Contacts of the helix formed by residues 303 - 310 (chain D) in PDB entry 1WLZ
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 TYR 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B MET* 5.2 3.8 - - + -
291B ASN* 3.7 25.4 + - - -
254D PHE* 3.7 54.2 + + + -
255D GLU* 4.9 3.2 + - - -
258D ASP* 2.6 36.1 + - + +
263D ASN* 3.2 33.8 + - - -
264D THR* 3.2 16.4 - - - -
265D ILE* 3.9 11.4 - - + -
301D LEU* 3.1 10.8 + - + -
302D LYS* 1.3 71.2 - - - +
304D PRO* 1.3 81.5 - - + +
306D PHE* 3.4 7.4 - - - +
307D LEU* 2.9 31.5 + - + +
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Residues in contact with PRO 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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227B HIS* 3.7 21.0 - - + +
228B MET* 4.2 18.4 - - - -
291B ASN* 3.6 28.9 - - + +
263D ASN* 3.1 30.1 - - + +
302D LYS* 3.5 4.7 - - + -
303D TYR* 1.3 105.8 - - + +
305D ASP* 1.3 61.5 + - - +
307D LEU* 3.3 3.3 + - + +
308D SER 3.1 17.7 + - - -
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Residues in contact with ASP 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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227B HIS* 5.2 2.0 - - - -
294D PRO* 4.3 13.9 - - + -
302D LYS* 3.3 24.8 + - + +
304D PRO* 1.3 78.9 - - - +
306D PHE* 1.3 64.6 + - - +
308D SER* 3.3 7.9 + - - -
309D ARG* 3.0 25.1 + - - +
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Residues in contact with PHE 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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239D LEU* 3.7 28.9 - - + -
243D VAL* 3.6 31.9 - - + -
250D ILE* 4.8 3.8 - - + -
254D PHE* 3.7 34.5 - + - -
270D PHE* 3.9 13.7 - + - -
293D MET* 3.7 19.3 - - - -
294D PRO* 3.8 15.0 - - + +
301D LEU* 4.3 8.7 - - + -
302D LYS 3.0 13.9 + - - +
303D TYR* 3.2 10.7 + - - +
305D ASP* 1.3 77.4 - - - +
307D LEU* 1.3 65.4 + - + +
309D ARG* 3.2 1.7 + - - -
310D PHE* 2.9 59.6 + + - +
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Residues in contact with LEU 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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227B HIS 4.6 2.0 - - - +
228B MET* 3.5 33.9 - - + -
243D VAL* 4.3 7.6 - - + +
247D TYR* 3.6 34.8 - - + +
250D ILE* 4.4 9.2 - - + -
251D THR* 3.7 16.2 - - + -
254D PHE* 3.8 28.9 - - + -
303D TYR* 2.9 21.3 + - + +
304D PRO* 3.6 4.0 - - + +
306D PHE* 1.3 86.7 - - + +
308D SER* 1.3 56.3 + - - +
310D PHE 3.5 0.5 + - - -
311D SER* 2.6 38.7 + - - -
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Residues in contact with SER 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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227B HIS* 3.8 28.0 + - - -
304D PRO 3.1 11.0 + - - -
305D ASP* 3.7 9.6 - - - -
306D PHE 3.3 0.2 - - - -
307D LEU* 1.3 79.4 - - - +
309D ARG* 1.3 63.2 + - - +
310D PHE 3.6 0.2 + - - -
311D SER* 3.7 16.7 + - - -
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Residues in contact with ARG 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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240D HIS* 3.7 12.8 - - - -
294D PRO* 5.7 3.1 - - + -
305D ASP 3.0 18.0 + - - +
306D PHE* 3.6 4.9 - - - +
308D SER* 1.3 78.4 - - - +
310D PHE* 1.3 75.3 + - + +
311D SER 3.7 1.6 + - - -
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Residues in contact with PHE 310 (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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236D LEU* 3.6 18.8 - - + -
239D LEU* 3.5 25.8 - - + -
240D HIS* 3.6 52.8 + + - +
243D VAL* 3.3 34.5 - - + +
244D THR* 3.7 2.3 - - - +
292D GLU 4.8 3.8 - - - -
293D MET* 3.3 26.7 - - + -
294D PRO* 4.7 7.4 - - + -
306D PHE* 2.9 42.3 + + - +
309D ARG* 1.3 88.3 - - + +
311D SER* 1.3 58.8 + - - +
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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