Contacts of the helix formed by residues 227 - 236 (chain B) in PDB entry 1R37
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 227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLN* 1.3 72.3 + - - +
228B PRO* 1.3 68.0 - - - +
229B LEU* 2.8 26.2 + - - +
230B ALA* 3.2 23.6 + - + +
231B GLU* 3.2 22.9 + - - +
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Residues in contact with PRO 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 4.5 2.5 - - + -
221B ILE* 4.1 23.6 - - + -
223B ALA* 4.3 12.6 - - + +
226B GLN 3.0 11.2 - - - +
227B ASP* 1.3 88.1 - - - +
229B LEU* 1.3 57.4 + - - +
231B GLU* 3.8 1.1 - - + +
232B ILE* 2.9 38.2 + - + +
256B VAL* 4.3 12.6 - - + -
257B TYR* 3.6 38.4 - - + +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ASP* 2.8 11.3 + - - +
228B PRO* 1.3 76.4 - - + +
230B ALA* 1.3 62.3 + - - +
232B ILE* 3.8 4.7 - - + +
233B ARG* 2.8 48.9 + - - +
256B VAL* 3.8 40.8 - - + +
257B TYR* 4.8 1.6 - - + -
259B LYS* 4.4 19.7 - - + -
260B ALA* 3.7 34.8 - - + +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ASP* 3.2 26.9 + - + +
229B LEU* 1.3 78.7 - - - +
231B GLU* 1.3 56.8 + - - +
233B ARG* 3.4 10.1 + - - +
234B ARG* 3.0 26.7 + - - +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B VAL 5.5 0.7 - - - +
221B ILE* 3.8 21.4 - - + +
226B GLN* 3.1 37.9 + - - +
227B ASP 3.2 10.7 + - - +
228B PRO* 3.8 0.7 - - + +
229B LEU 3.2 0.6 - - - -
230B ALA* 1.3 77.5 - - - +
232B ILE* 1.3 61.4 + - - +
234B ARG* 2.7 40.8 + - - +
235B ILE* 2.9 56.4 + - - +
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Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 3.5 34.3 - - + -
200B ILE* 4.7 7.6 - - + -
202B VAL* 6.1 0.2 - - + -
221B ILE* 3.8 15.3 - - + -
228B PRO 2.9 30.4 + - - +
229B LEU* 3.9 5.4 - - + +
231B GLU* 1.3 72.2 - - - +
233B ARG* 1.3 64.5 + - - +
235B ILE* 4.5 6.7 - - - +
236B THR* 2.8 36.2 + - + +
240B GLY* 4.9 0.9 - - - -
241B VAL* 3.8 25.8 - - + -
257B TYR* 4.2 11.2 - - + -
260B ALA* 4.1 25.6 - - + +
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B LEU* 2.8 38.5 + - - +
230B ALA* 3.4 8.9 - - - +
232B ILE* 1.3 78.2 - - - +
234B ARG* 1.3 56.4 + - - +
236B THR* 4.1 4.0 - - - -
237B GLU* 3.0 7.1 + - - -
238B SER* 2.7 60.4 + - - +
240B GLY* 5.5 6.0 - - - +
259B LYS* 4.2 17.6 + - - +
260B ALA* 5.2 3.2 - - - +
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Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B TYR* 5.2 8.9 - - - -
230B ALA 3.0 14.1 + - - +
231B GLU* 2.7 43.2 + - - +
233B ARG* 1.3 75.6 - - - +
235B ILE* 1.3 78.9 + - - +
237B GLU* 3.2 15.9 + - - +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B THR* 5.5 2.5 - - + +
198B THR* 5.5 1.6 - - + -
200B ILE* 3.7 31.2 - - + -
219B TYR* 3.6 63.0 + - + -
221B ILE* 4.6 5.4 - - + -
231B GLU* 2.9 41.8 + - - +
232B ILE 3.5 3.6 + - - +
234B ARG* 1.3 87.3 - - - +
236B THR* 1.3 62.8 + - + +
237B GLU* 3.5 6.6 + - - +
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B THR* 4.2 19.3 - - + +
200B ILE* 4.4 4.9 - - + -
232B ILE* 2.8 23.2 + - + +
233B ARG* 3.7 3.1 + - - -
235B ILE* 1.3 77.0 - - + +
237B GLU* 1.3 69.2 + - - +
238B SER 3.8 0.2 + - - -
239B LYS* 3.1 19.8 + - - +
240B GLY* 2.8 47.0 + - - +
241B VAL* 4.0 16.2 - - + -
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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