Contacts of the helix formed by residues 299 - 309 (chain B) in PDB entry 6W01
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 LEU 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B PHE 5.1 0.2 + - - -
197B GLN* 3.6 29.2 - - - +
199B ARG* 4.1 2.7 - - - +
207B ARG* 3.9 31.9 - - + +
208B SER* 4.9 3.1 - - - -
211B GLU* 3.5 22.7 - - - +
298B LEU* 1.3 73.3 - - - +
300B LEU* 1.3 67.0 + - - +
301B ASP* 3.7 29.8 - - + +
302B ASP* 2.9 38.2 + - - +
303B PHE 3.1 9.2 + - - -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B MET* 3.9 14.8 - - + +
211B GLU* 2.9 26.9 + - + +
214B PHE* 3.6 28.5 - - + -
222B PHE* 3.6 29.6 - - + -
233B PHE* 4.0 25.1 - - + -
237B VAL* 4.7 7.2 - - + -
251B LEU* 5.0 2.9 - - + -
253B ILE* 4.4 20.2 - - + -
298B LEU 3.2 3.9 + - - -
299B LEU* 1.3 72.2 - - - +
301B ASP* 1.3 57.0 + - - +
303B PHE* 3.3 12.8 + - + +
304B VAL* 2.9 29.7 + - + +
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B SER* 2.5 38.0 + - - -
210B MET* 3.7 34.5 + - + +
211B GLU* 4.3 1.9 - - - +
299B LEU* 3.1 18.0 - - + +
300B LEU* 1.3 74.5 - - - +
302B ASP* 1.3 58.2 + - - +
304B VAL* 3.4 2.6 + - - +
305B GLU* 2.9 28.5 + - - +
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B TYR* 3.5 37.0 + - + +
195B PHE 4.7 10.4 + - - +
197B GLN* 4.8 2.4 + - - -
298B LEU* 4.6 8.2 - - + +
299B LEU* 2.9 38.1 + - + +
301B ASP* 1.3 75.7 - - - +
303B PHE* 1.3 60.9 + - - +
305B GLU* 3.1 8.2 + - - +
306B ILE* 2.8 35.0 + - + +
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Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PHE* 3.6 36.3 - + - -
236B ILE* 3.7 23.3 - - + -
237B VAL* 3.8 13.2 - - + -
251B LEU* 3.8 38.8 - - + -
296B ILE* 5.7 0.4 - - + -
298B LEU* 4.3 18.0 - - + +
299B LEU 3.1 6.3 + - - +
300B LEU* 3.8 9.9 - - + +
302B ASP* 1.3 77.9 - - - +
304B VAL* 1.3 62.2 + - - +
306B ILE* 3.2 11.7 + - + +
307B ILE* 3.0 29.7 + - + +
330B PHE* 4.8 9.9 - + - -
342B PHE* 3.7 35.9 - + - -
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 3.8 28.5 - - + -
226B TYR* 5.6 1.1 - - + +
228B LEU* 4.2 11.4 - - + -
233B PHE* 3.6 29.8 - - + -
300B LEU* 2.9 21.6 + - + +
301B ASP 3.7 5.2 - - - +
303B PHE* 1.3 76.8 - - - +
305B GLU* 1.3 63.0 + - - +
307B ILE* 3.4 6.6 + - - +
308B LYS* 3.0 51.4 + - + +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B TYR* 2.6 34.2 + - - +
301B ASP 2.9 15.0 + - - +
302B ASP* 3.5 10.0 - - - +
304B VAL* 1.3 78.5 - - - +
306B ILE* 1.3 57.3 + - - +
308B LYS* 4.0 3.5 - - - +
309B SER* 2.5 40.3 + - - +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B TYR* 3.6 37.9 - - + +
298B LEU* 3.9 27.6 - - + -
302B ASP 2.8 21.1 + - - +
303B PHE* 3.2 8.7 + - + +
305B GLU* 1.3 79.7 - - - +
307B ILE* 1.3 63.2 + - - +
309B SER* 3.3 9.2 + - - -
310B GLN* 3.0 26.3 + - - +
321B VAL* 3.9 33.2 - - + -
323B ILE* 5.0 1.1 - - + -
330B PHE* 5.7 2.2 - - + -
342B PHE* 4.1 23.1 - - + -
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 5.0 1.3 - - + -
231B TYR* 3.7 47.5 - - + +
233B PHE* 4.3 13.7 - - + -
236B ILE* 3.8 18.6 - - + -
303B PHE* 3.0 23.8 + - + +
304B VAL* 3.6 13.9 - - - +
306B ILE* 1.3 78.0 - - - +
308B LYS* 1.3 69.3 + - + +
310B GLN* 3.3 24.4 + - + +
312B LEU* 4.8 0.7 - - - +
332B LEU* 5.2 1.8 - - + -
339B VAL* 4.2 12.8 - - + -
342B PHE* 4.0 29.2 - - + -
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TYR 3.1 23.0 + - - -
227B LYS* 3.2 23.6 + - - +
228B LEU* 3.8 17.7 - - + -
231B TYR* 3.9 35.5 + - + +
304B VAL* 3.0 32.6 + - + +
305B GLU* 4.2 4.5 - - - +
307B ILE* 1.3 81.0 - - + +
309B SER* 1.3 59.2 + - - +
310B GLN 3.2 5.2 + - - +
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Residues in contact with SER 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLU* 2.5 30.4 + - - +
306B ILE* 3.6 8.0 - - - -
307B ILE 3.2 1.0 - - - -
308B LYS* 1.3 75.5 - - - +
310B GLN* 1.3 65.5 + - - +
311B ASP 3.9 0.9 + - - -
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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