Contacts of the strand formed by residues 221 - 230 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191D TYR 4.0 10.0 + - - -
213D GLN 3.3 13.9 - - - -
214D TYR* 4.0 8.8 - - - -
219D GLY 4.1 1.2 + - - -
220D TYR* 1.3 75.7 - - - +
222D GLY* 1.3 57.6 + - - -
244D GLY* 3.5 4.9 - - - -
245D TYR* 2.8 33.5 + - - -
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Residues in contact with GLY 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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211D LYS 4.7 0.2 - - - -
212D GLY* 3.3 2.8 - - - -
213D GLN* 3.1 35.8 + - - +
221D GLY* 1.3 74.6 - - - -
223D ALA* 1.3 61.0 + - - +
242D TYR* 4.0 8.5 - - - -
243D SER 3.3 11.4 - - - -
244D GLY* 3.9 1.6 - - - -
245D TYR 3.9 14.3 + - - -
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Residues in contact with ALA 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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211D LYS 3.4 7.4 - - - +
212D GLY* 4.8 2.9 - - - -
222D GLY* 1.3 74.6 - - - +
224D GLU* 1.3 60.6 + - - +
225D LEU* 4.1 11.7 - - + -
241D VAL 3.8 0.9 - - - +
242D TYR* 3.3 9.4 - - - -
243D SER* 2.8 38.5 + - - +
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Residues in contact with GLU 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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39D TYR* 4.3 7.4 + - - -
68D LYS* 4.1 7.1 + - - -
209D SER 3.9 0.9 - - - +
210D ALA* 3.3 3.5 + - - -
211D LYS* 2.7 73.8 + - + +
223D ALA* 1.3 73.7 - - - +
225D LEU* 1.3 63.7 + - - +
238D TYR* 4.0 7.4 + - - +
240D GLN* 3.6 39.2 - - + +
241D VAL 3.3 3.8 - - - +
242D TYR* 3.6 24.0 - - + -
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Residues in contact with LEU 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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209D SER 3.3 4.3 - - - +
210D ALA* 3.7 26.5 - - + -
223D ALA* 5.3 9.9 - - + -
224D GLU* 1.3 79.4 - - - +
226D GLY* 1.3 58.0 + - - +
240D GLN* 3.4 5.0 - - - +
241D VAL* 2.8 52.8 + - + +
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Residues in contact with GLY 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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207D VAL 4.4 0.2 - - - -
208D LEU* 3.5 6.8 - - - +
209D SER* 2.8 47.1 + - - +
225D LEU* 1.3 75.5 - - - +
227D LEU* 1.3 61.8 + - - +
238D TYR* 4.0 11.9 - - - -
239D THR 3.3 9.2 - - - -
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Residues in contact with LEU 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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206D ALA* 4.4 13.7 - - + -
207D VAL 3.5 5.8 - - - +
208D LEU* 3.5 26.2 - - + -
226D GLY* 1.3 75.8 - - - +
228D SER* 1.3 73.1 + - - +
229D TYR* 5.7 2.2 - - + -
237D LEU 3.8 0.5 - - - +
238D TYR* 3.4 4.4 - - - -
239D THR* 2.9 43.8 + - + +
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Residues in contact with SER 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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206D ALA* 3.4 6.8 - - - +
207D VAL* 3.1 28.8 + - - +
227D LEU* 1.3 78.8 - - - +
229D TYR* 1.3 62.3 + - - +
236D ARG* 2.8 28.0 + - - -
237D LEU 3.0 11.9 - - - -
238D TYR* 4.0 3.8 - - - -
264D MET* 3.8 13.5 - - - -
267D ASP* 2.5 29.0 + - - -
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Residues in contact with TYR 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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203D LEU 5.2 0.7 - - - -
205D ASP* 3.7 23.4 + - + +
206D ALA* 3.6 38.4 - - + -
227D LEU* 5.7 2.0 - - + -
228D SER* 1.3 75.4 - - - +
230D PRO* 1.3 94.7 - - + +
231D ILE 3.4 0.2 + - - -
236D ARG* 4.0 3.8 - - - -
237D LEU* 2.7 49.2 + - + +
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Residues in contact with PRO 230 (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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205D ASP* 3.4 44.9 - - + +
229D TYR* 1.3 110.9 - - + +
231D ILE* 1.3 60.6 + - - +
232D THR 3.5 16.6 - - - +
235D VAL 3.7 7.0 - - - +
236D ARG* 3.6 21.7 - - + +
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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