Contacts of the helix formed by residues 301 - 305 (chain G) 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 ASN 301 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335E TYR* 3.0 30.5 + - - +
339E LEU* 3.9 10.5 - - - +
289G LYS* 3.0 28.6 - - - +
300G GLY* 1.3 72.0 - - - -
302G LEU* 1.3 55.6 + - - +
303G VAL 3.1 2.5 - - - -
304G MET* 2.8 63.1 + - + +
356G MET* 3.4 19.1 - - - +
359G SER* 3.3 20.1 + - - +
360G ASP* 2.7 12.9 + - - +
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Residues in contact with LEU 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G ILE* 6.0 0.2 - - + -
299G MET* 3.6 13.2 + - + +
301G ASN* 1.3 76.2 - - - +
303G VAL* 1.3 63.0 + - + +
305G GLN* 3.0 58.3 + - - +
356G MET 3.5 14.3 + - - +
357G MET* 3.5 17.9 - - - +
360G ASP* 3.0 23.0 + - + +
361G ARG* 3.9 16.4 - - - +
367G ALA* 3.6 20.2 - - + +
370G LEU* 3.7 24.7 - - + +
371G ALA* 4.0 13.2 - - + -
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Residues in contact with VAL 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271G TYR* 3.6 20.9 - - + -
286G MET* 3.4 46.0 - - + +
287G GLU 3.2 21.5 - - - +
288G GLY* 3.6 0.4 - - - -
299G MET* 3.3 39.7 - - + +
300G GLY 3.6 7.9 - - - +
302G LEU* 1.3 82.4 - - + +
304G MET* 1.3 62.2 + - - +
305G GLN* 3.2 3.7 + - - +
306G CYS 4.4 1.0 + - - -
307G CYS* 3.9 2.6 + - - +
310G TRP* 3.5 18.6 - - + -
370G LEU* 5.6 2.7 - - + -
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Residues in contact with MET 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E LEU* 5.6 1.8 - - + -
19G PHE* 3.6 9.7 - - - +
289G LYS* 3.5 17.9 - - + +
300G GLY 4.4 0.7 - - - +
301G ASN* 2.8 57.6 + - + +
303G VAL* 1.3 76.8 - - - +
305G GLN* 1.3 63.8 + - - +
306G CYS 2.9 4.7 + - - -
307G CYS* 3.2 22.6 + - - -
310G TRP* 3.4 42.6 - - + -
336G ASP* 4.7 5.2 - - - +
340G MET* 4.1 19.0 - - - +
356G MET* 3.5 24.5 - - + +
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Residues in contact with GLN 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G PHE* 3.5 12.5 + - - -
274G ILE* 3.7 15.7 - - + +
286G MET* 5.8 0.4 - - - +
301G ASN 3.9 0.8 + - - -
302G LEU* 3.0 28.1 + - - +
303G VAL* 4.6 4.4 + - - +
304G MET* 1.3 77.4 - - - +
306G CYS* 1.3 79.9 + - + +
353G ARG* 3.2 34.8 - - + +
356G MET* 3.8 12.8 - - - +
357G MET* 3.4 18.5 - - + +
370G LEU 3.1 23.2 + - - -
371G ALA* 3.7 0.7 - - - -
372G TYR* 3.0 31.7 + - + -
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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