Contacts of the strand formed by residues 243 - 248 (chain N) in PDB entry 6DZT
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 243 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194N TYR 3.8 0.3 - - - +
195N GLN* 3.4 2.9 - - - -
196N GLN* 2.8 36.1 + - - -
242N ALA* 1.3 75.4 - - - +
244N TYR* 1.3 64.1 + - - +
245N TYR* 3.6 36.9 + - + +
258N SER 5.4 0.2 - - - +
259N GLY* 4.0 4.9 - - - -
260N THR 3.3 26.0 - - - +
261N LYS* 3.5 32.5 + - + +
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Residues in contact with TYR 244 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N GLN* 2.8 31.2 + - - +
179N ILE* 3.8 26.9 - - + -
193N TRP* 4.8 2.0 - - + -
194N TYR 3.3 5.6 - - - +
195N GLN* 3.0 39.9 + - + -
205N LEU* 3.6 14.8 - - + -
220N PHE* 4.0 3.7 - + - -
231N LEU* 3.7 21.8 - - + -
233N ILE* 3.7 22.7 - - + +
240N ASP* 3.0 32.3 + - - +
242N ALA* 3.8 17.0 - - + -
243N THR* 1.3 75.0 - - - +
245N TYR* 1.3 55.5 + - - +
260N THR* 2.9 22.2 + - - +
262N LEU* 3.8 16.2 - - + -
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Residues in contact with TYR 245 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61N GLN* 3.5 9.3 + - - -
66N GLY* 5.0 5.0 - - - -
67N LEU* 3.6 39.3 - - + -
164N GLN* 3.4 2.7 - - - +
193N TRP* 3.4 9.6 - - - -
194N TYR* 2.9 45.9 + - + +
196N GLN* 3.1 42.0 + - + -
202N PRO* 5.6 0.9 - - + -
243N THR* 3.6 27.4 + - + +
244N TYR* 1.3 73.6 - - - +
246N CYS* 1.3 60.6 + - - +
256N PHE* 4.5 10.5 - - + -
257N GLY 3.8 18.4 - - - +
258N SER 4.2 5.8 - - - -
259N GLY* 3.9 20.0 - - - -
261N LYS* 5.8 0.3 + - - -
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Residues in contact with CYS 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162N MET* 4.0 6.6 - - - +
164N GLN* 3.6 23.3 - - - +
181N CYS* 2.0 48.7 - - + -
191N LEU* 4.0 4.3 - - + -
192N SER 3.3 10.8 - - - +
193N TRP* 3.6 17.7 - - + -
245N TYR* 1.3 75.4 - - - +
247N LEU* 1.3 59.8 + - - +
248N GLN 4.3 0.2 + - - -
255N THR 4.1 0.7 - - - +
256N PHE* 3.2 3.4 - - - +
257N GLY* 2.8 27.4 + - - +
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Residues in contact with LEU 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N TRP* 6.2 0.4 - - + -
129N LEU* 3.8 23.8 - - + -
191N LEU* 3.4 5.7 - - - -
192N SER* 2.8 37.1 + - - -
194N TYR* 3.5 39.6 - - + +
245N TYR 4.2 0.6 + - - -
246N CYS* 1.3 73.3 - - - +
248N GLN* 1.3 80.2 + - - +
249N HIS* 3.9 12.9 + - + -
254N TYR* 3.9 16.2 - - + -
255N THR 3.7 7.0 - - - +
256N PHE* 3.7 38.1 - - + -
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Residues in contact with GLN 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N ILE* 4.1 18.0 - - + +
162N MET* 3.6 18.5 - - - +
187N ILE* 3.4 38.7 - - + +
190N TYR 3.4 4.3 - - - -
191N LEU* 4.0 3.7 - - + +
246N CYS 4.2 0.4 - - - -
247N LEU* 1.3 88.4 - - - +
249N HIS* 1.3 59.7 + - - +
250N GLY 3.3 17.9 + - - -
251N GLU* 3.5 10.4 + - - +
253N PRO 3.2 22.8 + - - -
254N TYR* 3.5 9.7 - - - +
255N THR* 3.0 37.6 + - - +
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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