Contacts of the helix formed by residues 219 - 224 (chain E) in PDB entry 2Q5E
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 219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D HIS* 6.0 2.3 - - - -
225D PHE* 5.6 2.6 - - - -
1E MG 4.0 4.3 - - - -
217E ASP* 3.0 8.1 + - - -
218E ASN* 1.3 92.7 + - - +
220E PRO* 1.3 59.8 - - - +
221E ALA* 3.1 10.5 - - - -
222E SER* 2.7 42.3 + - - -
223E TYR* 3.8 7.9 - - - -
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Residues in contact with PRO 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D PHE 5.8 0.7 - - - +
195D HIS* 6.0 4.3 - - + -
196D GLN 6.3 1.1 - - - +
218E ASN 3.4 11.0 - - - +
219E SER* 1.3 83.0 - - - +
221E ALA* 1.3 62.5 + - - +
223E TYR* 3.1 46.2 + - + +
224E ILE* 3.8 3.6 + - - +
232E PRO* 6.5 0.2 - - + -
134F THR* 3.9 6.2 + - - +
135F THR 3.5 23.7 + - - +
136F HIS* 3.4 37.9 - - + +
137F GLN* 5.7 0.7 - - + +
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Residues in contact with ALA 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E CYS* 3.9 24.9 - - - -
199E TYR 4.1 2.5 - - - +
200E VAL* 3.5 10.6 - - - +
219E SER* 3.0 8.3 + - - -
220E PRO* 1.3 78.2 - - - +
222E SER* 1.3 63.4 + - - +
223E TYR 3.2 0.7 + - - -
224E ILE* 3.5 27.7 - - + +
134F THR* 4.2 10.5 + - + -
136F HIS* 5.5 0.8 - - - -
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Residues in contact with SER 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E TYR 4.0 12.0 + - - -
200E VAL* 3.4 2.3 - - - +
201E LYS* 2.8 53.5 + - - +
215E ILE* 4.9 0.7 - - - -
217E ASP* 3.1 33.7 + - - -
219E SER* 2.7 25.4 + - - -
221E ALA* 1.3 73.5 - - - +
223E TYR* 1.3 57.4 + - - -
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Residues in contact with TYR 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E LYS 4.5 6.7 - - - +
203E LEU* 6.0 0.7 - - + -
215E ILE* 4.2 27.6 - - + -
217E ASP* 4.1 21.6 + - + -
218E ASN 5.7 0.2 - - - -
219E SER 3.8 14.8 - - - -
220E PRO* 3.1 36.4 + - + +
222E SER* 1.3 80.6 - - - +
224E ILE* 1.3 62.1 + - - +
225E PHE 3.1 3.1 - - - -
226E HIS* 3.1 23.9 + - + +
227E PRO* 3.1 29.0 - - + +
230E ALA* 3.7 26.7 - - + -
231E VAL 5.8 0.2 - - - -
232E PRO* 3.9 25.2 - - + +
135F THR 4.5 6.0 + - - -
137F GLN* 5.6 1.2 - - - +
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Residues in contact with ILE 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ASP* 4.2 15.5 - - + +
195E HIS* 4.0 19.3 - - + +
198E CYS* 4.6 6.1 - - - -
200E VAL* 3.8 19.1 - - + +
220E PRO 4.2 1.3 - - - +
221E ALA* 3.5 25.6 + - + +
222E SER 3.7 1.0 + - - -
223E TYR* 1.3 75.6 - - - +
225E PHE* 1.3 73.4 + - + +
227E PRO* 3.8 10.5 - - - +
133F GLY* 4.1 19.4 - - - +
134F THR* 3.8 35.9 - - + +
135F THR* 5.4 5.0 - - - +
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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