Contacts of the helix formed by residues 209 - 223 (chain B) in PDB entry 2QPA
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 GLU 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B TRP* 3.8 24.3 + - + +
208B GLY* 1.3 75.1 - - - +
210B SER* 1.3 63.9 + - - +
211B GLU 4.0 0.2 - - - -
212B LYS* 4.3 12.8 - - + -
213B LEU* 3.5 21.9 + - + +
216B GLN* 6.3 1.3 - - - +
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Residues in contact with SER 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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202B LEU* 4.0 13.2 - - - +
206B TRP 3.6 12.0 + - - -
207B MET* 3.3 39.5 - - - -
208B GLY 3.4 3.8 + - - -
209B GLU* 1.3 75.8 - - - +
211B GLU* 1.3 54.8 + - - +
212B LYS 2.5 18.6 + - - -
213B LEU* 3.2 8.9 + - - +
214B VAL* 3.4 13.0 + - - +
252B ILE* 4.4 8.1 - - - -
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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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210B SER* 1.3 75.4 - - - +
212B LYS* 1.3 56.3 + - - +
214B VAL* 4.2 8.9 - - - +
215B LYS* 4.8 5.4 - - - +
252B ILE* 3.2 30.9 - - + +
255B GLU* 4.1 22.7 - - + +
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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
----------------------------------------------------------
209B GLU* 4.5 14.8 - - + +
210B SER 2.5 14.1 + - - -
211B GLU* 1.3 74.5 - - - +
213B LEU* 1.3 60.8 + - - +
214B VAL 2.9 6.3 + - - -
215B LYS* 3.4 10.3 + - - +
216B GLN* 3.2 27.0 + - - +
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Residues in contact with LEU 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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122B ALA* 6.6 0.2 - - + -
123B ILE* 4.9 11.0 - - + +
202B LEU* 5.9 7.9 - - + -
206B TRP* 6.4 1.1 - - + -
209B GLU* 3.5 19.0 + - + +
210B SER 3.2 4.0 + - - +
212B LYS* 1.3 78.0 - - - +
214B VAL* 1.3 57.2 + - + +
216B GLN* 3.1 22.2 - - + +
217B LEU* 3.0 27.4 + - - +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 5.6 11.4 - - + -
210B SER 3.4 18.4 - - - +
211B GLU* 4.2 11.4 - - - -
212B LYS 2.9 0.6 - - - -
213B LEU* 1.3 73.6 - - + +
215B LYS* 1.3 67.6 + - - +
216B GLN 3.0 1.1 - - - -
217B LEU* 3.0 18.3 + - - +
218B PHE* 3.2 36.1 + - + -
252B ILE* 5.0 6.1 - - + +
255B GLU* 3.5 30.1 - - + -
256B LEU* 4.4 12.8 - - + +
259B GLN* 4.6 1.1 - - + -
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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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211B GLU 4.8 6.5 - - - +
212B LYS* 3.4 9.5 + - - +
214B VAL* 1.3 79.1 - - - +
216B GLN* 1.3 53.6 + - + +
218B PHE* 3.2 1.9 + - - +
219B ALA* 2.6 39.6 + - + +
255B GLU* 3.2 42.8 + - + +
259B GLN* 3.3 19.8 + - - +
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Residues in contact with GLN 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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120B SER* 4.8 15.9 - - - -
121B SER 6.1 0.2 - - - +
123B ILE* 5.6 0.2 - - + -
212B LYS* 3.2 17.4 + - - +
213B LEU* 3.1 26.8 - - + +
215B LYS* 1.3 78.3 - - + +
217B LEU* 1.3 61.8 + - - +
219B ALA* 3.5 6.4 - - - +
220B MET* 3.0 37.8 + - + +
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Residues in contact with LEU 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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123B ILE* 4.2 14.1 - - + -
124B LEU 4.8 0.7 - - - +
195B PHE* 3.5 41.2 - - + +
196B SER 4.1 8.5 - - - +
197B VAL* 3.4 28.5 - - + -
213B LEU 3.0 11.9 + - - +
214B VAL* 3.0 12.1 + - - +
216B GLN* 1.3 79.3 - - - +
218B PHE* 1.3 69.6 + - + +
219B ALA 3.1 0.2 + - - -
220B MET* 3.1 16.6 + - + +
221B ALA 3.3 8.8 + - - -
229B ILE* 3.2 35.1 - - + +
231B ILE* 4.5 4.0 - - + -
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Residues in contact with PHE 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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214B VAL* 3.2 28.2 + - + -
215B LYS 3.2 1.9 + - - +
217B LEU* 1.3 81.4 - - + +
219B ALA* 1.3 64.6 + - - +
221B ALA* 3.4 1.2 + - - +
222B ARG* 2.7 39.6 + - - +
229B ILE* 4.0 39.0 - - + -
231B ILE* 4.7 3.1 - - + -
256B LEU* 4.0 30.5 - - + -
259B GLN* 3.4 63.9 - - + +
260B MET* 4.4 2.2 - - + -
270B VAL* 5.3 4.7 - - + +
272B VAL* 4.1 17.0 - - + -
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Residues in contact with ALA 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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215B LYS* 2.6 25.2 + - + +
216B GLN* 3.5 8.5 - - - +
218B PHE* 1.3 72.6 - - - +
220B MET* 1.3 54.3 + - + +
222B ARG* 3.0 11.2 - - - +
223B GLU* 2.7 53.0 + - - +
259B GLN* 5.2 0.2 - - - +
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Residues in contact with MET 220 (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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119B LEU 5.2 7.4 - - - -
120B SER* 4.0 21.5 - - - -
123B ILE* 3.9 27.8 - - + +
125B SER* 5.1 6.3 - - - -
195B PHE* 3.6 21.3 - - + -
216B GLN* 3.0 33.9 + - + +
217B LEU* 3.5 16.4 - - + +
219B ALA* 1.3 77.1 - - + +
221B ALA* 1.3 60.3 + - - +
223B GLU* 3.1 17.0 - - - +
224B ASN* 2.9 33.0 + - - +
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Residues in contact with ALA 221 (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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195B PHE* 3.6 23.0 - - + -
217B LEU 3.3 2.8 + - - -
218B PHE 3.9 1.1 - - - +
220B MET* 1.3 75.4 - - - +
222B ARG* 1.3 60.3 + - - +
224B ASN* 2.6 31.8 + - - -
225B LYS* 3.2 2.4 + - - +
227B SER* 3.0 25.1 + - - +
229B ILE* 3.3 33.7 - - + -
270B VAL* 4.0 4.9 - - + -
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Residues in contact with ARG 222 (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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218B PHE* 2.7 39.0 + - - +
219B ALA* 3.0 12.3 - - - +
221B ALA* 1.3 74.9 - - - +
223B GLU* 1.3 59.2 + - + +
225B LYS* 3.2 35.5 - - - +
259B GLN* 4.2 21.4 + - - +
263B VAL* 3.6 30.4 - - - +
270B VAL* 4.1 13.8 - - + +
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Residues in contact with GLU 223 (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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219B ALA* 2.7 46.3 + - - +
220B MET* 3.1 16.9 + - - +
222B ARG* 1.3 73.9 - - + +
224B ASN* 1.3 64.3 + - - +
225B LYS 3.9 0.7 - - - -
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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