Contacts of the helix formed by residues 200 - 212 (chain B) in PDB entry 4M6W
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 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B LEU 3.3 5.3 + - - -
196B GLU* 2.9 28.3 + - - -
199B VAL* 1.3 81.1 - - - +
201B GLN* 1.3 86.2 - - - +
203B VAL* 3.4 5.5 + - - +
204B ALA* 3.1 13.8 + - - -
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Residues in contact with GLN 201 (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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192B ILE* 5.7 0.3 - - - +
196B GLU* 2.8 20.2 + - - +
199B VAL 4.3 6.6 + - - +
200B GLY* 1.3 84.4 - - - +
202B ALA* 1.3 71.6 + - + +
203B VAL* 4.9 4.7 - - + +
204B ALA* 3.3 2.8 + - - +
205B GLN* 3.2 20.1 + - - +
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Residues in contact with ALA 202 (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 GLN* 1.3 82.8 - - + +
203B VAL* 1.3 55.7 + - + +
205B GLN* 3.2 7.0 + - - +
206B GLN* 2.7 41.9 + - - +
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Residues in contact with VAL 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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168B GLY 3.9 14.8 - - - +
169B VAL* 4.2 12.3 - - + -
173B LYS* 3.8 35.7 - - - +
199B VAL* 4.1 22.0 - - + +
200B GLY 3.4 7.6 + - - +
201B GLN* 3.4 4.4 - - + +
202B ALA* 1.3 77.8 - - + +
204B ALA* 1.3 61.3 - - - +
206B GLN* 3.2 12.8 + - - +
207B ILE* 3.1 24.4 + - + +
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Residues in contact with ALA 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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192B ILE* 4.3 8.1 - - + +
195B LEU* 3.5 50.0 - - + +
196B GLU* 3.6 9.4 - - + +
199B VAL* 3.8 7.8 - - - +
200B GLY 3.1 17.3 + - - +
201B GLN 3.5 9.4 - - - +
203B VAL* 1.3 78.3 - - - +
205B GLN* 1.3 59.9 + - - +
207B ILE* 3.6 1.4 + - - -
208B HIS* 3.4 17.2 + - - +
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Residues in contact with GLN 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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192B ILE* 4.2 34.0 - - + +
201B GLN 3.2 9.3 + - - +
202B ALA* 3.2 9.5 + - - +
204B ALA* 1.3 76.5 - - - +
206B GLN* 1.3 59.3 + - - +
208B HIS* 3.9 6.3 + - - +
209B ALA* 2.9 40.0 + - - +
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Residues in contact with GLN 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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167B PRO* 3.3 35.4 - - + +
168B GLY* 3.6 23.2 + - - +
202B ALA* 2.7 25.5 + - - +
203B VAL* 3.2 17.5 + - - +
205B GLN* 1.3 75.1 - - - +
207B ILE* 1.3 59.7 + - - +
209B ALA* 4.0 5.9 - - + +
210B PHE* 3.4 17.8 + - - +
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Residues in contact with ILE 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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166B ILE* 4.2 17.0 - - + -
167B PRO 4.1 11.0 - - - +
169B VAL* 4.0 21.3 - - + -
177B LEU* 3.8 27.8 - - + -
187B LEU* 5.0 10.1 - - + +
195B LEU* 4.3 19.3 - - + -
199B VAL* 4.1 13.5 - - + -
203B VAL* 3.1 17.5 + - + +
204B ALA* 3.9 4.3 - - - +
205B GLN 3.3 0.2 - - - -
206B GLN* 1.3 76.8 - - - +
208B HIS* 1.3 64.2 + - - +
210B PHE* 3.4 3.5 + - - +
211B PHE* 3.3 42.3 + - + -
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Residues in contact with HIS 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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1998A LYS* 6.0 2.2 + - - -
188B SER 5.4 5.6 - - - -
190B ALA 3.3 24.9 - - - -
191B SER* 4.9 2.6 - - - -
192B ILE* 3.6 42.8 + - + +
195B LEU* 4.1 6.0 - - + +
204B ALA 3.4 11.2 + - - +
205B GLN* 3.5 7.4 + - - +
207B ILE* 1.3 76.6 - - - +
209B ALA* 1.3 60.4 + - - +
211B PHE* 3.5 6.0 + - + +
212B THR* 3.0 56.6 + - + -
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Residues in contact with ALA 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 GLN* 2.9 33.5 + - - +
206B GLN* 4.2 7.0 - - - +
207B ILE 3.3 0.2 - - - -
208B HIS* 1.3 74.3 + - - +
210B PHE* 1.3 61.1 + - - +
212B THR* 2.9 25.7 - - - +
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Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1971A GLU 5.4 1.8 - - - -
1972A ALA* 4.3 23.8 - - + -
1975A PHE* 3.8 35.7 - + + -
1997A VAL* 3.4 34.0 - - + +
165B GLN 5.1 1.3 - - - -
166B ILE* 3.7 35.2 - - + -
167B PRO* 3.7 24.7 - - + -
206B GLN 3.4 13.9 + - - +
207B ILE 3.5 9.0 - - - +
209B ALA* 1.3 80.8 - - - +
211B PHE* 1.3 76.2 + + - +
213B GLN 4.0 7.3 - - - +
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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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1975A PHE* 4.9 1.1 - + - -
1996A SER* 3.5 8.7 - - - -
1997A VAL* 3.7 31.5 + - + -
1998A LYS* 3.2 38.4 + - + +
166B ILE* 4.0 24.0 - - + -
184B ILE* 4.5 15.7 - - + -
187B LEU* 3.5 23.1 - - + -
188B SER* 3.7 42.0 - - - +
195B LEU* 6.5 0.2 - - + -
207B ILE* 3.3 38.0 + - + +
208B HIS* 3.5 6.9 + - + +
210B PHE* 1.3 85.6 - + - +
212B THR* 1.3 62.8 + - - +
213B GLN 3.6 2.1 - - - +
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Residues in contact with THR 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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1996A SER* 4.6 0.4 - - - -
1998A LYS* 4.8 12.7 - - + +
208B HIS* 3.0 42.9 + - + -
209B ALA* 2.9 23.0 - - - +
211B PHE* 1.3 71.9 - - - +
213B GLN* 1.3 79.3 + - + +
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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