Contacts of the helix formed by residues 247 - 258 (chain C) in PDB entry 1IXR
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 LYS 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C LEU* 3.9 25.7 + - + +
241C ASP* 5.2 0.4 - - - +
246C GLU* 1.3 74.3 - - + +
248C ARG* 1.3 55.3 - - + +
250C ARG* 2.8 27.7 + - - +
251C GLU* 2.7 62.4 + - + +
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Residues in contact with ARG 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU* 2.7 9.2 + - + +
247C LYS* 1.3 79.2 - - + +
249C ASP* 1.3 52.4 + - - +
251C GLU* 2.9 29.8 + - - +
252C ILE* 2.7 41.6 + - + +
274C LEU* 2.4 56.0 + - - +
275C SER 4.5 0.6 + - - -
276C GLU* 3.5 27.8 + - - +
281C LEU* 6.4 0.2 - - - +
285C HIS* 4.1 29.4 - - + +
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Residues in contact with ASP 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ARG* 4.2 17.2 + - - -
245C LEU* 4.1 12.1 - - + -
246C GLU* 2.4 57.8 + - - +
248C ARG* 1.3 65.4 - - - +
250C ARG* 1.3 63.9 + - - +
252C ILE* 3.1 14.2 + - - +
253C LEU* 3.0 29.3 + - + +
285C HIS* 4.4 18.1 + - - +
288C TYR* 5.9 0.3 - - - +
289C LEU* 2.9 34.5 - - + +
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Residues in contact with ARG 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLU* 6.0 3.4 - - + +
245C LEU* 5.4 2.8 - - + +
246C GLU* 3.6 3.1 + - - +
247C LYS* 2.8 31.1 + - - +
249C ASP* 1.3 79.5 - - - +
251C GLU* 1.3 56.4 + - - +
253C LEU* 3.2 12.2 + - + +
254C GLU* 2.6 73.7 + - - +
311C HIS* 6.2 1.8 - - + -
312C LEU* 3.6 27.0 - - - +
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Residues in contact with GLU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LYS* 2.7 66.6 + - + +
248C ARG* 2.9 45.0 + - - +
250C ARG* 1.3 73.6 - - + +
252C ILE* 1.3 69.4 + - - +
254C GLU* 2.9 17.7 + - - +
255C VAL* 2.7 25.3 + - + +
274C LEU* 4.6 1.8 - - + -
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ARG* 2.7 36.0 + - + +
249C ASP* 3.2 14.4 - - - +
251C GLU* 1.3 70.2 - - - +
253C LEU* 1.3 55.0 + - + +
255C VAL* 2.6 11.4 + - - +
256C LEU* 2.6 39.2 + - + +
270C LEU* 4.8 6.7 - - + -
274C LEU* 3.5 35.2 - - + +
281C LEU* 4.0 13.2 - - + -
285C HIS* 3.6 37.2 - - + -
286C GLU* 5.2 1.1 - - + +
289C LEU* 4.4 20.9 - - + -
295C LEU* 5.2 5.8 - - + -
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C LEU* 3.8 24.0 - - + -
249C ASP* 3.0 29.0 + - + +
250C ARG* 3.4 9.4 - - + +
252C ILE* 1.3 78.1 - - + +
254C GLU* 1.3 56.4 + - - +
256C LEU* 2.7 12.0 + - + -
257C ILE* 2.4 44.3 + - + +
289C LEU* 4.9 15.5 - - + -
294C LEU* 4.2 17.5 - - + +
295C LEU* 5.5 1.8 - - + +
304C ALA* 5.5 5.8 - - + -
308C ALA* 3.9 28.9 - - + +
312C LEU* 4.7 14.6 - - - +
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Residues in contact with GLU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ARG* 2.6 64.0 + - - +
251C GLU* 3.0 20.1 - - - +
253C LEU* 1.3 70.7 - - - +
255C VAL* 1.3 55.6 + - + +
257C ILE* 3.7 7.2 - - - -
258C LEU* 2.6 57.0 + - + +
312C LEU* 4.6 5.6 - - - +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLU* 2.7 18.6 + - + +
252C ILE 2.6 11.7 + - - +
254C GLU* 1.3 73.3 - - + +
256C LEU* 1.3 64.4 + - - +
258C LEU* 4.9 0.2 - - - -
259C ARG* 3.1 34.7 + - + +
260C PHE* 3.0 34.2 - - + -
270C LEU* 5.3 1.1 - - + -
273C ALA* 4.2 17.9 - - + +
274C LEU* 4.1 20.4 - - + -
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C ILE* 2.6 21.0 + - + +
253C LEU* 2.7 18.8 + - + +
255C VAL* 1.3 74.3 - - - +
257C ILE* 1.3 51.1 + - - +
260C PHE* 3.3 5.9 - - + +
261C GLY 2.5 33.4 + - - +
263C GLY 4.2 4.7 - - - +
265C VAL* 3.3 32.8 - - + -
270C LEU* 3.7 22.2 - - + +
295C LEU* 5.0 7.9 - - + -
302C ARG* 4.7 6.3 - - + -
303C VAL* 3.5 7.2 - - - +
304C ALA* 3.2 46.4 - - + +
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Residues in contact with ILE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C LEU* 2.4 44.5 + - + +
254C GLU* 3.4 7.9 - - - +
256C LEU* 1.3 73.2 - - - +
258C LEU* 1.3 81.3 + - + +
261C GLY* 2.8 27.5 + - - -
262C GLY* 3.8 11.4 - - - +
304C ALA* 4.1 11.2 - - + -
308C ALA* 6.3 0.7 - - + -
309C ARG* 3.4 63.0 - - + +
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLU* 2.6 44.4 + - + +
255C VAL* 4.9 0.4 - - - -
257C ILE* 1.3 90.1 - - + +
259C ARG* 1.3 60.9 + - - +
261C GLY* 4.3 1.2 + - - -
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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