Contacts of the helix formed by residues 364 - 369 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233O LEU* 3.7 3.5 - - - +
240O HIS* 2.4 32.5 + - - -
298O VAL* 3.3 29.6 - - + -
360O ASP 4.3 0.6 + - - -
361O ARG 4.0 0.9 - - - +
362O TYR 3.3 2.0 - - - -
363O ARG* 1.3 81.7 - - - +
365O PRO* 1.3 78.3 - - - +
366O GLN* 2.7 38.3 + - - +
367O ALA* 3.1 3.3 + - - +
368O TYR* 2.9 21.5 + - - +
412O LEU* 4.2 4.5 - - - -
15P ARG* 3.1 16.6 + - - +
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Residues in contact with PRO 365 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240O HIS* 4.1 16.2 - - + +
241O THR* 4.0 15.9 - - + -
244O VAL* 3.3 14.0 - - + +
364O ASP* 1.3 98.4 - - - +
366O GLN* 1.3 61.6 + - - +
368O TYR* 3.5 9.7 - - + +
369O MET 3.1 20.3 + - - -
404O ILE* 3.5 32.6 - - + +
412O LEU* 4.2 4.2 - - + -
414O LEU* 3.9 20.6 - - + -
418O GLU* 4.7 0.9 - - - +
15P ARG* 3.8 12.1 - - - +
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Residues in contact with GLN 366 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227O MET* 3.2 36.1 + - - +
231O GLY 5.1 2.0 + - - -
240O HIS* 3.4 41.9 + - - +
243O ALA* 3.5 18.8 - - - +
244O VAL* 3.7 22.7 - - + +
247O ARG* 5.2 2.5 + - + +
298O VAL* 4.2 9.1 - - + +
299O MET* 4.1 13.4 - - + +
364O ASP* 2.7 23.9 + - - +
365O PRO* 1.3 79.8 - - - +
367O ALA* 1.3 57.8 + - - +
369O MET 4.2 0.2 + - - -
370O LEU* 3.3 27.5 + - - +
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Residues in contact with ALA 367 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298O VAL* 3.6 23.5 - - + +
299O MET* 3.9 20.4 - - + +
302O LEU* 3.5 9.9 - - + +
360O ASP* 3.3 26.7 - - + +
361O ARG 4.2 0.7 - - - -
364O ASP* 3.1 9.6 + - - +
366O GLN* 1.3 78.6 - - - +
368O TYR* 1.3 68.4 + - - +
370O LEU* 2.9 13.1 + - - +
371O ALA 3.2 8.8 + - - -
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Residues in contact with TYR 368 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361O ARG* 3.2 69.2 + - + +
362O TYR* 4.0 15.0 - + - -
364O ASP 2.9 14.4 + - - +
365O PRO* 3.2 11.2 + - + +
367O ALA* 1.3 78.1 - - - +
369O MET* 1.3 63.1 + - - +
370O LEU 3.3 0.3 + - - -
371O ALA* 3.4 8.1 + - - +
374O ASN* 2.8 29.2 + - - -
403O ILE* 3.5 37.6 + - + -
404O ILE* 4.0 9.4 - - + -
406O GLU* 4.4 2.8 - - - +
407O GLY* 3.3 27.4 + - - -
412O LEU* 4.2 14.4 - - + -
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Residues in contact with MET 369 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244O VAL* 3.1 51.4 - - + +
247O ARG* 4.0 9.0 - - + -
248O ALA* 3.5 24.2 - - + +
275O ILE* 4.0 15.5 - - - -
365O PRO 3.1 4.5 + - - +
366O GLN 4.7 0.7 - - - +
368O TYR* 1.3 82.8 - - - +
370O LEU* 1.3 72.0 + - + +
371O ALA 3.3 0.4 - - - -
374O ASN* 3.3 7.8 - - - +
375O ALA* 3.2 24.1 + - - -
378O VAL* 4.0 20.4 - - + -
400O CYS* 3.8 12.6 - - + -
403O ILE* 4.6 6.3 - - + -
404O ILE* 4.3 7.2 - - + -
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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