Contacts of the helix formed by residues 277 - 287 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B PHE* 3.5 4.9 - - - -
275B GLY 3.5 6.0 + - - +
276B VAL* 1.3 75.4 - - - +
278B TYR* 1.3 67.6 + - - +
279B ARG* 3.5 16.0 + - + +
280B LEU* 2.8 39.2 + - + +
281B THR* 2.9 13.5 + - - -
64E GLN* 5.7 0.2 - - - +
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Residues in contact with TYR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 5.9 3.6 - - - -
254B PRO* 3.8 22.0 + - - +
257B ILE* 3.3 37.0 - - + +
258B GLN* 3.8 26.4 - - - +
261B PHE* 3.2 41.9 - + + -
277B THR* 1.3 71.6 + - - +
279B ARG* 1.3 66.5 + - - +
281B THR* 2.8 15.8 + - - -
282B GLN* 3.0 33.3 + - + +
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.3 25.2 + - - +
14A ASP* 4.2 10.1 + - - +
17A LEU* 3.3 38.9 + - - +
18A ARG* 2.5 62.7 + - - +
21A GLY* 4.8 1.8 - - - -
22A ASP* 2.9 40.2 + - - +
277B THR* 3.2 13.8 + - + +
278B TYR* 1.3 81.2 - - - +
280B LEU* 1.3 56.8 + - - +
282B GLN* 3.4 9.2 + - - -
283B GLY 3.0 8.7 + - - -
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.8 3.8 - - - +
225B PRO* 3.7 19.7 - - + -
226B GLU* 3.9 21.1 - - + +
229B ILE* 3.6 14.1 - - + -
275B GLY 3.5 23.6 - - - +
276B VAL* 4.6 0.2 - - - -
277B THR* 2.8 25.0 + - + +
279B ARG* 1.3 75.1 - - - +
281B THR* 1.3 68.1 + - - +
282B GLN 3.0 1.6 - - - -
283B GLY* 3.0 4.0 + - - +
284B VAL* 2.9 42.5 + - + +
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Residues in contact with THR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ILE* 3.3 22.7 - - + +
257B ILE* 4.0 13.7 - - + -
260B ILE* 3.6 19.3 - - + +
261B PHE* 3.1 56.5 - - + +
276B VAL* 4.2 2.1 - - - +
277B THR 2.9 6.2 + - - -
278B TYR 2.8 8.0 + - - -
280B LEU* 1.3 76.0 - - - +
282B GLN* 1.3 60.2 + - - +
285B VAL* 3.0 32.7 + - + +
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Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 3.6 20.1 - - - +
15A ARG* 6.0 0.8 - - - +
18A ARG* 3.6 6.5 + - - +
257B ILE* 3.6 39.0 - - + +
278B TYR* 3.0 36.2 + - + +
279B ARG* 3.4 10.5 - - - +
280B LEU 3.0 0.2 - - - -
281B THR* 1.3 75.4 - - - +
283B GLY* 1.3 60.7 + - - +
285B VAL* 3.2 3.8 + - - -
286B LYS* 2.7 48.7 + - + +
288B ILE* 3.4 12.5 - - + +
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.8 13.2 - - - -
279B ARG 3.0 5.5 + - - -
280B LEU* 3.0 9.6 + - - -
282B GLN* 1.3 76.8 - - - +
284B VAL* 1.3 56.5 + - - +
287B ARG* 2.8 32.4 + - - -
288B ILE* 3.3 20.6 + - - +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B PHE* 5.5 2.7 - - + -
226B GLU* 4.2 19.1 - - + +
229B ILE* 3.4 40.2 - - + -
230B GLU* 3.8 32.8 - - + +
233B ARG* 4.6 0.8 - - - -
280B LEU* 2.9 30.0 + - + +
283B GLY* 1.3 73.5 - - - +
285B VAL* 1.3 60.5 + - - +
287B ARG* 2.6 36.8 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ILE* 4.2 4.9 - - + -
233B ARG* 3.9 30.9 + - - +
249B LEU* 4.5 5.8 - - + -
251B GLY* 4.1 27.6 - - - +
257B ILE* 5.1 5.4 - - + -
260B ILE* 3.8 42.2 - - + -
281B THR* 3.0 24.7 + - + +
282B GLN* 3.8 3.8 - - - +
284B VAL* 1.3 80.8 - - - +
286B LYS* 1.3 62.7 + - + +
287B ARG* 3.5 4.2 + - - +
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Residues in contact with LYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 4.4 22.2 - - - +
5B ATP 5.8 1.3 - - - +
84B ASP* 5.0 5.1 + - - -
86B SER* 5.8 0.6 + - - -
251B GLY* 2.9 38.8 - - - +
252B ASP* 2.7 36.3 + - - +
257B ILE* 4.3 6.5 - - - -
282B GLN* 2.7 33.8 + - + +
285B VAL* 1.3 75.1 - - + +
287B ARG* 1.3 72.1 + - - +
288B ILE* 3.3 14.3 + - + -
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B VAL 5.4 7.6 + - - -
212B ASN* 4.9 12.5 - - - +
213B PHE* 6.3 0.2 - - - -
230B GLU* 2.9 35.1 + - - -
233B ARG* 4.3 18.7 - - - +
234B MET* 5.0 3.0 - - - +
283B GLY 2.8 11.5 + - - -
284B VAL* 2.6 37.0 + - - +
285B VAL 3.3 4.4 - - - +
286B LYS* 1.3 80.7 - - - +
288B ILE* 1.3 63.3 + - - +
289B ILE* 3.9 9.2 + - - +
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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