Contacts of the strand formed by residues 221 - 232 (chain C) in PDB entry 1QD6
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 GLY 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191C TYR 4.0 8.9 + - - -
213C GLN* 3.2 15.5 - - - -
214C TYR* 4.0 8.1 - - - -
219C GLY 4.0 1.6 + - - -
220C TYR* 1.3 77.9 - - - +
222C GLY* 1.3 59.0 + - - -
244C GLY* 3.5 4.9 - - - -
245C TYR* 2.8 31.1 + - - -
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Residues in contact with GLY 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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212C GLY* 3.2 3.7 - - - -
213C GLN* 3.0 35.7 + - - +
221C GLY* 1.3 75.0 - - - -
223C ALA* 1.3 60.3 + - - +
242C TYR* 3.9 10.3 - - - -
243C SER 3.3 11.2 - - - -
244C GLY* 4.0 0.2 - - - -
245C TYR 3.8 14.5 + - - -
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Residues in contact with ALA 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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211C LYS 3.4 7.0 - - - +
212C GLY* 4.9 2.7 - - - -
222C GLY* 1.3 74.2 - - - +
224C GLU* 1.3 61.6 + - - +
225C LEU* 4.1 16.9 - - + +
241C VAL 3.8 0.7 - - - +
242C TYR* 3.3 8.7 - - - -
243C SER* 2.8 38.8 + - - +
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Residues in contact with GLU 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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39C TYR* 4.3 7.8 + - - -
68C LYS* 4.1 6.9 + - - -
209C SER* 3.8 0.9 + - - +
210C ALA* 3.3 3.8 - - - -
211C LYS* 2.7 70.6 + - + +
223C ALA* 1.3 74.0 - - - +
225C LEU* 1.3 64.1 + - - +
226C GLY 4.1 0.2 + - - -
238C TYR* 4.0 7.6 + - - +
240C GLN* 3.7 39.1 - - + +
241C VAL 3.3 3.4 - - - +
242C TYR* 3.7 23.8 - - + -
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Residues in contact with LEU 225 (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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209C SER 3.3 9.0 - - - +
210C ALA* 4.7 12.1 - - + -
223C ALA* 4.3 15.0 - - + +
224C GLU* 1.3 86.0 - - - +
226C GLY* 1.3 60.0 + - - +
239C THR 4.1 0.2 - - - +
240C GLN* 3.3 5.3 - - - +
241C VAL* 2.7 48.8 + - + +
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Residues in contact with GLY 226 (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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207C VAL 4.4 0.2 - - - -
208C LEU* 3.6 5.7 - - - +
209C SER* 2.8 46.1 + - - +
224C GLU 4.1 0.2 + - - -
225C LEU* 1.3 76.6 - - - +
227C LEU* 1.3 61.8 + - - +
238C TYR* 3.9 12.1 - - - -
239C THR 3.3 9.4 - - - -
240C GLN* 4.4 0.7 - - - -
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Residues in contact with LEU 227 (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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206C ALA* 4.5 7.4 - - + -
207C VAL 3.4 9.9 - - - +
208C LEU* 4.0 27.6 - - + -
226C GLY* 1.3 75.5 - - - +
228C SER* 1.3 75.0 + - - +
229C TYR* 5.8 1.6 - - + -
237C LEU 3.9 0.3 - - - +
238C TYR* 3.3 5.4 - - - -
239C THR* 2.9 43.9 + - - +
267C ASP* 5.1 0.2 - - - -
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Residues in contact with SER 228 (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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206C ALA* 3.4 6.6 - - - +
207C VAL* 3.1 31.3 + - - +
227C LEU* 1.3 79.6 - - - +
229C TYR* 1.3 61.7 + - - +
236C ARG* 2.8 28.9 + - - -
237C LEU 3.0 11.9 - - - -
238C TYR* 4.0 3.4 - - - -
264C MET* 3.8 13.2 - - - -
267C ASP* 2.6 27.1 + - - -
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Residues in contact with TYR 229 (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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203C LEU 5.1 0.7 - - - -
205C ASP* 4.0 16.9 + - + +
206C ALA* 3.6 38.4 - - + -
227C LEU* 5.8 2.2 - - + -
228C SER* 1.3 74.0 - - - +
230C PRO* 1.3 96.1 - - + +
231C ILE* 4.2 0.2 - - - +
236C ARG* 3.9 4.3 - - - -
237C LEU* 2.8 48.4 + - + +
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Residues in contact with PRO 230 (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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205C ASP* 3.5 40.6 - - + +
229C TYR* 1.3 112.0 - - + +
231C ILE* 1.3 59.3 + - - +
232C THR 3.9 15.5 - - - +
233C LYS* 5.7 0.9 - - - -
235C VAL 3.6 7.4 - - - +
236C ARG* 3.7 17.9 - - + +
237C LEU* 5.9 0.9 - - - +
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Residues in contact with ILE 231 (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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230C PRO* 1.3 74.1 - - - +
232C THR* 1.3 64.4 + - + +
235C VAL* 2.8 26.9 + - + +
236C ARG 3.9 5.4 - - - +
237C LEU* 3.4 55.6 - - + +
263C VAL* 4.3 6.7 - - + -
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Residues in contact with THR 232 (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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230C PRO* 3.5 13.2 - - - +
231C ILE* 1.3 81.5 - - + +
233C LYS* 1.3 78.3 + - - +
234C HIS* 2.9 10.1 + - + +
235C VAL* 2.9 48.5 + - + +
236C ARG* 5.1 0.7 - - - +
76D PRO 5.0 1.8 - - - +
77D LEU 3.9 17.2 + - - +
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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