Contacts of the helix formed by residues 230 - 237 (chain A) in PDB entry 2Y48
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 THR 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A GLN* 3.9 16.5 + - + +
229A LEU* 1.3 77.3 - - - +
231A PHE* 1.3 63.7 + - - +
232A GLU* 3.7 15.4 + - - +
233A ALA* 3.0 27.7 + - - +
234A THR* 2.8 26.0 + - - -
253A HIS* 3.6 4.7 - - - -
270A ILE* 3.8 27.8 - - + +
271A LYS* 3.7 24.9 - - + -
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Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A THR* 1.3 73.1 - - - +
232A GLU* 1.3 82.4 + - + +
234A THR* 3.3 2.2 + - - -
235A LEU* 3.0 42.1 + - + +
246A THR* 3.6 21.3 - - - -
249A VAL* 3.1 34.8 - - + -
250A HIS* 3.3 49.8 - + + +
253A HIS* 3.7 25.7 + - + +
271A LYS* 5.7 0.4 - - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A THR* 3.2 8.2 - - - +
231A PHE* 1.3 98.8 + - + +
233A ALA* 1.3 59.0 + - - +
234A THR 3.0 0.9 + - - -
235A LEU* 3.1 5.4 + - - +
236A GLN* 2.8 31.1 + - - +
271A LYS* 3.6 28.9 + - - -
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLN 5.9 0.2 - - - +
229A LEU* 4.7 11.9 - - + -
230A THR* 3.0 25.4 + - - +
232A GLU* 1.3 78.3 - - - +
234A THR* 1.3 61.0 + - - +
236A GLN* 3.5 8.4 - - - +
237A GLN* 3.0 36.8 + - - +
270A ILE* 5.7 5.4 - - + -
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A THR* 3.8 28.0 - - + +
220A LEU* 4.7 14.8 - - + +
229A LEU* 3.5 14.7 - - - +
230A THR 2.8 16.7 + - - -
231A PHE* 3.4 11.2 - - - -
232A GLU 3.0 0.2 - - - -
233A ALA* 1.3 76.2 - - - +
235A LEU* 1.3 64.4 + - - +
237A GLN* 3.2 12.5 + - - +
238A LEU* 3.3 32.2 + - + +
249A VAL* 4.4 10.5 - - + -
253A HIS* 3.5 18.0 - - + -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 3.0 29.1 + - + +
232A GLU* 3.8 4.0 - - - +
234A THR* 1.3 74.1 - - - +
236A GLN* 1.3 68.5 + - - +
238A LEU* 3.1 22.1 + - - +
243A ASN* 3.7 44.2 + - + +
246A THR* 3.8 28.9 - - + -
249A VAL* 4.1 22.0 - - + +
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Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLU 2.8 18.0 + - - +
233A ALA* 3.5 13.5 - - - +
235A LEU* 1.3 78.3 - - - +
237A GLN* 1.3 65.7 + - + +
238A LEU 3.5 4.3 + - - +
243A ASN* 5.6 0.3 + - - -
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Residues in contact with GLN 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 4.3 22.0 + - - +
220A LEU* 3.8 34.9 - - + +
229A LEU* 5.8 2.0 - - - +
233A ALA* 3.0 28.0 + - - +
234A THR 3.2 8.3 + - - +
236A GLN* 1.3 82.0 - - + +
238A LEU* 1.3 59.6 + - - +
239A GLU* 4.2 5.2 + - - +
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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