Contacts of the helix formed by residues 271 - 277 (chain C) in PDB entry 2IHU
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 TYR 271 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269C THR* 3.1 3.9 + - - -
270C GLY* 1.3 83.6 - - - +
272C MET* 1.3 59.4 + - - +
273C ASP 3.3 2.2 - - - -
274C GLY* 3.2 6.4 + - - +
275C ILE* 2.8 42.8 + - + +
412C PHE* 4.1 12.6 - + + -
415C HIS* 3.2 43.3 + + - +
495C LEU* 3.7 9.6 - - + -
498C LEU* 3.7 26.5 - - + +
499C TYR* 3.3 35.8 + - - -
502C ILE* 3.9 12.2 - - + +
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Residues in contact with MET 272 (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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265C TYR 6.0 0.2 - - - +
267C ALA 4.6 3.6 - - - +
268C VAL* 4.1 9.9 - - - -
269C THR* 3.2 17.7 + - - +
270C GLY 3.4 0.8 - - - -
271C TYR* 1.3 77.4 - - - +
273C ASP* 1.3 62.2 + - - +
275C ILE* 3.9 0.7 - - - +
276C LEU* 3.1 32.8 + - + +
280C ALA* 3.7 25.4 - - + -
281C LEU* 3.9 21.5 - - + -
284C MET* 4.1 18.8 - - + -
364C LEU* 4.3 1.6 - - + -
368C ILE* 4.0 26.2 - - + -
419C LEU* 3.7 44.9 - - + +
420C PHE* 5.6 0.2 - - + -
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Residues in contact with ASP 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLY 4.8 3.9 + - - +
271C TYR 3.3 0.2 - - - -
272C MET* 1.3 76.0 - - - +
274C GLY* 1.3 57.0 + - - +
277C ASN* 3.0 25.5 + - - -
278C PHE 3.2 24.3 + - - +
279C PRO* 4.2 6.1 - - + +
280C ALA* 2.8 10.2 + - - +
281C LEU* 2.8 47.4 + - + +
282C GLN* 4.8 6.2 + - - +
309C LYS* 5.7 0.7 - - - -
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Residues in contact with GLY 274 (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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270C GLY 5.4 0.2 + - - -
271C TYR* 3.2 8.9 + - - +
273C ASP* 1.3 77.7 - - - +
275C ILE* 1.3 65.3 + - - +
276C LEU 3.6 0.2 + - - -
277C ASN* 3.7 19.5 + - - +
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Residues in contact with ILE 275 (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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271C TYR* 2.8 28.8 + - + +
272C MET* 3.9 4.3 - - - +
274C GLY* 1.3 78.9 - - - +
276C LEU* 1.3 60.4 + - + +
277C ASN* 3.7 3.8 + - - -
367C ARG* 5.2 0.2 + - - -
371C PHE* 3.4 27.7 - - + -
412C PHE* 4.2 13.7 - - + -
415C HIS* 3.6 31.4 - - + -
416C TYR* 3.7 44.9 + - + +
419C LEU* 4.1 11.7 - - + -
420C PHE* 4.0 14.4 - - + -
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Residues in contact with LEU 276 (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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272C MET* 3.1 37.1 + - + +
275C ILE* 1.3 77.0 - - + +
277C ASN* 1.3 68.7 + - - +
278C PHE* 3.4 12.6 + - + +
280C ALA* 4.0 2.7 - - + -
364C LEU* 3.9 19.1 - - + -
367C ARG* 2.9 37.5 + - + +
368C ILE* 3.8 31.2 - - + -
371C PHE* 3.6 36.3 - - + -
420C PHE* 3.6 18.2 - - + -
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Residues in contact with ASN 277 (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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273C ASP 3.0 10.3 + - - +
274C GLY* 3.7 13.5 + - - +
275C ILE 3.4 4.9 + - - -
276C LEU* 1.3 79.2 - - - +
278C PHE* 1.3 60.4 + - - +
279C PRO* 5.0 0.3 - - - +
367C ARG* 4.9 6.5 + - - +
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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