Contacts of the helix formed by residues 232 - 241 (chain B) in PDB entry 3EGC
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 GLY 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ILE* 3.8 18.2 - - - +
191B VAL 5.3 3.4 - - - -
224B ALA 6.0 4.3 - - - -
231B ASN* 1.3 79.7 - - - +
233B ARG* 1.3 59.4 + - - +
234B ASP* 3.3 2.2 - - - -
235B GLY* 3.7 8.3 - - - -
236B ALA* 2.9 28.2 + - - +
256B ILE* 5.1 2.0 - - - -
259B GLY 4.4 2.3 - - - -
260B ALA 4.6 0.6 + - - -
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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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231B ASN* 3.3 9.8 + - + +
232B GLY* 1.3 76.5 - - - +
234B ASP* 1.3 75.4 + - - +
236B ALA* 3.0 2.5 + - - +
237B ILE* 2.8 44.5 + - + +
259B GLY* 3.3 28.3 - - - +
262B GLN* 3.6 34.1 - - - +
263B ALA 3.8 7.6 - - - +
266B VAL* 3.4 25.3 - - - +
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Residues in contact with ASP 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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232B GLY* 3.3 0.6 - - - -
233B ARG* 1.3 100.7 + - - +
235B GLY* 1.3 57.9 + - - +
237B ILE* 3.5 11.8 + - - +
238B LYS* 2.8 29.8 + - - +
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Residues in contact with GLY 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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190B ILE* 5.1 0.7 - - - -
223B ALA* 3.7 23.6 - - - -
224B ALA 5.6 3.4 - - - -
232B GLY* 3.5 10.8 + - - -
233B ARG 3.2 0.4 - - - -
234B ASP* 1.3 79.7 - - - +
236B ALA* 1.3 56.9 + - - +
238B LYS* 3.1 7.9 + - - +
239B VAL* 2.9 32.4 + - - +
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Residues in contact with ALA 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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190B ILE* 3.9 20.5 - - + +
232B GLY 2.9 18.3 + - - +
233B ARG 3.4 4.3 - - - +
235B GLY* 1.3 74.6 - - - +
237B ILE* 1.3 53.6 + - - +
239B VAL* 3.2 1.4 + - - +
240B LEU* 2.7 46.5 + - + +
249B LEU* 5.5 0.4 - - + -
260B ALA* 3.9 21.1 - - + -
263B ALA* 3.4 18.8 - - + -
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Residues in contact with ILE 237 (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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233B ARG* 2.8 57.5 + - + +
234B ASP* 3.6 11.2 - - - +
236B ALA* 1.3 73.0 - - - +
238B LYS* 1.3 62.4 + - - +
240B LEU 3.9 0.2 - - - -
241B THR* 3.1 30.8 + - + +
263B ALA* 3.5 21.5 - - + +
266B VAL* 3.7 19.1 - - + -
267B LEU* 4.1 20.0 - - + -
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Residues in contact with LYS 238 (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 GLU* 5.8 7.6 - - - +
234B ASP 2.8 15.9 + - - +
235B GLY* 3.4 10.5 - - - +
237B ILE* 1.3 76.6 - - - +
239B VAL* 1.3 68.9 + - + +
240B LEU 3.4 0.2 + - - -
241B THR* 3.4 16.7 + - - -
242B GLY* 3.8 6.4 + - - -
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Residues in contact with VAL 239 (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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190B ILE* 3.7 18.6 - - + -
220B GLU 3.3 25.2 - - - +
221B TRP* 3.7 20.3 - - - +
222B ILE 4.1 3.1 - - - +
223B ALA* 3.4 24.0 - - + -
235B GLY 2.9 19.0 + - - +
236B ALA 4.2 2.0 - - - +
238B LYS* 1.3 75.6 - - + +
240B LEU* 1.3 64.1 + - + +
241B THR 3.6 0.9 + - - -
242B GLY* 3.6 10.3 + - - -
245B ARG* 4.0 0.7 - - - +
246B PRO* 3.5 31.0 - - + +
249B LEU* 4.1 6.7 - - + -
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Residues in contact with LEU 240 (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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236B ALA* 2.7 30.7 + - + +
239B VAL* 1.3 73.5 - - + +
241B THR* 1.3 60.8 + - - +
242B GLY 3.3 3.6 - - - -
245B ARG* 3.3 25.9 - - - +
246B PRO* 4.2 20.4 - - + +
249B LEU* 3.9 28.3 - - + -
260B ALA* 5.1 1.6 - - + +
263B ALA* 4.6 8.3 - - + -
264B LEU* 3.8 26.5 - - + -
267B LEU* 3.6 19.7 - - + +
269B LEU* 4.2 7.2 - - + +
275B VAL* 3.8 24.0 - - + -
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Residues in contact with THR 241 (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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237B ILE* 3.1 20.4 + - + +
238B LYS* 3.4 9.9 + - - -
239B VAL 3.4 0.6 - - - -
240B LEU* 1.3 76.0 - - - +
242B GLY* 1.3 64.5 + - - +
267B LEU* 3.2 37.5 - - + -
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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