Contacts of the helix formed by residues 274 - 282 (chain A) in PDB entry 1RI5
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 THR 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASN* 5.4 1.8 - - - +
193A PHE* 5.2 0.3 - - - -
272A CYS 4.9 3.4 - - - +
273A LEU* 1.3 75.3 - - - +
275A ARG* 1.3 53.7 + - - +
276A GLU* 3.6 7.6 + - - +
277A GLU* 3.0 41.9 + - - +
278A SER* 2.7 38.0 + - - -
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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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273A LEU 4.1 0.2 + - - -
274A THR* 1.3 72.7 - - - +
276A GLU* 1.3 65.0 + - + +
278A SER* 3.2 8.5 + - - -
279A GLU* 3.0 34.2 + - - +
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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
----------------------------------------------------------
191A ASN* 3.2 35.6 + - + +
192A ASP* 4.2 25.4 + - - +
193A PHE* 4.2 22.1 - - + -
274A THR* 3.3 7.2 + - - +
275A ARG* 1.3 80.7 - - + +
277A GLU* 1.3 62.0 + - - +
279A GLU* 3.4 15.0 + - - +
280A VAL* 3.7 5.2 + - - +
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Residues in contact with GLU 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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42A LYS 4.4 10.0 - - - +
45A ASN* 2.7 40.0 + - - +
46A ILE* 4.0 17.0 + - + +
193A PHE* 3.8 22.3 - - + -
272A CYS 4.2 0.3 - - - +
273A LEU* 3.6 19.9 - - + +
274A THR* 3.0 43.7 + - - +
276A GLU* 1.3 73.2 - - - +
278A SER* 1.3 64.6 + - - +
280A VAL* 3.2 13.3 + - - +
281A VAL* 3.3 18.0 + - - +
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Residues in contact with SER 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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183A ARG* 4.5 0.2 + - - -
251A ILE* 3.6 19.5 - - - +
273A LEU* 3.6 19.2 + - - +
274A THR 2.7 29.6 + - - -
275A ARG* 3.2 10.2 + - - -
277A GLU* 1.3 73.8 - - - +
279A GLU* 1.3 54.7 + - - +
281A VAL* 4.5 3.4 - - - -
282A GLY* 2.7 33.1 + - - -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 2.6 46.0 + - - +
188A ARG* 3.5 33.6 + - - +
190A SER 4.7 3.8 - - - +
191A ASN* 3.2 27.2 + - - +
194A TYR* 4.4 5.7 + - + -
275A ARG* 3.0 23.9 + - - +
276A GLU* 3.4 14.4 - - - +
277A GLU 3.2 0.2 - - - -
278A SER* 1.3 77.9 - - - +
280A VAL* 1.3 61.0 + - - +
282A GLY 3.7 0.5 + - - -
283A ILE* 3.2 3.2 - - - +
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Residues in contact with VAL 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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46A ILE* 3.8 29.2 - - + -
50A ASN* 5.5 1.3 - - - +
193A PHE* 3.8 23.1 - - + -
194A TYR* 3.6 30.5 - - + -
214A PHE* 5.4 1.8 - - + -
216A LEU* 4.0 19.5 - - + -
276A GLU 4.1 5.8 - - - +
277A GLU 3.2 7.7 + - - +
279A GLU* 1.3 75.8 - - - +
281A VAL* 1.3 65.0 + - - +
283A ILE* 3.2 28.4 - - + +
284A TYR* 3.7 16.2 - - + -
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Residues in contact with VAL 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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46A ILE* 4.3 19.3 - - + -
49A ALA* 4.3 12.1 - - + -
50A ASN* 4.1 10.1 - - - +
53A ILE* 4.2 9.9 - - + -
250A PHE* 3.1 44.6 - - + +
251A ILE* 4.1 13.0 - - + -
254A TYR* 5.5 2.0 - - + -
273A LEU* 4.0 23.1 - - + -
277A GLU 3.3 14.7 + - - +
278A SER* 3.9 5.4 - - - +
280A VAL* 1.3 72.0 - - - +
282A GLY* 1.3 57.4 + - - +
283A ILE 3.0 11.2 + - - -
284A TYR* 3.4 8.2 + - - -
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Residues in contact with GLY 282 (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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179A VAL* 3.5 22.2 - - - +
183A ARG* 3.8 11.6 + - - -
250A PHE* 4.8 0.9 - - - -
251A ILE* 3.6 21.7 - - - +
278A SER 2.7 21.4 + - - -
280A VAL 3.3 0.6 - - - -
281A VAL* 1.3 70.8 - - - +
283A ILE* 1.3 59.1 + - - +
284A TYR 3.4 6.1 - - - +
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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