Contacts of the helix formed by residues 364 - 371 (chain C) in PDB entry 2I2X
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 ASP 364 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C LEU* 3.3 6.1 - - - +
240C HIS* 2.6 28.6 + - - +
298C VAL* 3.5 28.0 - - + -
360C ASP 4.3 0.6 + - - -
361C ARG 4.1 1.0 - - - +
362C TYR 3.4 2.2 - - - -
363C ARG* 1.3 79.2 - - + +
365C PRO* 1.3 76.1 - - - +
366C GLN* 3.0 38.7 + - - +
367C ALA 2.9 13.0 + - - +
368C TYR* 3.0 12.8 + - - +
412C LEU* 4.2 5.4 - - - -
15D ARG* 2.9 21.0 + - - +
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Residues in contact with PRO 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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240C HIS* 4.0 15.5 - - + -
241C THR* 4.0 19.7 - - + -
244C VAL* 3.5 24.1 - - + +
364C ASP* 1.3 95.5 - - - +
366C GLN* 1.3 62.5 + - - +
368C TYR* 4.1 8.1 - - + -
369C MET 3.1 19.8 + - - -
404C ILE* 3.5 18.4 - - + +
412C LEU* 4.2 4.9 - - + -
414C LEU* 3.8 22.2 - - + -
418C GLU* 4.9 1.1 - - - +
15D ARG* 3.7 11.0 - - - +
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Residues in contact with GLN 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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227C MET* 3.3 35.5 + - - +
230C GLY* 5.7 0.2 - - - -
231C GLY 5.0 2.8 + - - -
240C HIS* 3.5 40.9 + - - +
243C ALA* 3.6 19.2 - - - +
244C VAL* 3.9 22.0 - - + +
247C ARG* 5.2 2.5 + - + -
298C VAL* 4.2 11.2 - - + +
299C MET* 4.1 14.3 - - + +
364C ASP* 3.0 23.1 + - - +
365C PRO* 1.3 78.2 - - - +
367C ALA* 1.3 59.4 + - - +
369C MET 4.2 0.2 + - - -
370C LEU* 3.4 28.2 + - - +
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Residues in contact with ALA 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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298C VAL* 3.7 21.3 - - - +
299C MET* 4.0 17.5 - - + +
302C LEU* 3.5 10.4 - - + +
360C ASP* 3.2 29.2 - - + +
361C ARG 4.4 0.2 - - - -
364C ASP* 2.9 11.2 + - + +
366C GLN* 1.3 76.6 - - - +
368C TYR* 1.3 67.7 + - - +
370C LEU* 2.8 16.1 + - - -
371C ALA 3.1 9.2 + - - -
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Residues in contact with TYR 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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361C ARG* 3.2 62.3 + - + +
362C TYR* 4.1 12.9 + + - -
364C ASP 3.0 10.4 + - - +
365C PRO* 3.6 13.9 - - + +
367C ALA* 1.3 77.2 - - - +
369C MET* 1.3 61.4 + - - +
370C LEU 3.3 0.2 + - - -
371C ALA* 3.4 9.0 + - - +
374C ASN* 3.0 40.7 + - - -
403C ILE* 3.6 31.6 - - + -
404C ILE* 3.9 8.7 - - + -
406C GLU* 4.7 1.0 - - - +
407C GLY* 3.3 27.1 + - - -
412C LEU* 3.9 17.0 - - + -
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Residues in contact with MET 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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244C VAL* 3.4 37.0 - - + +
247C ARG* 3.7 17.7 - - + -
248C ALA* 3.5 33.2 - - + +
275C ILE* 3.8 13.7 - - + -
365C PRO 3.1 3.9 + - - +
366C GLN 4.6 0.9 - - - +
368C TYR* 1.3 82.4 - - - +
370C LEU* 1.3 67.8 + - + +
374C ASN* 3.5 7.2 - - - +
375C ALA* 3.3 19.8 + - - -
378C VAL* 3.8 27.6 - - + -
400C CYS* 4.0 13.9 - - + -
403C ILE* 4.6 8.5 - - + -
404C ILE* 4.0 6.7 - - + -
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Residues in contact with LEU 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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247C ARG* 3.8 22.0 - - + -
271C TYR* 3.9 24.9 - - + +
272C GLU* 4.6 0.2 - - - -
274C ILE* 3.6 28.7 - - + +
275C ILE* 4.0 8.5 - - + -
299C MET* 3.4 24.9 - - + -
302C LEU* 3.8 12.8 - - + -
303C VAL* 5.6 2.0 - - + -
305C GLN* 2.8 27.1 + - - -
366C GLN* 3.4 17.9 + - + +
367C ALA* 2.8 9.3 + - - +
369C MET* 1.3 100.7 - - + +
371C ALA* 1.3 61.0 + - - +
372C TYR 3.3 0.2 + - - -
375C ALA* 4.2 1.1 - - - -
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Residues in contact with ALA 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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302C LEU* 3.8 12.3 - - + +
305C GLN* 3.7 7.2 - - - -
357C MET* 3.5 22.4 - - + -
361C ARG* 3.7 13.7 - - + +
367C ALA 3.1 5.3 + - - -
368C TYR 3.4 14.6 - - - +
369C MET 3.3 0.2 - - - -
370C LEU* 1.3 75.2 - - - +
372C TYR* 1.3 60.1 + - - +
373C ASP* 3.3 11.4 - - - +
374C ASN* 2.9 23.0 + - - +
375C ALA 2.9 10.0 + - - -
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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