Contacts of the helix formed by residues 203 - 214 (chain B) in PDB entry 4GJ0
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 SER 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B GLN* 4.7 7.1 + - - -
201B ILE* 4.2 0.2 - - - +
202B HIS* 1.3 80.9 - - - +
204B PRO* 1.3 73.8 - - - +
205B GLU* 3.4 17.9 + - - +
206B GLU* 2.9 24.8 + - - +
207B GLN* 3.0 23.0 + - - +
242B TYR* 3.7 11.4 - - - +
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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
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203B SER* 1.3 88.0 - - - +
205B GLU* 1.3 73.2 + - - +
207B GLN* 3.4 1.3 + - + +
208B ASP* 2.8 40.0 + - - +
242B TYR* 3.7 30.5 - - + +
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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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170B PHE* 3.6 24.3 - - + -
171B GLN* 4.2 10.0 + - - +
203B SER* 3.1 19.2 + - - +
204B PRO* 1.3 88.3 - - - +
206B GLU* 1.3 63.9 + - - +
208B ASP* 3.4 10.1 + - - +
209B PHE* 3.0 17.5 + - - +
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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
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170B PHE* 3.7 16.3 - - + -
171B GLN* 4.9 4.9 - - - +
173B LYS* 2.9 23.5 + - - +
175B TYR* 2.4 34.4 + - + +
200B SER 3.3 11.2 - - - +
201B ILE* 3.5 2.8 - - + -
202B HIS* 2.7 36.4 + - - +
203B SER* 2.9 19.5 + - - +
205B GLU* 1.3 73.7 - - - +
207B GLN* 1.3 68.0 + - - +
209B PHE* 3.1 4.2 + - + +
210B LEU* 3.0 38.3 + - + +
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Residues in contact with GLN 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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201B ILE* 3.6 16.0 - - + +
203B SER 3.0 11.0 + - - +
204B PRO 3.6 6.3 - - - +
206B GLU* 1.3 75.2 - - - +
208B ASP* 1.3 61.9 + - - +
210B LEU* 3.1 6.2 + - - +
211B THR* 2.8 43.8 + - - +
242B TYR* 3.2 28.3 - - + +
244B ASN* 3.4 20.8 - - - +
262B MET* 3.6 17.2 - - - -
266B GLY 3.3 11.4 + - - -
268B TRP* 2.9 29.5 + - - -
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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
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204B PRO* 2.8 30.1 + - - +
205B GLU* 3.7 9.6 - - - +
206B GLU 3.2 0.2 - - - -
207B GLN* 1.3 80.1 - - - +
209B PHE* 1.3 61.1 + - - +
211B THR* 3.4 7.9 + - - -
212B LYS* 3.2 43.8 + - - +
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Residues in contact with PHE 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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168B ILE* 4.0 22.0 - - + -
169B ASN 4.2 7.2 - - - -
170B PHE* 3.6 48.0 - + + -
175B TYR* 3.5 32.5 - + - -
177B PHE* 4.0 16.8 - + - -
205B GLU 3.0 14.6 + - - +
206B GLU 3.1 6.9 + - - +
208B ASP* 1.3 76.7 - - - +
210B LEU* 1.3 71.0 + - + +
212B LYS* 3.4 11.9 + - + +
213B HIS* 2.8 55.8 + + - -
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Residues in contact with LEU 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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175B TYR* 3.8 26.9 - - + -
177B PHE* 3.9 24.4 - - + -
199B VAL* 4.2 10.8 - - + -
201B ILE* 3.6 40.8 - - + -
206B GLU* 3.0 24.0 + - + +
207B GLN* 3.5 11.0 - - - +
209B PHE* 1.3 77.7 - - + +
211B THR* 1.3 62.4 + - - +
213B HIS* 3.0 4.5 + - - +
214B ALA* 2.7 31.9 + - - +
262B MET* 4.2 11.2 - - + -
281B VAL* 4.2 10.5 - - + -
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Residues in contact with THR 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 GLN* 2.8 39.7 + - - +
208B ASP* 3.7 9.5 + - - -
210B LEU* 1.3 72.1 - - - +
212B LYS* 1.3 63.8 + - + +
213B HIS 3.3 0.5 + - - -
214B ALA* 3.3 21.2 + - - +
244B ASN* 5.3 0.2 + - - -
264B GLY 4.1 7.7 - - - +
265B SER* 3.5 25.9 + - - +
266B GLY* 3.4 8.9 - - - -
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Residues in contact with LYS 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* 3.2 31.7 + - - +
209B PHE* 3.6 12.8 - - + +
210B LEU 3.1 0.8 - - - -
211B THR* 1.3 77.0 - - + +
213B HIS* 1.3 72.5 + - + +
214B ALA 3.5 0.9 - - - +
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Residues in contact with HIS 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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168B ILE* 4.0 27.3 - - + +
177B PHE* 3.4 42.0 - + + +
209B PHE* 2.8 50.4 + + - -
210B LEU 3.0 3.2 + - - +
212B LYS* 1.3 87.6 - - + +
214B ALA* 1.3 66.0 + - - +
215B SER 3.8 0.7 + - - -
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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
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177B PHE* 4.8 5.2 - - - -
210B LEU 2.7 14.6 + - - +
211B THR* 3.3 17.3 + - - +
212B LYS 5.1 0.7 - - - +
213B HIS* 1.3 80.8 - - - +
215B SER* 1.3 68.9 + - - +
216B HIS* 3.6 1.6 + - - -
219B SER* 4.9 1.1 - - - +
262B MET* 3.5 26.9 - - + -
263B ARG 4.6 8.7 - - - +
264B GLY 4.8 4.6 - - - +
266B GLY* 5.7 0.2 - - - -
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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