Contacts of the helix formed by residues 211 - 222 (chain X) in PDB entry 2DQ7
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 ASN 211 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171X LYS* 3.9 2.0 - - - +
210X MET* 1.3 76.4 - - - +
212X ASN* 1.3 54.8 + - - +
213X ARG* 2.6 22.1 + - - +
214X GLU* 2.4 83.6 + - - +
215X VAL* 2.7 15.4 + - - -
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Residues in contact with ASN 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X LYS* 4.9 10.5 - - - +
169X PRO* 4.9 1.2 - - - +
170X ILE* 2.8 50.6 - - + +
171X LYS* 3.7 22.0 - - - +
211X ASN* 1.3 72.2 - - - +
213X ARG* 1.3 59.9 + - - +
215X VAL* 4.1 2.7 - - - -
216X LEU* 3.3 30.7 + - - +
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Residues in contact with ARG 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X ASN* 2.6 20.2 + - - +
212X ASN* 1.3 73.4 - - - +
214X GLU* 1.3 67.6 + - + +
216X LEU* 3.3 24.9 - - - +
217X GLU* 3.6 6.5 + - - +
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Residues in contact with GLU 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209X GLY 4.1 5.1 - - - +
210X MET* 3.7 23.1 - - + +
211X ASN* 2.4 57.2 + - - +
213X ARG* 1.3 72.5 - - + +
215X VAL* 1.3 63.5 + - - +
216X LEU 2.9 4.3 - - - -
217X GLU* 2.7 19.5 + - - +
218X GLN* 3.2 10.2 + - - +
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Residues in contact with VAL 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X ILE* 4.5 13.2 - - + +
171X LYS* 3.2 32.5 - - + +
207X TYR* 3.6 41.1 - - + -
210X MET* 3.4 33.3 - - + +
211X ASN 2.7 17.5 + - - +
212X ASN* 4.4 5.2 - - - +
214X GLU* 1.3 72.3 - - - +
216X LEU* 1.3 48.2 + - - +
218X GLN* 5.2 0.2 + - - -
219X VAL* 2.7 40.1 + - + +
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Residues in contact with LEU 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X ILE* 3.8 30.7 - - + +
175X PRO* 6.2 2.5 - - + -
178X ALA* 5.3 4.5 - - + +
179X LEU* 4.0 32.5 - - + +
212X ASN 3.3 19.3 + - - +
213X ARG* 3.3 19.1 - - - +
214X GLU 2.8 2.0 + - - -
215X VAL* 1.3 79.4 - - - +
217X GLU* 1.3 57.6 + - - +
219X VAL* 3.1 19.3 - - + +
220X GLU* 3.3 13.0 - - - +
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Residues in contact with GLU 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213X ARG 3.6 5.3 + - - +
214X GLU* 2.7 15.7 + - - +
216X LEU* 1.3 74.2 - - - +
218X GLN* 1.3 65.8 + - - +
220X GLU* 3.2 15.1 + - - +
221X ARG* 2.9 70.2 + - - +
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Residues in contact with GLN 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207X TYR* 4.2 14.5 - - - -
210X MET* 3.3 39.8 - - + +
214X GLU 3.2 7.0 + - - +
217X GLU* 1.3 79.4 - - - +
219X VAL* 1.3 64.7 + - - +
221X ARG* 3.1 12.6 + - - +
222X GLY 3.1 0.3 + - - -
223X TYR* 2.6 73.8 + - + +
224X ARG 3.0 20.6 + - - +
225X MET* 5.7 0.2 - - - +
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Residues in contact with VAL 219 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175X PRO* 4.2 19.0 - - + +
190X TRP* 3.3 39.7 - - + -
207X TYR* 4.9 8.3 - - + +
215X VAL* 2.7 32.2 + - + +
216X LEU* 3.1 17.3 - - + +
218X GLN* 1.3 75.9 - - - +
220X GLU* 1.3 73.6 + - - +
222X GLY* 2.9 5.7 + - - -
223X TYR 3.1 13.6 + - - +
224X ARG* 2.8 25.5 + - - +
245X LYS* 5.2 0.5 - - - -
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Residues in contact with GLU 220 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175X PRO* 5.6 6.0 - - - +
179X LEU* 4.6 17.7 - - + +
180X TYR* 5.7 0.9 + - - -
216X LEU 3.3 18.2 - - - +
217X GLU* 3.3 19.3 - - - +
218X GLN 3.1 0.6 - - - -
219X VAL* 1.3 80.9 - - + +
221X ARG* 1.3 66.2 + - + +
222X GLY 2.6 15.3 + - - -
245X LYS* 3.1 37.0 + - - +
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Residues in contact with ARG 221 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217X GLU* 2.9 61.0 + - - +
218X GLN* 3.6 7.9 - - - +
220X GLU* 1.3 78.2 - - + +
222X GLY* 1.3 57.2 + - - +
223X TYR* 3.6 26.4 - - + -
245X LYS* 5.0 1.3 - - - -
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Residues in contact with GLY 222 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X VAL 2.9 6.9 + - - -
220X GLU 2.6 13.1 + - - -
221X ARG* 1.3 75.3 - - - +
223X TYR* 1.3 70.3 + - - +
224X ARG* 3.5 21.1 + - - +
245X LYS* 4.9 8.1 - - - -
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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