Contacts of the strand formed by residues 168 - 174 (chain D) in PDB entry 3QEL
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 ILE 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D TRP* 3.3 1.8 - - - +
167D TYR* 1.3 87.9 - - + +
169D PHE* 1.3 64.0 + - - +
196D GLY 5.5 1.1 - - - +
197D TRP 5.4 0.2 - - - -
198D GLU* 3.6 22.9 - - + +
200D GLU* 3.1 30.5 - - + +
226D PRO* 3.6 28.0 - - + +
227D ILE* 3.7 13.7 + - - +
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Residues in contact with PHE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 4.3 9.4 - - + -
161D MET* 4.5 6.5 - - - -
166D TRP 5.0 0.4 - - - +
167D TYR 3.9 11.2 - - - -
168D ILE* 1.3 80.4 - - - +
170D SER* 1.3 67.8 + - - +
171D ILE* 4.2 2.2 - - + -
186D ILE* 3.7 31.0 - - + -
190D ILE* 3.8 18.2 - - + -
197D TRP* 3.9 24.5 - + + -
198D GLU 3.1 14.3 + - - +
199D LEU* 3.5 15.7 - - + -
200D GLU 2.7 32.2 + - - -
225D SER* 3.3 12.1 + - - -
227D ILE* 3.1 27.8 - - + +
229D LEU* 3.7 23.1 - - + -
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Residues in contact with SER 170 (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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169D PHE* 1.3 79.0 - - - +
171D ILE* 1.3 65.8 + - - +
199D LEU* 4.0 1.1 - - - -
200D GLU* 3.8 1.0 - - - +
201D GLU* 3.2 23.9 + - - +
223D LEU* 3.3 32.6 - - - +
224D GLN 5.0 0.9 + - - -
225D SER* 3.3 21.9 + - - -
227D ILE 3.0 6.8 + - - -
228D ILE* 3.6 7.5 - - - -
229D LEU 3.0 23.8 + - - -
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Residues in contact with ILE 171 (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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169D PHE* 4.2 6.7 - - + -
170D SER* 1.3 79.4 - - - +
172D VAL* 1.3 75.1 + - - +
173D THR* 3.8 23.3 - - + -
182D PHE* 4.2 8.3 - - + -
183D VAL* 4.0 23.6 - - + -
186D ILE* 3.9 37.7 - - + -
199D LEU* 3.8 21.8 - - + -
201D GLU 2.9 8.3 + - - +
202D VAL* 3.6 14.8 - - + -
203D LEU* 3.0 20.4 + - - +
228D ILE* 4.8 0.2 - - - -
229D LEU* 3.3 15.0 - - + +
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Residues in contact with VAL 172 (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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171D ILE* 1.3 85.6 - - - +
173D THR* 1.3 62.9 + - - +
203D LEU* 3.7 18.2 - - + +
205D LEU* 3.7 32.8 - - + -
220D LEU* 4.8 7.0 - - + -
223D LEU* 3.9 28.9 - - + -
228D ILE* 4.0 10.3 - - + -
229D LEU 2.7 12.5 + - - +
230D LEU* 3.2 23.3 - - + +
231D TYR 2.8 23.6 + - - -
240D ILE* 5.2 1.6 - - + -
256D TRP* 4.9 2.2 - - + -
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Residues in contact with THR 173 (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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171D ILE* 3.8 19.3 - - + -
172D VAL* 1.3 79.3 - - - +
174D THR* 1.3 73.5 + - - +
179D TYR* 3.7 26.0 - - + +
182D PHE* 4.3 2.9 - - + -
183D VAL* 4.2 14.2 - - + +
202D VAL* 5.9 0.7 - - - +
203D LEU 3.0 10.7 + - - +
204D LEU* 3.7 6.8 - - - +
205D LEU* 2.9 26.9 + - - +
230D LEU* 5.7 0.2 - - - -
231D TYR* 3.0 29.2 - - + -
232D CYS* 5.2 0.2 - - - -
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Residues in contact with THR 174 (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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173D THR* 1.3 89.0 + - - +
175D TYR* 1.3 60.4 + - - +
176D PHE* 3.2 13.9 + - - +
179D TYR* 3.3 15.2 - - - +
204D LEU* 3.6 6.1 - - - +
205D LEU* 3.3 16.2 - - + +
207D MET* 3.3 31.9 - - + -
230D LEU* 6.1 0.4 - - + -
231D TYR 3.1 5.0 + - - -
232D CYS* 3.6 14.7 - - + +
236D GLU* 2.7 29.8 + - - +
240D ILE* 4.0 13.5 - - + -
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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