Contacts of the helix formed by residues 285 - 291 (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 HIS 285 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C ARG* 4.1 21.6 - - + +
249C ASP* 4.4 15.7 + - - +
252C ILE* 3.6 25.7 - - + +
276C GLU* 3.4 26.5 + - - -
280C THR* 4.0 13.8 - - + +
281C LEU* 3.0 15.2 + - + +
284C VAL* 1.3 99.2 + - + +
286C GLU* 1.3 67.3 + - - +
287C PRO* 2.7 10.2 - - - +
288C TYR* 3.7 7.1 + - - +
289C LEU* 3.5 16.6 + - - +
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Residues in contact with GLU 286 (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* 6.1 1.6 - - + -
267C LEU* 3.6 11.4 - - - +
270C LEU* 5.1 0.3 - - - +
281C LEU* 3.2 18.0 + - + +
282C GLU* 2.9 33.6 - - - +
285C HIS* 1.3 75.5 - - - +
287C PRO* 1.4 70.3 - - + +
289C LEU* 3.3 11.7 - - + +
290C ILE* 3.1 23.3 + - + +
295C LEU* 4.0 14.5 - - + +
297C ARG* 2.9 13.5 + - - +
302C ARG* 2.4 58.9 + - - +
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Residues in contact with PRO 287 (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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147C ARG* 6.3 0.4 - - - +
167C TYR* 5.9 1.8 - - - +
282C GLU 3.3 18.4 - - - +
283C GLU 3.2 21.5 - - - +
284C VAL* 4.4 1.6 - - - -
285C HIS 2.7 15.0 - - - +
286C GLU* 1.4 96.3 - - - +
288C TYR* 1.3 67.1 + - - +
289C LEU 2.9 0.2 + - - -
290C ILE* 2.9 12.4 + - + +
291C ARG* 3.2 15.8 + - - +
297C ARG* 5.2 2.0 - - - +
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Residues in contact with TYR 288 (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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198C ARG* 3.9 22.2 + - - -
201C ARG* 2.6 68.4 - - + +
243C LEU* 4.2 7.9 + - - +
244C GLY* 4.3 2.5 - - - -
245C LEU* 3.4 33.2 - - + -
249C ASP* 5.9 0.4 - - - +
285C HIS 3.7 4.2 + - - +
287C PRO* 1.3 76.9 - - - +
289C LEU* 1.3 73.0 + - + +
291C ARG* 3.0 47.7 + - - +
292C GLN* 2.9 37.7 + - + +
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Residues in contact with LEU 289 (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* 4.4 19.1 - - + -
249C ASP* 2.9 35.7 - - + +
252C ILE* 4.4 24.9 - - + -
253C LEU* 4.9 13.2 - - + -
285C HIS 3.5 13.0 + - - +
286C GLU* 3.3 12.1 - - - +
287C PRO 2.9 0.6 + - - -
288C TYR* 1.3 87.1 - - + +
290C ILE* 1.3 65.0 + - - +
292C GLN 2.9 19.4 + - - +
294C LEU* 3.6 9.7 - - + +
295C LEU* 3.3 39.7 - - + +
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Residues in contact with ILE 290 (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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286C GLU 3.4 12.1 - - - +
287C PRO* 2.9 11.0 + - + +
289C LEU* 1.3 76.2 - - - +
291C ARG* 1.3 53.5 + - - +
292C GLN* 2.5 14.6 + - - -
293C GLY* 3.7 7.1 + - - -
294C LEU 4.4 1.2 + - - -
295C LEU* 3.0 39.2 - - + +
296C LYS* 5.2 2.7 - - + -
297C ARG* 3.4 55.9 - - + +
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Residues in contact with ARG 291 (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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167C TYR* 3.0 51.3 + - + +
201C ARG* 2.6 62.3 + - - +
202C GLY* 3.4 2.6 - - - +
203C THR* 4.5 1.0 + - - -
287C PRO* 3.4 6.5 - - - +
288C TYR* 3.0 47.5 + - - +
290C ILE* 1.3 72.8 - - + +
292C GLN* 1.3 67.5 + - - +
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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