Contacts of the helix formed by residues 270 - 276 (chain A) in PDB entry 5C51
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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269A HIS* 1.3 76.5 + - + +
271A VAL* 1.3 59.7 + - - +
272A SER* 3.3 6.8 + - - -
273A PHE* 3.4 34.0 + - + +
274A ASP* 2.9 12.5 - - - +
293A ASP* 2.9 19.9 + - - +
295A MET* 4.0 24.2 - - + +
843A GLN* 4.8 7.1 - - - +
845A VAL* 3.9 19.7 + - - +
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Residues in contact with VAL 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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197A PHE* 5.9 0.4 - - + +
266A VAL* 3.6 27.8 - - + +
267A VAL 4.2 2.0 - - - -
268A GLY* 3.5 24.0 + - - +
270A ASN* 1.3 73.7 - - - +
272A SER* 1.3 66.6 + - - +
274A ASP* 3.2 12.8 + - + +
275A ARG* 2.9 26.2 + - - +
291A PHE* 3.6 31.2 - - + -
292A LEU 3.9 2.0 - - - +
293A ASP* 3.0 32.4 + - + +
431A GLY* 6.5 1.3 - - - -
846A THR* 5.0 4.0 - - - +
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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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270A ASN* 3.2 5.8 - - - -
271A VAL* 1.3 85.3 - - - +
273A PHE* 1.3 56.9 + - - +
275A ARG* 3.2 15.0 + - - +
276A ALA* 2.9 28.6 + - - +
293A ASP* 4.1 1.6 + - - -
431A GLY* 4.5 7.8 + - - -
841A LEU* 5.6 0.2 - - - +
843A GLN* 3.6 13.2 - - - +
844A VAL* 2.3 52.6 + - - +
845A VAL* 4.5 0.3 - - - -
846A THR* 5.0 1.6 + - - -
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Residues in contact with PHE 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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199A VAL* 3.6 30.5 - - + -
201A VAL* 3.5 28.7 - - + -
270A ASN* 3.4 24.9 + - + +
271A VAL 3.3 0.4 - - - -
272A SER* 1.3 78.8 - - - +
274A ASP* 1.3 68.5 + - - +
276A ALA* 3.5 12.6 + - - +
277A HIS* 3.7 29.1 + + - -
843A GLN* 3.2 36.9 - - - +
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Residues in contact with ASP 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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197A PHE* 3.9 33.9 - - + +
198A ASP* 3.2 4.6 - - - +
199A VAL* 2.9 42.2 + - + +
266A VAL* 6.0 0.7 - - + -
268A GLY 5.0 0.3 - - - -
269A HIS 3.8 6.3 - - - +
270A ASN 2.9 23.7 - - - +
271A VAL* 3.2 16.8 + - + +
273A PHE* 1.3 81.4 - - - +
275A ARG* 1.3 62.7 + - - +
277A HIS* 3.0 20.3 + - - +
278A ILE* 3.4 15.6 - - - +
291A PHE* 5.5 0.9 - - + -
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Residues in contact with ARG 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 VAL 2.9 13.3 + - - +
272A SER* 3.3 16.6 - - - +
274A ASP* 1.3 73.7 - - - +
276A ALA* 1.3 61.7 + - - +
277A HIS 3.0 6.5 + - - -
278A ILE* 3.1 25.8 + - - +
281A GLN* 2.8 39.2 + - + +
291A PHE* 3.4 26.2 - - + -
431A GLY 3.4 19.5 + - - -
432A VAL* 3.2 36.1 + - - +
433A SER* 2.4 31.3 + - - +
434A TYR* 4.8 1.6 - - - +
841A LEU* 3.3 32.3 - - + +
843A GLN 5.8 1.1 - - - +
1129A PHE* 4.8 3.0 - - - -
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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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241A PRO* 4.9 1.7 - - - +
272A SER 2.9 12.5 + - - +
273A PHE 3.6 11.7 - - - +
274A ASP 3.2 0.4 - - - -
275A ARG* 1.3 76.8 - - - +
277A HIS* 1.3 63.8 + - + +
278A ILE 3.4 1.1 - - - -
282A TYR* 2.3 36.3 + - - +
812A MET* 3.3 19.6 - - + +
840A ILE* 5.1 0.4 - - + -
841A LEU* 4.1 22.4 - - + +
843A GLN* 4.1 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