Contacts of the helix formed by residues 277 - 287 (chain F) in PDB entry 1R4N
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 277 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F PHE* 3.5 4.7 - - - -
275F GLY 3.5 5.3 + - - +
276F VAL* 1.3 76.1 - - - +
278F TYR* 1.3 68.8 + - - +
279F ARG* 3.5 16.1 + - + +
280F LEU* 2.8 39.4 + - + +
281F THR* 2.9 12.5 + - - -
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Residues in contact with TYR 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU* 5.7 5.8 - - - -
254F PRO* 3.8 22.2 + - - +
257F ILE* 3.3 40.1 - - + +
258F GLN* 3.8 26.0 - - - +
261F PHE* 3.2 40.2 - + + -
277F THR* 1.3 73.9 + - - +
279F ARG* 1.3 60.6 + - - +
281F THR* 2.8 21.1 + - - -
282F GLN* 3.0 32.7 + - + +
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Residues in contact with ARG 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E GLU* 3.3 25.1 + - - +
14E ASP* 4.3 9.9 + - - +
17E LEU* 3.4 37.2 + - - +
18E ARG* 2.6 63.5 + - - +
21E GLY* 4.7 2.0 - - - -
22E ASP* 2.7 44.0 + - - +
277F THR* 3.1 14.2 + - + +
278F TYR* 1.3 81.1 - - - +
280F LEU* 1.3 57.3 + - - +
282F GLN* 3.4 8.6 + - - -
283F GLY 3.1 8.5 + - - -
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Residues in contact with LEU 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG* 4.9 3.4 - - - +
225F PRO* 3.7 18.6 - - + -
226F GLU* 4.0 21.3 - - + +
229F ILE* 3.6 13.5 - - + -
275F GLY 3.5 22.9 - - - +
276F VAL* 4.7 0.2 - - - -
277F THR* 2.8 28.9 + - + +
279F ARG* 1.3 71.5 - - - +
281F THR* 1.3 67.8 + - - +
282F GLN 3.0 1.8 - - - -
283F GLY* 3.0 4.1 + - - +
284F VAL* 2.9 43.1 + - + +
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Residues in contact with THR 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F ILE* 3.2 22.4 - - + +
257F ILE* 4.0 13.9 - - + -
260F ILE* 3.7 20.0 - - + +
261F PHE* 3.1 56.7 - - + +
276F VAL* 4.2 2.1 - - - +
277F THR 2.9 5.8 + - - -
278F TYR 2.8 8.0 + - - -
280F LEU* 1.3 75.9 - - - +
282F GLN* 1.3 59.7 + - - +
284F VAL 3.7 0.2 + - - -
285F VAL* 3.0 32.2 + - + +
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Residues in contact with GLN 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ASP* 3.6 20.3 - - - +
15E ARG* 6.2 0.2 - - - +
18E ARG* 3.6 6.6 + - - +
257F ILE* 3.6 37.3 - - + +
278F TYR* 3.0 33.9 + - + +
279F ARG* 3.5 12.4 - - - +
281F THR* 1.3 75.0 - - - +
283F GLY* 1.3 59.8 + - - +
285F VAL* 4.4 4.0 - - - -
286F LYS* 2.7 48.9 + - + +
288F ILE* 3.5 12.4 - - + +
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Residues in contact with GLY 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG* 3.8 14.1 - - - -
279F ARG 3.1 5.5 + - - -
280F LEU* 3.0 9.9 + - - -
282F GLN* 1.3 78.0 - - - +
284F VAL* 1.3 51.8 + - - +
287F ARG* 2.8 35.9 + - - -
288F ILE* 3.3 20.2 + - - +
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Residues in contact with VAL 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F PHE* 5.4 3.1 - - + -
226F GLU* 4.2 18.8 - - + +
229F ILE* 3.4 37.7 - - + -
230F GLU* 3.8 31.6 - - + +
233F ARG* 4.6 1.0 - - - -
280F LEU* 2.9 31.9 + - + +
283F GLY* 1.3 72.2 - - - +
285F VAL* 1.3 62.1 + - - +
287F ARG* 2.6 36.1 + - - +
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Residues in contact with VAL 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F ILE* 4.2 6.7 - - + -
233F ARG* 3.9 28.4 + - - +
249F LEU* 4.6 6.1 - - + -
251F GLY* 4.0 28.0 - - - +
257F ILE* 5.1 6.5 - - + -
260F ILE* 3.9 39.3 - - + -
281F THR* 3.0 26.2 + - + +
282F GLN* 3.8 3.8 - - - +
284F VAL* 1.3 81.9 - - - +
286F LYS* 1.3 63.2 + - + +
287F ARG* 3.5 3.8 + - - +
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Residues in contact with LYS 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ARG* 4.5 21.1 - - - +
7F ATP 5.6 1.7 + - - -
84F ASP* 5.0 4.6 + - - -
86F SER* 5.8 0.6 + - - -
251F GLY* 2.9 37.2 - - - +
252F ASP* 2.6 37.0 + - - +
257F ILE* 4.3 6.5 - - - +
282F GLN* 2.7 34.5 + - - +
285F VAL* 1.3 74.9 - - + +
287F ARG* 1.3 72.2 + - - +
288F ILE* 3.6 15.1 - - + -
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Residues in contact with ARG 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ATP 5.4 1.9 + - - -
211F VAL 5.4 6.8 + - - -
212F ASN* 4.9 11.5 - - - +
213F PHE* 6.3 0.2 - - - -
230F GLU* 2.9 35.5 + - - -
233F ARG* 4.4 18.2 - - - +
234F MET* 5.0 3.0 - - - +
283F GLY 2.8 13.1 + - - -
284F VAL* 2.6 37.1 + - - +
285F VAL 3.3 4.6 - - - +
286F LYS* 1.3 80.3 - - - +
288F ILE* 1.3 61.9 + - - +
289F ILE* 3.9 9.4 + - - +
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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