Contacts of the helix formed by residues 232 - 241 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190F ILE* 3.9 17.1 - - - +
191F VAL 5.7 2.2 - - - -
224F ALA 6.3 2.9 - - - -
231F ASN* 1.3 79.5 - - - +
233F ARG* 1.3 61.4 + - - +
234F ASP* 3.3 2.0 - - - -
235F GLY* 3.7 9.9 - - - -
236F ALA* 2.9 28.1 + - - +
256F ILE* 5.1 1.7 - - - +
259F GLY* 4.5 2.8 - - - -
260F ALA 4.6 0.7 + - - -
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Residues in contact with ARG 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F ASN* 3.3 7.8 + - + +
232F GLY* 1.3 77.9 - - - +
234F ASP* 1.3 69.1 + - - +
236F ALA* 3.1 2.1 + - - +
237F ILE* 2.7 61.3 + - + +
259F GLY* 3.4 30.7 - - - +
262F GLN* 3.6 31.5 - - - +
263F ALA 3.8 5.8 - - - +
266F VAL* 3.4 24.5 - - - +
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Residues in contact with ASP 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F GLY* 3.3 1.1 - - - -
233F ARG* 1.3 100.1 + - - +
235F GLY* 1.3 57.3 + - - +
237F ILE* 3.4 11.2 + - - +
238F LYS* 2.8 31.5 + - - +
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Residues in contact with GLY 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ILE* 4.4 1.3 - - - -
223F ALA* 3.6 24.7 - - - -
224F ALA 5.8 2.9 - - - -
232F GLY* 3.6 11.6 + - - -
233F ARG 3.3 0.8 - - - -
234F ASP* 1.3 76.4 - - - +
236F ALA* 1.3 63.6 + - - +
238F LYS* 3.2 7.1 + - - +
239F VAL* 3.0 27.0 + - - +
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Residues in contact with ALA 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ILE* 4.0 19.1 - - + +
232F GLY 2.9 19.3 + - - +
233F ARG 3.6 0.2 - - - +
235F GLY* 1.3 75.5 - - - +
237F ILE* 1.3 57.5 + - - +
239F VAL 3.8 0.3 - - - -
240F LEU* 2.8 42.5 + - + +
249F LEU* 5.3 0.4 - - + -
260F ALA* 3.9 21.1 - - + -
263F ALA* 3.5 22.0 - - + -
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Residues in contact with ILE 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F ARG* 2.7 60.3 + - + +
234F ASP* 3.6 11.4 - - - +
236F ALA* 1.3 71.5 - - - +
238F LYS* 1.3 62.7 + - - +
240F LEU 3.5 0.7 + - - -
241F THR* 3.1 31.0 + - + +
263F ALA* 3.6 20.8 - - + +
266F VAL* 3.8 18.8 - - + -
267F LEU* 4.1 21.3 - - + -
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Residues in contact with LYS 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F GLU* 5.0 8.0 + - - +
223F ALA* 6.2 2.7 - - + -
234F ASP 2.8 20.6 + - - +
235F GLY* 3.7 5.4 - - - +
236F ALA 3.2 0.2 - - - -
237F ILE* 1.3 73.1 - - - +
239F VAL* 1.3 68.6 + - + +
241F THR* 3.5 16.0 + - - +
242F GLY* 3.8 6.8 + - - -
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Residues in contact with VAL 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ILE* 3.7 10.1 - - + -
220F GLU 3.4 24.1 - - - +
221F TRP* 3.8 18.3 - - - +
222F ILE 4.3 1.6 - - - +
223F ALA* 3.6 26.9 - - + +
235F GLY 3.0 17.3 + - - +
236F ALA 4.4 1.8 - - - +
238F LYS* 1.3 77.9 - - + +
240F LEU* 1.3 61.9 + - + +
242F GLY* 3.5 11.3 + - - -
245F ARG* 4.0 1.0 - - - +
246F PRO* 3.7 33.3 - - + +
249F LEU* 4.0 13.7 - - + -
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Residues in contact with LEU 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236F ALA* 2.8 30.5 + - + +
239F VAL* 1.3 78.2 - - + +
241F THR* 1.3 59.8 + - - +
242F GLY 3.4 1.9 - - - +
245F ARG* 3.4 27.4 - - - +
246F PRO* 4.2 20.2 - - + +
249F LEU* 3.8 28.3 - - + -
260F ALA 5.0 0.9 - - - +
263F ALA* 4.5 8.3 - - + -
264F LEU* 3.8 25.1 - - + -
267F LEU* 3.6 17.3 - - + +
269F LEU* 4.2 5.9 - - + +
275F VAL* 3.7 25.4 - - + -
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Residues in contact with THR 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F ILE* 3.1 18.7 + - + +
238F LYS* 3.5 10.7 + - - +
239F VAL 3.4 0.2 - - - -
240F LEU* 1.3 76.0 - - - +
242F GLY* 1.3 64.9 + - - +
267F LEU* 3.2 37.0 - - + -
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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