9 4.1 - - - +
272A SER* 1.3 81.3 + - - +
274A PHE* 1.3 70.5 + - - +
276A THR* 4.0 8.8 - - - +
291A SER* 5.2 1.0 - - - -
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Residues in contact with PHE 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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217A ILE* 3.9 35.0 - - + -
221A MET* 3.4 35.8 - - + +
253A TYR* 3.6 14.8 - - + -
255A SER* 3.0 29.4 - - - -
256A PHE* 4.0 23.8 - + - -
271A TYR* 3.5 40.8 - + + -
273A ASP* 1.3 88.8 + - - +
275A LEU* 1.3 83.4 + - + +
276A THR* 3.8 4.7 - - - -
291A SER* 3.5 9.8 - - - +
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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