Contacts of the helix formed by residues 209 - 216 (chain B) in PDB entry 2QKW
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 ASP 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TYR 3.3 4.0 + - - -
208B ILE* 1.3 75.1 - - - +
210B PRO* 1.4 62.2 - - - +
211B GLU* 2.8 16.7 + - - +
212B TYR* 2.9 23.2 + - + +
213B PHE 2.9 22.7 + - - -
217B ARG 5.1 0.5 - - - +
219B THR* 4.5 2.3 + - - -
222B SER* 2.7 44.2 + - - +
225B TYR* 3.9 7.0 - - + -
226B SER* 4.7 1.4 + - - -
300B ARG* 2.7 44.4 + - - +
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Residues in contact with PRO 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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208B ILE 3.1 9.8 - - - +
209B ASP* 1.4 87.4 - - - +
211B GLU* 1.3 53.4 + - - +
213B PHE* 3.6 8.2 - - + +
214B ILE* 2.8 45.6 + - + +
225B TYR* 3.4 36.6 - - + +
295B LEU* 4.2 22.7 - - + +
300B ARG* 3.9 5.2 - - - +
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Residues in contact with GLU 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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209B ASP* 2.8 14.8 + - - +
210B PRO* 1.3 79.4 - - - +
212B TYR* 1.3 62.6 - - - +
214B ILE* 4.1 6.3 - - + -
215B LYS* 3.2 53.4 + - + +
217B ARG* 3.1 35.4 + - - +
219B THR* 5.1 1.6 + - - -
295B LEU 3.8 13.0 + - - +
296B SER* 3.4 12.8 - - - -
297B SER* 2.7 43.4 + - - -
298B GLU* 4.7 0.5 + - - +
300B ARG* 4.4 0.7 - - - +
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Residues in contact with TYR 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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163B ARG* 3.3 19.0 + - + -
199B TPO 3.9 14.6 - - - +
200B VAL 2.2 33.5 + - - -
201B VAL* 3.3 15.9 - - + +
202B LYS 3.2 31.5 + - - -
208B ILE* 4.5 12.1 - - + -
209B ASP* 2.9 27.2 + - + +
211B GLU* 1.3 79.6 - - - +
213B PHE* 1.3 55.0 + - - +
216B GLY 3.1 18.8 + - - -
217B ARG 3.3 27.8 + - - +
218B LEU* 3.8 35.0 - - + -
222B SER* 3.9 5.8 - - - +
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Residues in contact with PHE 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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96A ILE* 3.8 30.7 - - + -
201B VAL* 4.1 16.2 - - + +
205B LEU* 6.3 3.1 - - + -
208B ILE* 3.9 22.0 - - + +
209B ASP 2.9 12.2 + - - +
210B PRO* 3.2 11.4 + - + +
212B TYR* 1.3 78.8 - - - +
214B ILE* 1.3 79.2 + - + +
215B LYS 3.5 0.3 + - - -
216B GLY* 4.4 1.6 + - - -
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Residues in contact with ILE 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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210B PRO* 2.8 31.1 + - + +
211B GLU* 4.0 5.4 - - + +
213B PHE* 1.3 89.0 - - + +
215B LYS* 1.3 93.0 + - + +
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Residues in contact with LYS 215 (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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198B SEP 4.1 9.4 + - - -
211B GLU* 3.2 30.7 + - + +
213B PHE 4.8 0.2 - - - -
214B ILE* 1.3 106.6 - - + +
216B GLY* 1.3 59.6 + - - +
217B ARG* 3.3 32.9 + - + +
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Residues in contact with GLY 216 (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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198B SEP 3.8 13.5 + - - +
199B TPO 3.2 37.6 + - - +
201B VAL* 4.7 6.5 - - - -
212B TYR* 3.1 21.4 + - - -
213B PHE 4.4 1.2 + - - -
214B ILE 3.9 0.2 - - - -
215B LYS* 1.3 76.2 - - - +
217B ARG* 1.3 61.6 + - - +
218B LEU 3.7 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