Contacts of the helix formed by residues 361 - 373 (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 ILE 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265C TYR* 3.6 51.8 - - + +
283C THR* 3.7 24.0 - - + +
284C MET* 4.5 10.8 - - - -
358C ARG* 6.1 0.2 - - - +
359C HIS* 3.3 27.6 + - + +
360C ASP* 1.3 77.5 + - - +
362C GLU* 1.3 65.7 + - - +
363C PRO* 3.3 4.3 - - - -
364C LEU* 3.0 14.1 + - + +
365C ARG* 3.0 53.9 + - + +
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Residues in contact with GLU 362 (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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358C ARG* 5.2 2.4 + - - -
360C ASP* 3.0 18.8 + - - +
361C ILE* 1.3 79.3 + - - +
363C PRO* 1.4 60.7 - - + +
365C ARG* 3.1 41.0 + - - +
366C ALA* 2.8 31.6 + - - +
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Residues in contact with PRO 363 (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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278C PHE* 3.6 20.2 - - + -
283C THR* 5.3 4.7 - - + -
360C ASP* 3.8 19.1 - - - +
361C ILE* 3.4 6.7 - - - -
362C GLU* 1.4 93.7 - - + +
364C LEU* 1.3 55.1 + - - +
366C ALA* 3.5 6.3 + - + +
367C ARG* 3.1 26.9 + - - +
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Residues in contact with LEU 364 (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* 4.3 3.8 - - + -
276C LEU* 3.9 7.9 - - + -
278C PHE* 3.8 20.0 - - + -
280C ALA* 3.5 46.2 - - + +
283C THR* 3.8 18.8 - - + +
284C MET* 3.8 26.9 - - + +
361C ILE* 3.0 18.2 + - + +
363C PRO* 1.3 75.8 - - - +
365C ARG* 1.3 66.8 + - + +
367C ARG* 3.1 3.5 + - + +
368C ILE* 3.0 41.1 + - + +
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Residues in contact with ARG 365 (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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261C HIS 4.1 3.6 + - - -
262C GLU* 3.1 34.3 + - - +
264C ASN 3.6 15.2 + - - -
265C TYR* 3.5 18.9 - - - -
358C ARG* 3.8 13.7 - - - +
361C ILE* 3.0 37.5 + - + +
362C GLU* 3.4 39.1 + - - +
364C LEU* 1.3 75.6 - - + +
366C ALA* 1.3 61.8 + - - +
368C ILE* 3.5 9.3 + - + +
369C ALA* 3.1 25.6 + - - +
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Residues in contact with ALA 366 (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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362C GLU 2.8 16.5 + - - +
363C PRO* 3.7 8.3 - - + +
365C ARG* 1.3 76.7 - - - +
367C ARG* 1.3 62.0 + - - +
369C ALA* 3.5 6.3 + - - +
370C GLU* 3.1 24.6 + - - +
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Residues in contact with ARG 367 (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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275C ILE 5.2 0.2 + - - -
276C LEU* 2.9 35.2 + - + +
277C ASN* 4.9 8.1 + - - +
278C PHE* 3.7 37.5 - - + -
363C PRO 3.1 14.7 + - - +
364C LEU* 3.1 8.3 + - + +
366C ALA* 1.3 76.8 - - - +
368C ILE* 1.3 52.0 + - - +
370C GLU* 3.1 39.0 + - - +
371C PHE* 2.8 68.3 + - - +
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Residues in contact with ILE 368 (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* 4.0 17.3 - - + -
276C LEU* 3.8 23.1 - - + -
364C LEU* 3.0 39.8 + - + +
365C ARG* 3.9 7.9 - - + +
367C ARG* 1.3 73.9 - - - +
369C ALA* 1.3 57.7 + - - +
371C PHE* 3.3 6.9 + - - +
372C LEU* 2.9 41.8 + - + +
419C LEU 5.6 2.7 - - - +
420C PHE* 3.9 26.0 - - + -
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Residues in contact with ALA 369 (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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365C ARG 3.1 18.4 + - - +
366C ALA* 3.8 5.2 - - - +
368C ILE* 1.3 77.7 - - - +
370C GLU* 1.3 62.5 + - - +
372C LEU* 3.6 6.8 + - - +
373C ALA* 3.2 24.6 + - - +
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Residues in contact with GLU 370 (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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366C ALA 3.1 17.5 + - - +
367C ARG* 3.1 33.6 + - - +
369C ALA* 1.3 73.6 - - - +
371C PHE* 1.3 66.1 + - - +
373C ALA* 3.3 6.7 + - - +
374C ASP* 3.2 19.1 + - - -
375C PRO* 5.6 0.2 - - - +
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Residues in contact with PHE 371 (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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275C ILE* 3.4 34.5 - - + -
276C LEU* 3.6 21.1 - - + -
367C ARG* 2.8 46.7 + - - +
368C ILE 3.4 4.7 - - - +
370C GLU* 1.3 77.3 - - - +
372C LEU* 1.3 62.6 + - + +
374C ASP* 3.2 12.4 - - + +
385C HIS* 3.1 72.1 - + + -
416C TYR* 4.1 4.0 - + - -
420C PHE* 3.8 23.6 - + - -
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C ILE* 2.9 35.2 + - + +
369C ALA* 4.1 6.3 - - - +
371C PHE* 1.3 76.7 - - + +
373C ALA* 1.3 51.9 + - - +
374C ASP 3.3 0.9 - - - -
385C HIS* 3.7 25.4 - - + +
388C ILE* 4.9 1.1 - - + -
389C ASP* 3.0 39.7 - - + +
392C ASN* 4.9 4.9 - - - +
420C PHE* 3.6 47.3 - - + +
536C ARG* 2.7 24.1 + - - -
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Residues in contact with ALA 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C ALA 3.2 18.7 + - - +
370C GLU* 3.3 7.4 + - - +
371C PHE 3.2 0.4 - - - -
372C LEU* 1.3 74.7 - - - +
374C ASP* 1.3 66.4 + - - +
375C PRO* 2.9 13.5 - - - +
389C ASP* 4.8 3.6 - - - -
536C ARG* 3.5 6.2 + - - +
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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