Contacts of the helix formed by residues 203 - 214 (chain B) in PDB entry 4GWO
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 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B THR* 4.3 2.0 - - - +
150B GLU* 2.5 21.9 + - - +
166B TRP* 3.9 3.5 - - - -
168B ARG* 3.1 26.7 + - - -
197B TYR* 5.6 0.2 - - - -
202B THR* 1.3 72.1 - - - +
204B ARG* 1.3 64.5 + - - +
205B SER 3.2 2.9 - - - -
206B GLU* 3.1 16.8 + - - +
207B LEU* 3.5 4.2 + - - +
268B SER* 3.6 14.4 - - - -
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Residues in contact with ARG 204 (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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150B GLU* 3.5 1.8 + - - +
196B THR* 4.6 4.7 - - - +
197B TYR* 2.8 36.8 + - + +
198B THR* 3.5 12.8 - - - +
199B PHE* 3.3 39.1 - - + +
200B GLY 4.2 3.4 - - - +
201B PHE 2.9 18.0 + - - +
202B THR 3.2 0.8 + - - -
203B GLY* 1.3 78.7 - - - +
205B SER* 1.3 56.8 + - - +
207B LEU* 2.9 33.4 + - - +
208B ASP* 2.8 43.4 + - - +
218B PRO* 5.8 0.6 - - - +
220B ILE* 3.3 24.0 - - - +
223B THR* 3.8 16.6 - - - +
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLU* 4.1 16.8 + - - -
199B PHE* 5.9 7.6 - - - -
200B GLY 5.6 0.8 - - - +
204B ARG* 1.3 77.7 - - - +
206B GLU* 1.3 75.2 + - - +
208B ASP* 3.5 10.5 + - - +
209B THR* 2.6 35.4 + - - -
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 5.0 1.9 - - - +
150B GLU* 4.8 0.7 - - - +
168B ARG* 3.5 21.1 - - - +
203B GLY* 3.1 18.2 + - - +
205B SER* 1.3 97.1 + - - +
207B LEU* 1.3 61.6 + - - +
209B THR* 3.5 8.0 + - - -
210B ALA* 3.1 23.9 + - - +
265B PHE* 4.1 4.1 - - + +
266B SER* 3.7 25.8 + - - +
267B HIS 3.7 10.1 - - - +
268B SER* 2.3 33.8 + - - +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 5.1 5.3 - - - +
194B LEU* 5.0 4.0 - - + -
196B THR* 4.1 25.1 - - + +
203B GLY 3.5 4.9 + - - +
204B ARG* 2.9 24.4 + - - +
206B GLU* 1.3 76.0 - - - +
208B ASP* 1.3 81.0 + - - +
210B ALA* 3.4 1.9 + - - +
211B PHE* 3.0 56.0 + - + -
218B PRO* 4.7 2.0 - - + -
220B ILE* 4.1 15.7 - - + -
242B VAL* 4.2 24.5 - - + -
265B PHE* 3.9 19.3 - - + -
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Residues in contact with ASP 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 4.5 13.3 - - - +
204B ARG* 2.8 58.2 + - - +
205B SER* 4.0 9.2 - - - +
206B GLU 3.3 0.2 - - - -
207B LEU* 1.3 81.5 - - - +
209B THR* 1.3 53.8 + - - +
211B PHE* 3.2 6.0 + - - +
212B ASN* 2.7 39.6 + - + +
218B PRO* 5.2 4.3 - - - +
220B ILE* 5.0 0.3 - - - +
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Residues in contact with THR 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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205B SER* 2.6 24.0 + - - -
206B GLU* 3.6 8.9 + - - -
208B ASP* 1.3 76.3 - - - +
210B ALA* 1.3 65.3 + - - +
212B ASN* 4.6 3.4 - - - +
213B ARG* 3.0 71.4 + - + +
266B SER* 5.5 5.6 - - - +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 3.3 18.6 - - + +
206B GLU 3.1 14.9 + - - +
207B LEU 3.8 1.6 - - - +
208B ASP 3.3 0.4 - - - -
209B THR* 1.3 80.1 - - - +
211B PHE* 1.3 62.7 + - - +
213B ARG* 4.1 3.5 - - - +
214B ALA* 3.2 17.8 + - - +
264B ILE 3.4 25.1 - - - +
265B PHE* 3.7 16.4 - - + -
266B SER 5.5 0.9 - - - +
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Residues in contact with PHE 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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186B ILE* 3.7 20.9 - - + -
189B LEU* 3.5 28.5 - - + -
190B ALA* 3.6 24.9 - - + -
194B LEU* 3.9 11.0 - - + -
207B LEU* 3.0 61.0 + - + +
208B ASP* 3.8 3.6 - - - +
210B ALA* 1.3 75.4 - - - +
212B ASN* 1.3 62.9 + - - +
214B ALA 3.2 5.4 + - - -
216B LEU* 3.1 44.6 + - + +
218B PRO* 3.8 35.4 - - + -
265B PHE* 4.2 7.2 - + - -
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Residues in contact with ASN 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 ASP* 2.7 22.7 + - + +
209B THR* 4.0 4.7 - - - +
211B PHE* 1.3 73.1 - - - +
213B ARG* 1.3 63.3 + - + +
215B GLY* 2.9 22.6 + - - +
216B LEU 4.2 5.9 - - - +
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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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209B THR* 3.0 43.9 + - + +
210B ALA* 4.4 2.9 - - - +
212B ASN* 1.3 82.2 - - + +
214B ALA* 1.3 58.6 + - - +
215B GLY 3.1 1.8 + - - -
266B SER* 5.5 4.2 + - - -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 4.0 25.1 - - + -
187B GLU* 4.4 8.2 - - - +
210B ALA 3.2 17.2 + - - +
211B PHE 3.2 5.6 + - - +
212B ASN 3.1 1.4 - - - -
213B ARG* 1.3 76.3 - - - +
215B GLY* 1.3 54.0 + - - +
216B LEU* 3.0 25.4 + - + +
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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