Contacts of the strand formed by residues 333 - 338 (chain D) in PDB entry 6WNX
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 VAL 333 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294D ALA* 3.3 17.8 - - - +
295D CYS* 3.4 10.3 - - - -
306D GLY* 3.6 20.6 - - - -
307D SER 3.2 7.6 + - - +
310D ASN 3.8 22.2 - - - +
311D THR 3.9 11.4 - - - +
312D ILE* 3.8 22.2 - - + -
329D HIS* 3.6 24.2 - - + -
332D LEU* 1.3 71.9 - - - +
334D ARG* 1.3 59.4 + - - +
335D CYS 4.0 15.3 - - - +
336D ILE* 4.5 1.1 - - + -
345D SER* 4.0 11.2 - - - -
346D GLY 3.8 6.1 - - - +
347D ALA* 4.3 1.1 - - - +
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Residues in contact with ARG 334 (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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131D TYR* 3.9 11.1 + - - -
171D LEU 5.6 2.0 + - - -
294D ALA* 3.9 5.9 + - - +
295D CYS* 3.6 10.9 - - - +
332D LEU* 3.5 13.4 + - + +
333D VAL* 1.3 72.6 - - - +
335D CYS* 1.3 58.6 + - - +
346D GLY 2.9 7.8 + - - +
347D ALA* 4.7 1.3 - - - -
348D TYR* 3.9 15.9 - - + -
382D VAL 3.1 24.9 - - - +
383D PHE* 3.0 39.1 + - + +
32F ASP* 2.7 37.9 + - - -
34F GLY* 3.4 18.8 + - - -
35F ILE* 3.6 33.1 - - - +
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Residues in contact with CYS 335 (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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295D CYS* 3.5 13.0 - - - -
333D VAL* 4.0 0.9 - - - +
334D ARG* 1.3 76.7 - - - +
336D ILE* 1.3 64.4 - - - +
345D SER* 3.5 3.1 - - - -
346D GLY* 2.9 29.4 + - - +
382D VAL* 3.7 18.8 - - - -
383D PHE 3.6 13.7 - - - +
384D ARG* 3.6 33.7 - - - +
385D LEU* 3.6 26.9 - - - +
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Residues in contact with ILE 336 (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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295D CYS* 3.3 21.7 - - + +
296D LEU* 3.6 28.4 - - - +
297D GLN* 4.3 8.4 - - + +
304D VAL* 3.5 31.0 - - + +
305D SER 4.3 5.6 - - - +
306D GLY 4.6 0.4 - - - +
312D ILE* 3.6 39.3 - - + -
333D VAL* 4.5 2.2 - - + -
335D CYS* 1.3 75.9 - - - +
337D ARG* 1.3 79.8 + - - +
343D ILE* 3.9 13.9 - - + -
344D VAL 3.4 8.7 - - - +
345D SER* 4.2 3.4 - - - -
384D ARG* 6.0 0.3 + - - -
385D LEU* 5.0 1.0 - - - +
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Residues in contact with ARG 337 (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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257D ASP* 4.6 6.3 + - - -
296D LEU 5.0 2.8 + - - -
297D GLN* 3.0 52.6 + - - +
336D ILE* 1.3 85.2 + - - +
338D PHE* 1.3 65.1 + - - +
343D ILE* 3.4 5.9 - - - +
344D VAL 2.9 30.8 + - - +
384D ARG* 4.6 21.8 - - - +
385D LEU* 3.3 34.1 - - + +
386D GLN* 4.6 9.1 - - - +
387D PHE* 3.7 21.5 - - + +
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Residues in contact with PHE 338 (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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297D GLN* 2.7 62.4 + - + +
299D ARG* 3.8 46.3 + - + -
302D LEU* 3.9 31.0 - - + -
304D VAL* 3.8 26.9 - - + -
337D ARG* 1.3 77.7 + - - +
339D ASP* 1.3 73.4 + - - +
342D ARG 3.1 17.3 - - - +
343D ILE* 4.0 12.1 - - + -
357D LEU* 4.3 8.3 - - + -
387D PHE* 3.7 9.1 - - - -
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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