Contacts of the strand formed by residues 182 - 186 (chain D) in PDB entry 1TLF
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 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D VAL* 5.6 0.4 - - + -
174D LEU* 4.1 22.2 - - + -
175D VAL* 4.5 2.7 - - + -
179D HIS* 3.5 38.1 - - + +
180D GLN 3.2 5.6 + - - +
181D GLN* 1.3 77.9 - - - +
183D ALA* 1.3 71.3 + - - +
184D LEU* 4.3 4.7 - - + -
205D LEU* 4.1 25.1 - - + -
210D ILE* 4.3 9.2 - - + -
212D PRO* 3.0 29.6 - - - +
213D ILE* 3.2 9.0 + - - +
241D ALA* 3.6 12.8 - - + +
243D LEU* 4.1 23.1 - - + -
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Residues in contact with ALA 183 (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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182D ILE* 1.3 77.9 - - - +
184D LEU* 1.3 63.2 + - - +
213D ILE* 4.6 0.4 - - + -
214D ALA* 3.2 13.9 - - + +
232D MET* 3.0 37.2 - - + -
239D PRO* 3.9 12.9 - - + +
241D ALA 3.1 7.1 + - - -
242D MET* 3.4 10.7 - - + +
243D LEU 3.0 23.7 + - - -
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Residues in contact with LEU 184 (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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182D ILE* 4.3 2.7 - - + -
183D ALA* 1.3 78.3 - - - +
185D LEU* 1.3 57.2 + - - +
186D ALA 3.9 0.9 - - - +
198D LEU* 3.8 24.0 - - + -
201D TRP* 3.9 24.9 - - + -
202D HIS* 4.1 12.8 - - + +
205D LEU* 3.7 21.8 - - + -
212D PRO* 3.9 25.8 - - + -
214D ALA 2.8 9.9 + - - +
215D GLU* 3.4 11.5 - - + -
216D ARG* 2.7 33.5 + - - +
242D MET* 6.4 0.2 - - - -
243D LEU* 3.5 28.9 - - + -
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Residues in contact with LEU 185 (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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183D ALA 5.6 0.2 - - - +
184D LEU* 1.3 73.1 - - - +
186D ALA* 1.3 56.2 + - - +
201D TRP* 3.8 2.0 - - - -
216D ARG* 3.3 15.9 - - + +
218D GLY 4.4 0.4 - - - +
225D GLY* 4.1 14.4 - - - -
228D GLN* 3.8 31.0 - - + -
229D THR* 3.8 22.0 - - - +
242D MET* 4.8 9.4 - - + -
243D LEU 2.8 13.7 + - - +
244D VAL* 3.4 26.5 - - + +
245D ALA* 2.8 32.4 + - - +
249D MET* 4.2 17.4 - - + +
253D ALA* 4.1 10.3 - - + -
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Residues in contact with ALA 186 (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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184D LEU 3.9 0.4 - - - -
185D LEU* 1.3 75.6 - - - +
187D GLY* 1.3 60.0 + - - +
189D LEU* 4.4 2.7 - - + -
194D ALA 5.1 2.0 - - - +
198D LEU* 4.0 35.7 - - + -
201D TRP* 4.3 5.4 - - + -
215D GLU* 5.9 0.7 - - + -
216D ARG 2.7 10.0 + - - +
217D GLU* 2.9 22.7 - - + -
218D GLY* 2.8 32.4 + - - -
245D ALA* 3.7 5.2 - - + -
249D MET* 4.1 2.6 - - - +
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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