Contacts of the helix formed by residues 220 - 230 (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 LEU 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with GLN 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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143B SER 4.3 4.4 + - - -
144B GLN* 3.7 40.6 + - - +
146B LEU* 4.7 0.2 - - - +
147B PHE* 3.1 51.4 - - + +
216B VAL* 2.9 5.7 + - + +
217B GLY* 3.6 20.2 - - - +
220B LEU* 1.3 76.8 - - - +
222B GLU* 1.3 58.7 + - + +
224B LEU* 4.0 0.5 - - - +
225B SER* 2.7 49.5 + - - +
261B PRO 4.5 2.5 + - - +
262B ILE* 5.4 0.2 - - - -
265B SER* 3.0 28.7 + - - -
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Residues in contact with GLU 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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217B GLY 2.9 23.9 + - - +
218B LYS* 3.3 40.5 - - - +
220B LEU 2.9 1.4 + - - -
221B GLN* 1.3 75.4 - - + +
223B PRO* 1.3 69.2 - - + +
224B LEU 3.1 1.6 - - - -
225B SER* 3.1 17.1 + - - -
226B ILE* 3.3 14.4 + - - +
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Residues in contact with PRO 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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218B LYS 3.5 14.1 - - - +
219B LEU* 3.6 18.4 - - - +
220B LEU 3.0 18.6 - - - +
222B GLU* 1.3 93.3 - - + +
224B LEU* 1.3 58.5 + - + +
226B ILE* 3.3 15.4 - - + +
227B LEU* 3.2 26.9 + - - +
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Residues in contact with LEU 224 (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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147B PHE* 3.9 21.1 - - + -
220B LEU* 3.1 43.1 + - + +
221B GLN 4.2 2.0 - - - +
222B GLU 3.1 0.6 - - - -
223B PRO* 1.3 77.1 - - + +
225B SER* 1.3 67.0 + - - +
226B ILE 3.0 1.6 - - - -
227B LEU* 3.3 26.8 + - + +
228B GLY* 2.9 20.8 + - - -
262B ILE* 3.7 22.7 - - + +
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Residues in contact with SER 225 (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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221B GLN* 2.7 39.5 + - - +
222B GLU* 3.4 8.0 - - - -
224B LEU* 1.3 76.3 - - - +
226B ILE* 1.3 62.7 + - - +
228B GLY* 3.4 0.7 + - - -
229B ALA* 3.1 27.7 + - - +
262B ILE* 3.6 16.6 - - - +
265B SER* 4.2 1.2 + - - -
266B LEU* 3.8 25.4 - - - +
269B GLN* 5.3 3.9 + - - -
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Residues in contact with ILE 226 (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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222B GLU 3.3 10.9 + - - +
223B PRO* 3.3 18.6 - - + +
224B LEU 3.0 0.8 - - - -
225B SER* 1.3 79.5 - - - +
227B LEU* 1.3 77.8 + - + +
228B GLY 2.9 2.1 + - - -
229B ALA* 3.3 13.1 + - + +
230B SER* 3.3 10.0 + - - -
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Residues in contact with LEU 227 (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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223B PRO 3.2 10.6 + - - +
224B LEU* 3.3 29.1 + - + +
226B ILE* 1.3 88.2 - - + +
228B GLY* 1.3 56.1 + - - +
230B SER* 3.0 25.0 - - - -
233B GLY* 3.4 11.6 - - - -
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Residues in contact with GLY 228 (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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224B LEU 2.9 16.8 + - - -
225B SER 3.7 2.7 - - - -
226B ILE 2.9 2.0 - - - -
227B LEU* 1.3 75.3 - - - +
229B ALA* 1.3 55.9 + - - -
230B SER 3.0 12.7 + - - +
233B GLY* 4.0 10.5 - - - -
259B MET* 4.4 16.6 - - - -
262B ILE* 4.4 11.7 - - - -
263B TRP* 4.4 4.1 + - - -
266B LEU* 4.5 1.6 - - - -
284B ILE* 3.5 16.6 - - - +
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Residues in contact with ALA 229 (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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225B SER 3.1 12.4 + - - +
226B ILE* 3.3 5.1 + - + +
228B GLY* 1.3 71.3 - - - +
230B SER* 1.3 66.8 + - - +
266B LEU* 3.4 22.6 - - + +
282B ASN* 4.2 15.5 - - + +
283B THR 5.9 0.2 - - - +
284B ILE* 3.7 25.0 + - + +
364B TYR* 4.3 9.4 + - - -
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Residues in contact with SER 230 (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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226B ILE 3.3 8.1 + - - -
227B LEU* 3.0 26.0 - - - -
228B GLY 3.0 1.7 - - - +
229B ALA* 1.3 85.5 - - - +
231B LEU* 1.3 65.4 + - - +
232B TRP* 3.1 18.9 + - - +
233B GLY 3.3 7.2 + - - -
234B ALA* 3.2 22.3 + - - +
284B ILE* 4.0 2.1 - - - +
364B TYR* 4.7 0.9 - - - -
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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