Contacts of the helix formed by residues 230 - 237 (chain F) in PDB entry 4GOO
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119D TYR* 3.7 11.0 + - - -
185F ALA* 4.8 3.1 - - + +
186F PRO 4.6 14.4 + - - +
187F LEU* 4.8 13.9 - - + +
228F HIS* 4.1 13.5 - - - +
229F ASP* 1.3 80.0 + - - +
231F MET* 1.3 71.9 + - + +
232F LEU* 3.0 29.2 - - + +
233F THR* 3.1 20.5 + - + +
234F ARG* 3.2 25.6 + - - +
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Residues in contact with MET 231 (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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119D TYR* 3.5 27.4 + - + -
122D LEU* 4.4 15.0 - - + -
124D ARG* 4.2 32.8 - - + +
132D ASN* 3.8 41.7 - - - +
133D VAL* 4.4 6.3 - - - -
134D PRO* 3.3 28.0 - - + +
230F THR* 1.3 78.5 - - + +
232F LEU* 1.3 69.5 + - + +
235F GLU* 3.1 25.0 + - + +
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Residues in contact with LEU 232 (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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185F ALA* 5.5 1.1 - - + -
186F PRO* 4.4 21.5 - - + +
203F LEU* 4.6 14.6 - - + -
230F THR* 3.0 15.8 - - + +
231F MET* 1.3 89.9 - - + +
233F THR* 1.3 60.5 + - + +
235F GLU* 3.1 11.3 + - + +
236F TRP* 2.9 67.1 + - + +
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Residues in contact with THR 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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185F ALA* 3.6 30.1 - - + -
227F ASN* 3.9 14.8 - - - +
228F HIS 2.9 29.1 + - - +
230F THR* 3.1 21.3 + - - -
232F LEU* 1.3 75.2 - - - +
234F ARG* 1.3 57.1 + - - +
236F TRP* 3.5 12.0 + - + -
237F TYR* 2.9 50.0 + - + -
264F LEU* 3.5 7.2 - - - +
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Residues in contact with ARG 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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92D TYR* 3.8 4.3 + - - +
119D TYR* 3.6 27.4 - - - -
134D PRO* 3.9 11.9 - - + -
135D PHE 3.6 20.4 + - - +
136D GLY* 4.0 9.6 + - - -
137D ARG* 3.6 30.6 - - - +
229F ASP* 2.7 42.3 + - - +
230F THR 3.2 15.1 + - - +
231F MET 3.7 4.0 - - - +
232F LEU 3.2 0.2 - - - -
233F THR* 1.3 80.1 + - - +
235F GLU* 1.3 67.7 + - - +
237F TYR 3.9 0.4 - - - +
238F GLN* 3.2 21.5 + - - +
242F LEU* 4.2 19.8 - - + +
244F VAL* 3.6 17.4 - - - +
264F LEU* 4.6 8.0 - - + +
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Residues in contact with GLU 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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92D TYR* 4.8 0.7 - - - -
95D ARG* 2.7 47.7 + - - -
132D ASN* 3.4 12.4 - - - +
134D PRO* 3.8 12.6 - - + +
231F MET* 3.1 16.1 + - + +
232F LEU* 3.1 14.8 + - + +
234F ARG* 1.3 80.7 - - - +
236F TRP* 1.3 70.8 + - + +
237F TYR 3.3 0.2 + - - -
238F GLN* 3.0 35.6 + - - +
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Residues in contact with TRP 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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185F ALA* 4.2 7.2 - - + -
186F PRO* 5.1 0.4 - - + -
203F LEU* 4.2 28.7 + - + -
206F GLN* 3.6 39.0 - - + +
207F ALA* 3.4 35.7 - - + +
210F ALA* 3.3 23.8 - - + +
214F GLU* 4.7 7.1 - - - +
227F ASN* 4.8 0.4 - - - -
232F LEU* 2.9 54.4 + - + +
233F THR* 3.7 27.6 - - + +
235F GLU* 1.3 84.5 - - + +
237F TYR* 1.3 74.6 + - + +
238F GLN* 3.4 3.7 + - - +
268F TYR* 4.1 1.0 + - - -
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Residues in contact with TYR 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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182F PRO* 4.4 3.3 - - - +
206F GLN* 4.8 6.5 - - - +
209F LEU* 5.0 2.8 - - + +
210F ALA* 3.8 14.1 - - + -
225F ILE* 3.4 38.4 - - + +
227F ASN* 3.1 35.5 + - + +
233F THR* 2.9 36.4 + - - +
234F ARG 3.9 2.7 - - - -
235F GLU 3.3 0.2 - - - -
236F TRP* 1.3 92.4 - + + +
238F GLN* 1.3 56.4 - - - +
239F ARG 3.1 3.8 - - - -
240F ALA* 2.8 19.7 + - + -
242F LEU* 3.6 16.7 - - + +
264F LEU* 3.9 17.5 - - + -
266F ALA* 3.9 23.1 - - + -
268F TYR* 3.5 22.0 - - - +
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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