Contacts of the helix formed by residues 200 - 207 (chain B) in PDB entry 2VQO
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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158B HIS* 3.3 30.5 - - - -
194B ASP* 3.5 2.9 + - - -
198B HIS 3.4 3.4 + - - -
199B HIS* 1.3 73.0 - - - +
201B ASN* 1.3 64.3 + - - -
202B GLY 3.2 3.8 + - - -
203B THR* 3.2 10.6 + - - -
204B GLN* 3.2 8.7 + - - +
215B TYR* 3.2 28.0 + - - -
217B SER* 4.1 1.2 + - - -
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Residues in contact with ASN 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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159B HIS* 2.8 53.0 + - - +
161B GLU* 2.7 34.3 + - - +
166B MET* 3.4 12.8 - - - +
199B HIS* 3.0 17.9 + - + +
200B GLY* 1.3 72.9 - - - +
202B GLY* 1.3 62.2 + - - +
204B GLN* 3.7 2.1 + - - +
205B GLN* 3.2 23.2 + - - +
228B PRO* 3.8 9.7 - - + +
230B SER* 3.4 23.8 - - - +
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 5.6 1.6 - - - +
158B HIS 3.0 13.0 + - - -
160B ALA 3.5 21.5 - - - +
161B GLU* 4.1 12.1 - - - -
172B ASN* 3.5 6.2 - - - +
201B ASN* 1.3 79.5 - - - +
203B THR* 1.3 59.5 + - - +
205B GLN* 3.5 5.8 + - - +
206B ALA* 3.0 28.2 + - - +
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Residues in contact with THR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B HIS* 3.8 15.8 + - - +
172B ASN* 3.0 24.3 + - - +
174B VAL* 5.4 1.1 - - + +
175B ALA* 4.5 6.3 - - + +
192B ILE* 3.9 28.3 - - + -
194B ASP* 4.7 0.7 + - - -
200B GLY 3.2 3.9 + - - -
202B GLY* 1.3 72.1 - - - +
204B GLN* 1.3 66.4 + - - +
206B ALA* 3.4 10.6 + - - -
207B PHE* 3.4 24.4 + - + +
215B TYR* 3.8 33.8 - - + -
286B SER* 4.9 2.9 + - - -
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Residues in contact with GLN 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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199B HIS* 2.9 33.4 + - + +
200B GLY 3.2 6.5 + - - +
201B ASN 3.9 7.9 - - - +
203B THR* 1.3 78.5 - - - +
205B GLN* 1.3 62.7 + - - +
207B PHE 3.8 1.1 - - - -
208B TYR* 3.1 52.4 + - + +
215B TYR* 3.8 20.6 - - + -
230B SER* 5.5 1.0 - - - -
235B GLU* 3.0 20.9 - - - +
245B ASN* 3.0 20.3 + - - +
247B ASN* 2.9 23.4 + - - +
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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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161B GLU* 3.3 29.6 + - + +
162B GLU* 3.0 38.2 + - - +
201B ASN 3.2 16.2 + - - +
202B GLY 3.5 5.1 - - - +
204B GLN* 1.3 81.4 - - - +
206B ALA* 1.3 62.9 + - - +
207B PHE 3.2 0.9 + - - -
208B TYR* 3.5 14.7 + - - +
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Residues in contact with ALA 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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70B VAL* 4.5 14.8 - - + -
175B ALA* 4.3 12.3 - - + -
179B LYS* 3.1 31.5 + - - +
202B GLY 3.0 17.4 + - - +
203B THR 3.7 1.1 - - - +
204B GLN 3.3 0.6 - - - -
205B GLN* 1.3 76.9 - - - +
207B PHE* 1.3 79.5 + - + +
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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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175B ALA* 3.4 36.6 - - + -
178B ALA* 3.4 26.2 - - + -
179B LYS* 3.6 26.9 - - + -
182B GLN* 4.1 5.2 - - - -
192B ILE* 3.8 11.0 - - + -
203B THR* 3.4 23.0 + - + +
204B GLN* 3.8 2.2 - - - +
205B GLN 3.2 0.4 - - - -
206B ALA* 1.3 82.5 - - + +
208B TYR* 1.3 59.7 + - - +
209B SER 3.2 4.4 + - - -
210B ASP* 3.2 22.2 + - + +
213B VAL* 3.6 44.0 - - + -
215B TYR* 5.6 3.4 - - + -
245B ASN* 5.9 0.2 - - - -
1408B K 2.7 30.0 - - - -
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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