Contacts of the helix formed by residues 272 - 278 (chain A) in PDB entry 3SRH
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A LEU 5.9 0.2 + - - -
213A ALA 4.3 11.1 + - - -
215A VAL* 5.6 1.8 - - - +
243A PHE* 4.2 19.5 - - + -
244A ILE 4.1 3.5 - - - +
245A ARG* 3.7 21.2 - - - +
270A ILE* 3.8 0.5 - - - +
271A GLU* 1.3 81.3 + - - +
273A HIS* 1.3 64.6 + - - +
274A GLU* 3.4 25.9 + - - +
275A GLY* 2.9 29.6 + - - -
276A VAL* 3.3 14.4 + - - +
296A LEU* 3.8 10.0 - - - +
299A GLU* 3.8 26.9 + - + +
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Residues in contact with HIS 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 PRO* 4.2 4.7 - - + +
212A GLY* 3.2 36.8 + - - +
213A ALA 5.9 0.4 - - - +
272A ASN* 1.3 73.7 - - - +
274A GLU* 1.3 62.3 + - - +
276A VAL* 3.0 10.8 + - - +
277A ARG* 2.7 58.6 + - - +
299A GLU* 3.2 28.2 + - - +
300A ILE* 3.4 31.5 - - + +
301A PRO* 4.5 8.6 - - + +
304A LYS* 6.2 0.6 - - - +
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Residues in contact with GLU 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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213A ALA 4.1 6.0 + - - +
214A ALA* 3.4 35.7 - - - +
215A VAL 4.1 4.2 + - - +
245A ARG* 3.4 30.7 - - + +
246A LYS* 4.5 7.6 + - - -
272A ASN* 3.3 14.6 + - - +
273A HIS* 1.3 76.8 - - - +
275A GLY* 1.3 66.2 + - - +
277A ARG* 3.2 9.5 + - + +
278A ARG* 2.9 55.6 + - + +
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Residues in contact with GLY 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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244A ILE 3.9 15.9 - - - -
245A ARG* 4.0 3.0 - - - +
270A ILE* 3.9 14.3 - - - +
272A ASN* 2.9 22.2 + - - -
274A GLU* 1.3 75.1 - - - +
276A VAL* 1.3 59.5 + - - +
278A ARG 3.5 2.1 - - - -
279A PHE* 3.1 23.9 + - - +
282A ILE* 3.6 13.2 - - - +
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Residues in contact with VAL 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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270A ILE* 3.7 21.3 - - + +
272A ASN 3.3 10.0 + - - +
273A HIS* 3.0 10.4 + - - +
275A GLY* 1.3 73.5 - - - +
277A ARG* 1.3 69.3 + - - +
279A PHE* 3.2 20.7 - - - +
296A LEU* 4.2 13.9 - - + -
300A ILE* 5.5 4.0 - - + -
308A ALA* 4.3 19.1 - - + -
311A MET* 3.5 23.1 - - + +
312A MET* 4.4 3.8 - - + -
315A ARG* 5.1 2.1 + - - -
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Residues in contact with ARG 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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212A GLY* 5.0 9.5 + - - -
273A HIS* 2.7 63.5 + - - +
274A GLU* 3.2 12.1 + - + +
276A VAL* 1.3 80.4 - - - +
278A ARG* 1.3 65.3 + - + +
279A PHE* 3.3 4.0 + - - +
280A ASP* 4.9 1.0 + - - +
315A ARG* 5.5 2.4 + - - -
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Residues in contact with ARG 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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245A ARG 3.7 17.5 - - - +
246A LYS* 3.5 24.4 - - - +
274A GLU* 2.9 39.0 + - + +
275A GLY 3.5 4.5 - - - +
277A ARG* 1.3 81.6 - - + +
279A PHE* 1.3 61.6 + - - +
280A ASP* 3.3 2.9 - - - -
281A GLU* 2.7 55.0 + - + +
282A ILE* 3.3 9.5 + - - +
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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