Contacts of the helix formed by residues 211 - 220 (chain B) in PDB entry 3QNQ
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 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA 5.8 0.2 - - - -
116B PRO* 4.4 15.2 - - - +
201B ARG* 6.4 1.1 - - - -
204B PHE* 3.6 15.1 - - - +
205B GLU* 5.8 0.4 - - - -
209B PHE 3.4 4.0 - - - +
210B GLY* 1.3 81.3 - - - +
212B ILE* 1.3 63.7 + - - +
213B HIS* 2.9 50.0 + - - -
214B ASN* 3.6 6.1 - - - +
215B VAL* 3.7 12.0 + - - +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ALA* 4.2 34.8 + - + +
115B THR* 6.0 0.4 - - + -
148B VAL* 3.6 26.5 - - + -
151B ILE* 6.4 0.9 - - + -
152B ILE* 4.9 8.3 - - + -
197B VAL* 4.8 4.0 - - + +
200B ILE* 3.6 30.5 - - + -
201B ARG* 4.1 25.6 - - + +
204B PHE* 4.7 8.5 - - + -
211B SER* 1.3 71.0 - - - +
213B HIS* 1.3 66.4 + - - +
214B ASN 2.9 5.8 + - - -
215B VAL* 3.0 24.7 - - + +
216B VAL* 3.1 15.2 + - + +
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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
----------------------------------------------------------
114B ALA 5.4 0.2 + - - -
115B THR* 4.5 15.8 - - + +
116B PRO* 4.5 9.7 - - + +
140B LEU* 3.1 46.2 - - + +
144B GLN 5.8 2.2 - - - +
145B GLY* 6.2 1.1 - - - -
148B VAL* 4.8 13.5 - - + -
211B SER* 2.9 25.7 + - - -
212B ILE* 1.3 82.8 - - - +
214B ASN* 1.3 90.1 + - + +
216B VAL* 3.8 6.4 - - - +
217B GLY* 2.8 24.9 + - - -
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Residues in contact with ASN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 3.2 30.5 - - + +
210B GLY 3.4 6.5 - - - +
211B SER* 3.6 16.1 - - - +
212B ILE 2.9 0.4 + - - -
213B HIS* 1.3 94.3 - - + +
215B VAL* 1.3 56.5 + - - +
216B VAL 3.0 1.3 - - - -
217B GLY* 3.0 1.4 + - - -
218B LYS* 2.7 55.2 + - - +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.2 47.8 - - + -
209B PHE* 3.7 29.3 - - + +
211B SER 3.7 4.8 + - - +
212B ILE* 3.0 16.8 - - + +
214B ASN* 1.3 79.1 - - - +
216B VAL* 1.3 66.3 + - + +
219B LEU* 3.1 51.7 + - + +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 4.2 35.7 - - + +
148B VAL* 4.2 8.1 - - + +
151B ILE* 4.8 17.0 - - + -
212B ILE* 3.1 28.9 + - + +
213B HIS* 3.8 5.6 - - - +
214B ASN 3.0 0.4 - - - -
215B VAL* 1.3 89.4 - - + +
217B GLY* 1.3 58.7 + - - +
220B LEU* 2.9 48.6 + - + +
221B GLN* 2.9 4.9 + - + -
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Residues in contact with GLY 217 (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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213B HIS 2.8 18.8 + - - -
214B ASN* 3.0 1.5 + - - -
216B VAL* 1.3 78.7 - - - +
218B LYS* 1.3 59.7 + - - +
221B GLN* 3.6 17.9 - - - -
222B GLU* 2.9 38.3 + - - +
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Residues in contact with LYS 218 (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 PHE* 4.4 16.4 - - + -
214B ASN* 2.7 38.4 + - - +
215B VAL 4.1 2.7 - - - +
217B GLY* 1.3 74.4 - - - +
219B LEU* 1.3 65.9 + - + +
222B GLU* 3.3 35.0 - - - +
223B PRO* 3.5 16.3 - - - +
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Residues in contact with LEU 219 (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 PHE* 4.1 23.1 - - + -
215B VAL* 3.1 38.1 + - + +
218B LYS* 1.3 82.7 - - + +
220B LEU* 1.3 68.4 + - + +
223B PRO* 3.6 13.5 - - - +
224B LEU* 5.7 0.3 - - - +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 4.3 16.8 - - + -
151B ILE* 4.1 25.8 - - + -
216B VAL* 2.9 24.0 + - + +
218B LYS 3.5 0.6 - - - -
219B LEU* 1.3 87.8 - - + +
221B GLN* 1.3 68.6 + - - +
222B GLU 2.9 3.5 + - - -
223B PRO* 3.0 11.5 - - - +
224B LEU* 3.1 39.3 + - + +
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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
------------------------------------------------------------
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