Contacts of the helix formed by residues 298 - 309 (chain D) in PDB entry 2WTK
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 ASN 298 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260D MET* 4.1 20.9 - - + +
294D ILE* 2.8 38.3 + - - +
295D LEU 3.4 3.6 - - - +
296D LEU 3.0 0.6 - - - -
297D LYS* 1.3 79.1 - - - +
299D GLN* 1.3 54.8 + - - +
300D ALA 3.4 2.0 - - - -
301D LYS* 3.1 21.4 + - + +
302D LEU* 2.7 40.7 + - + +
429E TRP* 3.7 10.2 - - + -
430E GLU* 3.0 45.4 + - - +
431E PHE* 4.6 0.8 - - - -
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Residues in contact with GLN 299 (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 LEU 2.8 12.8 + - - +
296D LEU* 3.1 27.6 + - + +
297D LYS 3.5 0.8 - - - -
298D ASN* 1.3 76.1 - - - +
300D ALA* 1.3 64.3 + - - +
302D LEU* 3.2 2.5 + - - +
303D ILE* 2.9 35.9 + - + +
330D ILE* 2.8 41.6 + - + +
331D ARG* 3.7 9.5 + - - +
333D LEU* 3.4 25.0 + - + +
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Residues in contact with ALA 300 (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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298D ASN 3.4 0.6 - - - -
299D GLN* 1.3 78.3 - - - +
301D LYS* 1.3 60.4 + - + +
303D ILE* 3.1 13.4 + - - +
304D GLU* 2.8 29.2 + - - +
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Residues in contact with LYS 301 (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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264D ARG* 5.2 1.8 - - - +
297D LYS 4.7 9.4 + - - +
298D ASN* 3.1 30.1 + - - +
300D ALA* 1.3 78.2 - - + +
302D LEU* 1.3 53.2 + - - +
304D GLU* 3.3 6.8 + - - +
305D PHE* 2.7 36.0 + - - +
428E ASP* 3.8 31.6 - - - +
429E TRP* 4.0 16.2 - - + +
430E GLU* 2.8 33.0 + - - +
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Residues in contact with LEU 302 (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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260D MET* 4.3 9.0 - - + -
263D LEU* 4.9 4.3 - - + -
278D PHE* 3.9 25.8 - - + -
295D LEU* 3.8 42.8 - - + +
298D ASN* 2.7 27.3 + - + +
299D GLN 3.5 4.3 - - - +
301D LYS* 1.3 71.0 - - - +
303D ILE* 1.3 60.2 + - - +
305D PHE* 4.3 0.9 - - - -
306D LEU* 2.8 48.7 + - + +
330D ILE* 4.2 17.9 - - + -
429E TRP* 3.6 28.3 - - + -
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Residues in contact with ILE 303 (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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299D GLN* 2.9 37.4 + - + +
300D ALA* 3.5 10.3 - - - +
302D LEU* 1.3 77.0 - - - +
304D GLU* 1.3 59.6 + - - +
306D LEU* 4.5 2.4 - - - +
307D SER* 2.5 37.3 + - - +
327D VAL* 4.1 13.1 - - + +
330D ILE* 3.9 14.6 - - + -
331D ARG* 3.6 56.1 - - + +
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Residues in contact with GLU 304 (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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300D ALA 2.8 16.0 + - - +
301D LYS* 3.8 6.5 - - - +
303D ILE* 1.3 76.6 - - - +
305D PHE* 1.3 66.1 + - - +
307D SER* 3.6 4.1 - - - -
308D LYS* 3.1 50.3 + - + +
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Residues in contact with PHE 305 (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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263D LEU* 3.5 48.2 - - + -
264D ARG* 4.0 37.2 - - + +
301D LYS 2.7 21.8 + - - +
302D LEU* 3.7 2.0 - - - +
304D GLU* 1.3 73.2 - - - +
306D LEU* 1.3 72.9 + - + +
308D LYS* 3.0 8.0 + - - +
309D PHE* 2.9 52.3 + + + +
429E TRP* 3.7 22.2 - + + -
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Residues in contact with LEU 306 (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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263D LEU* 5.1 4.9 - - + -
275D PHE* 3.9 31.4 - - + -
278D PHE* 4.6 15.3 - - + -
302D LEU* 2.8 33.8 + - + +
303D ILE 4.5 0.2 - - - +
305D PHE* 1.3 83.7 - - + +
307D SER* 1.3 60.6 + - - +
309D PHE* 3.2 15.0 + - + -
323D LYS* 3.2 25.6 - - + +
326D LEU* 4.4 15.3 - - + -
327D VAL* 3.8 21.8 - - + -
330D ILE* 3.8 30.3 - - + -
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Residues in contact with SER 307 (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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303D ILE* 2.5 31.0 + - - +
304D GLU* 3.6 5.8 - - - -
305D PHE 3.2 0.6 - - - -
306D LEU* 1.3 78.3 - - - +
308D LYS* 1.3 66.8 + - - +
311D ASN* 3.3 19.6 + - - +
323D LYS* 3.8 4.0 + - - +
327D VAL* 4.3 13.1 - - - +
331D ARG* 5.6 1.0 + - - -
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Residues in contact with LYS 308 (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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304D GLU* 3.1 42.2 + - + +
305D PHE* 3.0 5.8 + - - +
307D SER* 1.3 84.3 - - - +
309D PHE* 1.3 64.9 + - - +
310D GLN 3.0 4.2 + - - -
311D ASN* 3.3 27.4 + - - +
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Residues in contact with PHE 309 (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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263D LEU* 4.2 9.4 - - + -
271D GLN* 3.6 45.3 - - + -
272D PHE* 4.2 1.6 - - - -
275D PHE* 3.4 40.8 - + + -
305D PHE* 2.9 40.5 + + + +
306D LEU* 3.2 23.2 + - + +
307D SER 3.4 0.2 - - - -
308D LYS* 1.3 73.5 - - - +
310D GLN* 1.3 86.6 + - - +
319D PHE* 3.7 26.8 - + - -
323D LYS* 3.2 21.9 + - + +
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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