Contacts of the helix formed by residues 246 - 258 (chain C) 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 HIS 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242C ALA* 2.9 21.4 + - + +
243C VAL 3.6 2.2 - - - -
245C SER* 1.3 107.0 + - - +
247C TYR* 1.3 67.3 + - - +
248C HIS 3.4 2.2 - - - -
249C ALA* 3.3 9.1 + - + +
250C ILE* 2.9 28.4 + - + +
277C ARG* 3.9 32.7 + - - +
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Residues in contact with TYR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C VAL* 2.9 23.0 + - + +
244C THR* 4.3 7.2 + - - +
245C SER 3.7 1.4 - - - -
246C HIS* 1.3 75.7 - - - +
248C HIS* 1.3 61.9 + - - +
250C ILE* 3.8 4.3 - - - +
251C THR* 2.8 46.1 + - + -
307C LEU* 3.6 35.3 - - + +
308C SER* 4.8 1.6 + - - -
311C SER* 3.6 37.4 + - - -
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Residues in contact with HIS 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C HIS 3.4 0.6 - - - -
247C TYR* 1.3 82.2 - - + +
249C ALA* 1.3 65.9 + - - +
251C THR* 3.2 10.8 + - + +
252C GLN* 3.0 28.8 + - + +
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C HIS* 3.3 14.3 + - + +
248C HIS* 1.3 82.7 - - + +
250C ILE* 1.3 61.4 + - - +
252C GLN* 3.3 8.8 + - - +
253C GLU* 3.1 24.3 + - - +
277C ARG* 3.4 26.6 + - - +
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Residues in contact with ILE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C LEU* 6.5 0.4 - - + -
242C ALA* 3.6 27.1 - - + +
243C VAL* 3.8 18.6 - - + +
246C HIS* 2.9 20.7 + - + +
247C TYR* 3.8 4.0 - - - +
249C ALA* 1.3 74.5 - - - +
251C THR* 1.3 66.3 + - - +
253C GLU* 3.0 9.3 + - - +
254C PHE* 3.0 52.2 + - + -
273C ILE* 4.8 9.2 - - + -
277C ARG* 3.8 34.3 - - + +
306C PHE* 5.0 2.9 - - + -
307C LEU* 4.2 8.3 - - + -
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Residues in contact with THR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C TYR* 2.8 37.2 + - + -
248C HIS* 3.5 11.4 - - + +
250C ILE* 1.3 77.0 - - - +
252C GLN* 1.3 59.2 + - - +
254C PHE* 3.2 13.2 + - - +
255C GLU* 2.9 44.6 + - + +
303C TYR* 4.9 6.7 - - + -
307C LEU* 3.6 21.6 - - + +
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Residues in contact with GLN 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C HIS* 3.0 20.0 + - + +
249C ALA* 3.5 11.9 - - - +
251C THR* 1.3 79.5 - - - +
253C GLU* 1.3 57.1 + - + +
255C GLU* 3.7 13.8 - - - +
256C ASN* 2.9 39.9 + - - +
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ALA 3.1 13.7 + - - +
250C ILE* 3.0 15.8 + - - +
252C GLN* 1.3 73.3 - - - +
254C PHE* 1.3 67.3 + - - +
256C ASN* 3.3 8.8 + - - +
257C PHE* 3.2 34.3 + - + -
273C ILE* 3.7 35.7 - - + +
276C ARG* 5.5 4.0 - - - +
277C ARG* 2.7 42.3 + - - +
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Residues in contact with PHE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ILE* 3.0 32.7 + - + -
251C THR* 3.4 7.0 - - - +
253C GLU* 1.3 76.8 - - - +
255C GLU* 1.3 58.2 + - - +
257C PHE* 3.2 2.3 + - - -
258C ASP* 2.9 31.8 + - - +
265C ILE* 3.5 34.8 - - + +
270C PHE* 4.4 5.4 - + - -
273C ILE* 3.3 24.9 - - + -
301C LEU* 4.2 11.0 - - + -
303C TYR* 3.5 41.1 - + + -
306C PHE* 3.6 27.8 - + - -
307C LEU* 3.6 25.4 - - + -
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C THR* 2.9 34.1 + - + +
252C GLN* 3.7 13.8 - - - +
254C PHE* 1.3 76.2 - - - +
256C ASN* 1.3 64.6 + - - +
257C PHE 3.3 0.3 + - - -
258C ASP* 3.3 21.4 + - - +
259C THR* 4.2 1.6 + - - -
261C LYS* 5.0 17.1 + - - +
303C TYR* 3.6 20.8 + - - +
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Residues in contact with ASN 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C GLN* 2.9 28.2 + - - +
253C GLU* 3.3 7.8 + - - +
254C PHE 3.3 0.2 - - - -
255C GLU* 1.3 79.2 - - - +
257C PHE* 1.3 64.9 + - + +
259C THR* 3.7 15.8 - - - +
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Residues in contact with PHE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 3.3 36.6 - - + -
253C GLU* 3.2 22.5 + - + -
254C PHE 3.2 7.2 + - - +
256C ASN* 1.3 79.2 - - + +
258C ASP* 1.3 57.4 + - - +
259C THR* 3.0 17.8 + - - +
265C ILE* 3.9 8.3 - - + -
269C GLU* 3.6 57.5 - - + +
272C ALA* 4.7 3.4 - - + -
273C ILE* 3.8 22.9 - - + -
300C ARG* 5.5 1.7 + - - -
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Residues in contact with ASP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C PHE 2.9 17.0 + - - +
255C GLU* 3.3 12.5 + - - +
257C PHE* 1.3 73.7 - - - +
259C THR* 1.3 63.2 - - - +
260C MET 4.0 1.2 + - - -
261C LYS* 3.1 19.6 + - - +
262C THR* 2.8 33.4 + - - +
263C ASN* 2.7 28.9 + - - +
264C THR 3.2 21.6 + - - +
300C ARG* 4.7 3.8 + - - +
303C TYR* 3.6 12.5 + - + -
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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