Contacts of the helix formed by residues 211 - 218 (chain B) in PDB entry 4G1U
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 GLN 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B LEU* 3.2 21.1 + - + +
208B GLY* 3.4 8.4 + - - +
209B LEU 3.2 1.0 - - - -
210B LEU* 1.3 84.3 + - - +
212B ALA* 1.3 56.7 + - - +
213B ARG 3.0 11.6 + - - -
214B GLN* 3.1 31.3 + - + +
215B LEU* 3.1 20.8 + - - +
235B ALA* 4.7 6.1 - - - -
238B ARG* 4.0 44.9 + - + +
239B LEU* 3.9 25.6 - - + +
242B LEU* 5.3 4.9 - - + -
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Residues in contact with ALA 212 (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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208B GLY 3.5 2.6 + - - -
209B LEU* 3.5 11.2 + - - +
210B LEU 3.3 2.0 - - - -
211B GLN* 1.3 76.0 - - - +
213B ARG* 1.3 60.9 + - + +
215B LEU* 3.9 4.7 - - - -
216B ASN* 3.3 28.0 + - - -
276B HIS* 3.5 26.7 - - - +
277B ARG* 3.8 14.8 - - + +
280B LEU* 3.5 26.2 - - + -
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Residues in contact with ARG 213 (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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210B LEU 4.9 7.9 - - - +
211B GLN 3.0 0.8 + - - -
212B ALA* 1.3 77.1 - - + +
214B GLN* 1.3 78.6 + - - +
216B ASN* 3.1 17.6 + - - +
217B LEU* 3.1 24.0 + - + +
277B ARG* 4.6 25.9 - - + +
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Residues in contact with GLN 214 (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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210B LEU 4.2 14.8 + - - -
211B GLN* 3.3 37.8 + - + +
213B ARG* 1.3 81.0 - - - +
215B LEU* 1.3 56.5 + - - +
217B LEU* 3.2 9.8 + - - +
218B LEU* 2.8 37.1 + - + +
230B VAL* 4.6 16.6 - - + +
231B ASN 5.8 0.2 + - - -
235B ALA* 3.8 25.5 - - + +
239B LEU* 5.2 1.8 - - + -
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Residues in contact with LEU 215 (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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74B THR 4.4 2.5 - - - +
75B ILE* 4.3 21.1 - - + +
78B GLY* 3.6 25.8 - - - -
208B GLY 4.9 4.0 - - - +
211B GLN* 3.1 18.4 + - + +
212B ALA* 3.8 5.8 - - - +
213B ARG 3.1 0.2 - - - -
214B GLN* 1.3 77.6 - - - +
216B ASN* 1.3 60.0 + - - +
218B LEU* 3.8 7.4 + - + +
219B GLN* 3.4 29.3 + - - +
239B LEU* 3.6 41.0 - - + +
276B HIS* 3.2 48.5 - - + +
280B LEU* 5.2 3.1 - - + -
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Residues in contact with ASN 216 (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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212B ALA 3.3 13.0 + - - +
213B ARG* 3.1 11.5 + - - +
215B LEU* 1.3 76.7 - - - +
217B LEU* 1.3 64.6 + - + +
219B GLN* 3.1 23.3 + - - +
220B LEU 4.2 0.3 + - - -
275B ASP* 3.1 34.9 + - - -
276B HIS* 3.1 25.7 + - - +
277B ARG* 4.5 10.9 - - - +
100C PHE* 3.4 20.9 - - - -
108C MET* 3.6 20.2 - - - +
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Residues in contact with LEU 217 (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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213B ARG* 3.1 22.4 + - + +
214B GLN* 3.9 4.5 - - - +
216B ASN* 1.3 77.9 - - + +
218B LEU* 1.3 61.7 + - - +
219B GLN 3.1 0.9 + - - -
220B LEU* 3.2 17.0 + - - +
225B ALA* 3.3 16.1 - - + +
228B LEU* 3.9 13.2 - - + -
230B VAL* 3.4 33.9 - - + -
108C MET* 3.4 43.3 - - + +
111C ALA* 3.9 16.4 - - + -
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Residues in contact with LEU 218 (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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78B GLY 5.4 3.1 - - - +
79B LEU* 4.8 11.0 - - + -
81B ARG* 3.0 29.6 + - - +
139B ARG* 5.5 1.8 - - - +
214B GLN 2.8 19.1 + - - +
215B LEU* 4.0 7.2 - - + +
217B LEU* 1.3 74.5 - - - +
219B GLN* 1.3 68.0 + - - +
221B GLY* 3.2 5.8 + - - -
222B ASP* 4.3 10.5 - - - +
225B ALA* 4.1 13.2 - - + -
230B VAL* 4.7 4.0 - - + -
232B VAL* 3.6 33.9 - - + -
235B ALA* 3.6 30.5 - - + -
236B LYS* 4.6 4.5 - - + +
239B LEU* 4.1 19.1 - - + -
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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