Contacts of the helix formed by residues 202 - 212 (chain B) in PDB entry 4IXU
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 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ASN* 2.8 26.3 + - - +
155B SER* 4.6 3.6 + - - -
200B ASP 5.0 0.7 - - - +
201B VAL* 1.3 75.3 - - - +
203B PRO* 1.3 76.5 - - + +
204B PRO* 3.9 11.9 - - + -
205B GLU* 2.8 24.9 + - + +
206B HIS* 2.9 19.3 + - - +
406B 38I 2.9 62.5 + - + +
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Residues in contact with PRO 203 (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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329A GLY* 4.6 9.2 - - - +
201B VAL 3.8 2.2 - - - +
202B ASP* 1.3 84.0 - - + +
204B PRO* 1.3 73.9 - - + +
206B HIS* 3.1 9.9 + - + +
207B PHE* 3.0 21.3 + - - +
406B 38I 4.3 14.8 - - + -
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Residues in contact with PRO 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASN* 3.7 15.9 - - - +
153B THR* 3.5 39.0 - - + +
202B ASP* 3.5 6.7 - - + -
203B PRO* 1.3 99.0 - - + +
205B GLU* 1.3 56.8 + - - +
207B PHE* 3.3 9.5 + - + +
208B ILE* 3.0 33.4 + - - +
406B 38I 5.1 4.9 - - + -
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Residues in contact with GLU 205 (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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146B ALA* 3.7 8.3 + - + +
147B ASP* 3.1 12.6 + - - -
148B ILE* 3.0 44.7 + - + +
149B ASN* 3.4 33.9 + - - +
161B GLY 4.1 0.3 - - - +
200B ASP 4.4 1.7 - - - +
201B VAL* 3.7 14.7 - - + -
202B ASP* 2.8 38.4 + - + +
204B PRO* 1.3 74.3 - - - +
206B HIS* 1.3 62.8 + - - +
208B ILE* 3.1 5.2 + - - +
209B LEU* 2.9 33.3 + - - +
406B 38I 3.9 6.6 + - - -
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Residues in contact with HIS 206 (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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328A GLU* 2.9 31.8 + - + +
329A GLY* 3.6 30.9 + - - +
201B VAL* 3.7 5.9 - - + +
202B ASP 2.9 10.5 + - - +
203B PRO 3.1 8.3 + - - +
205B GLU* 1.3 76.9 - - - +
207B PHE* 1.3 65.8 + - - +
209B LEU* 3.4 6.4 + - - +
210B LYS* 3.0 61.4 + - + +
216B TYR* 3.9 9.6 + - - -
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Residues in contact with PHE 207 (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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203B PRO 3.0 12.0 + - - +
204B PRO* 3.4 13.2 - - + +
206B HIS* 1.3 80.7 - - - +
208B ILE* 1.3 62.0 - - + +
210B LYS* 3.2 4.9 + - - +
211B ASN* 2.7 68.4 + - + +
212B TYR* 5.4 2.5 - + - -
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Residues in contact with ILE 208 (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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148B ILE* 3.5 50.0 - - + +
150B THR* 4.1 19.5 - - + -
153B THR* 4.6 12.3 - - + +
171B LEU* 4.2 11.7 - - + -
204B PRO 3.0 22.6 + - - +
205B GLU* 3.1 8.0 + - - +
207B PHE* 1.3 84.9 - - + +
209B LEU* 1.3 62.7 + - - +
212B TYR* 3.0 52.4 + - + +
214B ILE* 4.2 3.1 - - + +
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Residues in contact with LEU 209 (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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328A GLU 5.5 1.3 - - - +
146B ALA* 4.3 9.2 - - + -
148B ILE* 4.4 10.3 - - + -
195B TYR* 3.6 32.8 - - + -
198B LEU* 4.0 17.7 - - + -
201B VAL* 4.4 12.8 - - + -
205B GLU 2.9 20.5 + - - +
206B HIS* 3.8 6.5 - - - +
208B ILE* 1.3 76.0 - - - +
210B LYS* 1.3 64.1 + - + +
213B ASP* 3.1 3.1 + - - -
214B ILE* 2.9 53.7 + - + +
216B TYR* 4.0 31.9 - - + -
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Residues in contact with LYS 210 (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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328A GLU* 4.5 3.7 + - - -
206B HIS* 3.0 48.2 + - + +
207B PHE* 3.7 4.3 - - - +
209B LEU* 1.3 76.8 - - + +
211B ASN* 1.3 66.0 + - - +
213B ASP* 3.2 15.1 + - - +
216B TYR* 3.3 33.7 + - + -
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Residues in contact with ASN 211 (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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207B PHE* 2.7 50.3 + - + +
210B LYS* 1.3 73.8 - - - +
212B TYR* 1.3 95.8 + - + +
213B ASP* 3.3 0.9 + - - +
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Residues in contact with TYR 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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170B GLU* 3.4 41.7 + - + -
171B LEU* 4.0 18.3 - - + +
174B LYS* 3.7 29.8 + - - +
190B SER* 3.4 22.9 + - - +
207B PHE* 5.4 3.4 - + - -
208B ILE* 3.0 48.0 + - + +
211B ASN* 1.3 100.8 + - + +
213B ASP* 1.3 70.7 + - - +
214B ILE* 3.2 15.8 + - + -
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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