Contacts of the helix formed by residues 214 - 220 (chain D) in PDB entry 4QG0
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 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D ILE* 3.6 8.3 - - - +
148D LYS 2.8 19.6 + - - -
149D GLN 3.4 16.8 + - - -
150D LEU 5.5 0.2 - - - -
151D GLY 4.9 0.2 - - - -
164D ARG* 3.1 29.7 + - - +
210D HIS* 3.8 15.8 + - - -
211D GLY 2.7 17.1 + - - +
213D PHE* 1.3 77.6 - - - +
215D HIS* 1.3 61.2 + - - -
217D PHE* 2.9 28.1 + - - +
218D ASP* 3.7 4.3 + - - +
703D DUT 6.0 0.2 - - - -
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Residues in contact with HIS 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ARG* 3.9 7.9 - - - -
210D HIS* 3.9 4.2 - + - -
213D PHE 3.1 1.4 + - - -
214D SER* 1.3 76.6 - - - +
216D MET* 1.3 57.0 + - - +
218D ASP* 3.3 14.8 + - - -
219D GLY* 2.7 35.3 + - - -
220D ARG* 5.2 0.3 - - - +
233D HIS* 3.9 15.9 - + - -
703D DUT 2.7 107.1 + + + +
706D EDO 5.5 2.9 - - - -
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Residues in contact with MET 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D PRO 3.8 9.9 - - - +
213D PHE* 3.2 24.6 + - + +
214D SER 3.1 0.8 - - - -
215D HIS* 1.3 76.8 - - - +
217D PHE* 1.3 63.9 + - + +
220D ARG* 2.9 30.7 + - - +
221D PHE* 3.0 14.1 + - + +
383D ASP* 3.5 46.0 + - + +
386D ILE* 3.6 21.1 - - + -
387D THR* 3.3 26.0 - - - +
390D PHE* 3.7 33.9 - - + -
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Residues in contact with PHE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D GLY* 3.8 20.0 - - - +
212D PRO* 3.3 31.5 + - + +
214D SER 2.9 10.3 + - - +
216D MET* 1.3 88.2 - - + +
218D ASP* 1.3 59.4 + - + +
221D PHE* 3.6 28.9 - + + -
222D ILE* 3.0 57.1 + - + +
231D TRP* 4.5 7.4 - - - -
390D PHE* 5.0 1.8 - + - -
409D ILE* 4.0 11.0 - - + -
413D ILE* 3.9 13.7 - - + -
419D TYR* 3.8 17.0 - + - -
422D LEU* 3.7 30.5 - - + -
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Residues in contact with ASP 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D HIS* 5.3 1.3 - - - -
214D SER 3.7 3.3 + - - +
215D HIS* 3.3 29.4 + - - +
217D PHE* 1.3 77.6 - - + +
219D GLY* 1.3 69.1 + - - +
222D ILE* 4.7 1.5 - - - +
223D PRO* 3.5 16.4 - - - +
231D TRP* 4.0 34.3 - - + +
232D THR* 4.6 4.7 - - - +
233D HIS* 3.0 42.6 + - + +
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Residues in contact with GLY 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D HIS* 2.7 24.6 + - - -
218D ASP* 1.3 77.2 + - - +
220D ARG* 1.3 62.6 + - - +
223D PRO* 3.5 13.5 - - - +
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Residues in contact with ARG 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D HIS 5.2 0.2 - - - +
216D MET* 2.9 18.2 + - - +
219D GLY* 1.3 84.6 - - - +
221D PHE* 1.3 64.9 + - - +
223D PRO* 3.6 3.6 - - - +
224D LEU* 3.4 28.9 + - + +
375D GLN* 4.9 1.6 + - - -
380D ASN* 3.4 28.9 + - - +
383D ASP* 4.0 27.8 + - - +
384D THR* 3.3 32.0 + - - +
387D THR* 3.6 15.3 - - + +
501D ASP* 2.9 40.7 + - - -
503D ILE* 5.3 1.8 - - - +
706D EDO 4.8 4.4 + - - -
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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