Contacts of the helix formed by residues 214 - 224 (chain C) in PDB entry 2Q41
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 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C LYS* 3.5 26.9 + - - +
211C GLU* 2.8 33.2 + - + +
213C PHE* 1.3 83.0 - - - +
215C LYS* 1.3 68.3 + - - +
216C PRO* 3.4 13.7 - - + -
217C PHE* 3.4 12.9 + - - +
218C PHE* 3.4 15.9 + - - -
251C ASN* 4.6 4.5 + - - +
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C PHE 4.1 0.6 + - - -
214C GLU* 1.3 72.3 + - - +
216C PRO* 1.3 71.2 - - + +
218C PHE* 3.2 5.8 + - - -
219C GLN 3.0 18.4 + - - -
251C ASN* 3.0 45.4 + - + +
254C GLU* 3.9 20.1 + - + +
255C ILE* 3.3 26.3 - - + +
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Residues in contact with PRO 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C GLU* 3.4 14.1 - - + -
215C LYS* 1.3 96.3 - - + +
217C PHE* 1.3 59.5 - - - +
219C GLN* 3.3 16.5 + - + +
220C SER* 3.4 12.1 + - - -
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Residues in contact with PHE 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 3.8 19.5 - - + -
184C VAL* 4.0 27.8 - - + -
187C LEU* 3.6 24.0 - - + -
200C VAL* 3.9 23.6 - - + -
211C GLU* 3.7 14.6 - - + +
212C LEU* 3.1 58.6 - - + -
214C GLU* 3.4 8.8 + - - +
215C LYS 3.3 0.4 - - - -
216C PRO* 1.3 79.0 - - - +
218C PHE* 1.3 71.9 + + - +
220C SER* 3.2 16.7 + - - -
221C VAL* 3.3 19.7 + - + +
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Residues in contact with PHE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C LEU 3.8 15.7 - - - -
213C PHE* 3.4 28.9 - + - -
214C GLU 3.4 17.2 + - - -
215C LYS* 3.2 7.2 + - - +
217C PHE* 1.3 84.6 - + - +
219C GLN* 1.3 64.1 + - - +
221C VAL* 3.2 7.1 + - + -
222C ALA 3.0 18.7 + - - -
231C VAL* 5.0 1.8 - - + -
233C THR* 3.8 34.1 - - + -
248C ILE* 4.5 12.3 - - + -
251C ASN* 4.3 14.8 - - + -
252C CYS* 4.1 21.8 - - - -
255C ILE* 3.1 19.0 - - + +
256C PHE* 3.3 32.4 - + + -
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Residues in contact with GLN 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LYS 3.0 7.8 + - - +
216C PRO* 3.5 13.2 - - + +
217C PHE 3.2 0.2 - - - -
218C PHE* 1.3 76.7 - - - +
220C SER* 1.3 58.0 + - - +
222C ALA* 3.4 9.7 + - - +
223C ARG* 3.1 33.4 + - - +
255C ILE* 3.3 38.5 + - + +
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Residues in contact with SER 220 (chain C).
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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184C VAL 5.2 2.7 - - - -
187C LEU* 2.9 41.0 + - - +
188C LYS* 3.5 12.1 + - - -
216C PRO 3.4 7.2 + - - -
217C PHE* 3.2 12.0 + - - -
218C PHE 3.2 0.2 - - - -
219C GLN* 1.3 79.3 - - - +
221C VAL* 1.3 58.8 + - - +
223C ARG* 3.3 15.4 - - - +
224C ALA* 2.9 31.7 + - - +
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Residues in contact with VAL 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU* 3.4 23.1 - - + -
198C VAL* 3.6 27.4 - - + -
217C PHE* 3.3 31.6 - - + +
218C PHE* 3.2 15.2 + - + +
220C SER* 1.3 76.4 - - - +
222C ALA* 1.3 57.8 + - - +
224C ALA* 3.1 4.3 + - - +
225C LEU* 2.9 36.3 + - + +
231C VAL* 3.2 35.2 - - + -
256C PHE* 3.9 2.9 - - + -
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PHE 3.0 13.4 + - - +
219C GLN* 3.5 16.2 - - - +
220C SER 3.2 0.2 - - - -
221C VAL* 1.3 78.5 - - - +
223C ARG* 1.3 61.4 + - - +
225C LEU* 3.4 17.5 + - - +
255C ILE* 3.7 22.2 - - + +
256C PHE* 3.7 16.7 - - + -
282C THR* 3.9 18.0 - - + +
283C GLU* 6.0 0.2 - - - +
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Residues in contact with ARG 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU 4.2 8.3 + - - -
188C LYS* 4.7 7.0 + - - +
190C ALA 3.4 24.0 + - - -
192C GLU* 3.0 50.8 + - - +
193C GLY 2.7 30.3 + - - -
219C GLN* 3.1 29.9 + - - +
220C SER* 3.3 24.0 - - - +
222C ALA* 1.3 76.7 - - - +
224C ALA* 1.3 52.3 + - - +
225C LEU 3.8 0.3 - - - +
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Residues in contact with ALA 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU* 3.8 26.7 - - + +
190C ALA* 4.3 15.9 - - + -
191C ALA 3.9 8.5 - - - -
192C GLU* 4.6 0.2 - - - +
193C GLY 3.8 0.7 - - - -
194C SER* 2.9 10.7 + - - -
195C TYR* 2.9 29.9 + - + +
198C VAL* 5.3 1.1 - - + -
220C SER 2.9 20.2 + - - +
221C VAL 3.1 4.7 + - - +
223C ARG* 1.3 78.3 - - + +
225C LEU* 1.3 59.7 + - + +
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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