Contacts of the helix formed by residues 219 - 229 (chain D) in PDB entry 6Q2J
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 THR 219 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D PRO* 1.3 78.4 - - - +
220D CYS* 1.3 63.9 + - - +
221D LEU* 3.9 6.7 + - - +
222D SER* 3.1 28.3 + - - -
223D VAL* 3.2 19.9 + - - +
291D CYS* 3.9 0.7 - - - -
292D THR 3.9 12.1 - - - +
295D THR* 4.2 27.8 - - + +
296D ILE* 3.9 32.1 - - + +
304D CYS* 4.9 2.5 - - - -
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Residues in contact with CYS 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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219D THR* 1.3 71.5 - - - +
221D LEU* 1.3 60.8 + - - +
223D VAL* 3.3 3.6 + - - +
224D ILE* 3.0 33.6 + - - +
291D CYS* 2.0 59.9 - - - -
293D CYS* 3.7 17.0 - - - -
304D CYS* 3.8 19.2 - - - +
307D PHE* 4.4 12.3 - - + -
308D GLN* 3.9 14.4 - - - +
311D LEU* 5.0 2.4 - - + +
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D THR* 3.2 6.0 - - - +
220D CYS* 1.3 77.9 - - - +
222D SER* 1.3 57.7 + - - +
224D ILE* 3.3 4.7 + - - +
225D ARG* 2.9 56.9 + - - +
256D GLU* 5.4 2.5 - - - +
296D ILE* 3.8 30.7 - - + -
300D GLU* 3.9 31.9 - - + +
303D LEU* 3.7 33.7 - - + -
304D CYS* 4.3 13.0 - - + +
307D PHE* 3.9 15.7 - - + -
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Residues in contact with SER 222 (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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218D PRO* 4.8 7.6 - - - -
219D THR* 3.1 25.7 + - - -
221D LEU* 1.3 75.0 - - - +
223D VAL* 1.3 62.1 + - - +
225D ARG* 3.7 12.3 + - - +
226D SER* 2.9 29.8 + - - -
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Residues in contact with VAL 223 (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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218D PRO* 4.0 21.8 - - + -
219D THR 3.2 15.5 + - - +
220D CYS* 3.3 9.8 + - - +
222D SER* 1.3 77.2 - - - +
224D ILE* 1.3 57.2 + - + +
226D SER* 3.4 4.3 + - - -
227D CYS* 2.9 25.1 + - - +
286D VAL* 3.4 38.9 - - + +
287D LEU* 3.8 21.3 - - + +
289D VAL* 4.7 9.4 - - + +
291D CYS* 4.0 14.1 - - + -
311D LEU* 4.7 8.1 - - + -
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Residues in contact with ILE 224 (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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220D CYS 3.0 17.4 + - - +
221D LEU 3.8 3.8 - - - +
223D VAL* 1.3 74.6 - - - +
225D ARG* 1.3 59.5 + - - +
227D CYS* 3.7 2.8 - - + +
228D GLN* 3.0 50.3 + - + +
237D TYR* 4.3 23.1 - - + +
256D GLU* 4.9 7.4 - - + +
287D LEU* 3.8 15.9 - - + -
307D PHE* 3.7 44.4 - - + -
311D LEU* 3.8 26.5 - - + -
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Residues in contact with ARG 225 (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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221D LEU* 2.9 52.8 + - - +
222D SER* 3.7 13.6 + - - +
224D ILE* 1.3 77.2 - - - +
226D SER* 1.3 56.3 + - - +
228D GLN* 3.8 4.0 - - - +
229D ASN* 3.0 45.6 + - - +
256D GLU* 2.9 38.3 + - - -
300D GLU* 5.3 8.1 + - - -
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Residues in contact with SER 226 (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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222D SER 2.9 19.0 + - - -
223D VAL* 3.8 4.5 - - - -
225D ARG* 1.3 76.3 - - - +
227D CYS* 1.3 63.4 + - - +
229D ASN* 3.7 10.7 + - - +
230D ASP* 3.8 13.9 + - - +
286D VAL* 3.8 25.5 - - - +
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Residues in contact with CYS 227 (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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223D VAL 2.9 17.4 + - - +
224D ILE* 3.7 6.3 - - + +
225D ARG 3.2 0.2 - - - -
226D SER* 1.3 77.0 - - - +
228D GLN* 1.3 59.1 + - + +
230D ASP 2.9 27.9 + - - +
233D CYS* 2.0 63.4 - - - +
234D ARG* 3.7 0.7 + - - -
237D TYR* 3.8 12.1 - - - -
286D VAL* 3.7 4.4 - - + +
287D LEU* 3.7 23.3 - - + -
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Residues in contact with GLN 228 (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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224D ILE* 3.0 30.4 + - + +
225D ARG* 4.3 3.4 - - - +
227D CYS* 1.3 79.9 - - + +
229D ASN* 1.3 62.6 + - - +
230D ASP 3.2 3.4 + - - -
231D GLU* 5.7 0.5 - - - +
234D ARG* 4.3 28.5 + - + -
237D TYR* 3.9 25.0 - - + -
254D GLU* 3.8 39.6 + - - +
255D ASP 5.5 0.4 - - - +
256D GLU* 5.0 9.9 - - - +
307D PHE* 6.0 1.0 - - - -
76F TYR* 6.6 0.2 - - - -
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Residues in contact with ASN 229 (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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225D ARG* 3.0 35.2 + - - +
226D SER* 4.1 7.3 - - - +
227D CYS 3.2 0.8 - - - -
228D GLN* 1.3 78.6 - - - +
230D ASP* 1.3 57.7 + - - +
231D GLU* 5.9 1.7 - - - +
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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