Contacts of the helix formed by residues 245 - 256 (chain C) in PDB entry 1ZWS
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 SER 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C GLU* 2.3 46.2 + - - -
243C HIS 3.7 1.7 + - - -
244C THR* 1.3 84.4 - - - +
246C GLU* 1.3 61.8 + - - +
247C LEU* 3.4 12.5 + - - +
248C ALA 2.8 16.6 + - - -
249C LYS* 3.2 9.5 + - - +
274C TRP* 3.7 0.7 + - - -
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Residues in contact with GLU 246 (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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244C THR 5.4 0.2 - - - +
245C SER* 1.3 70.5 - - - +
247C LEU* 1.3 56.2 + - - +
249C LYS* 3.3 36.7 + - - +
250C ASP* 2.7 37.0 + - - +
253C ARG* 4.5 11.5 + - - +
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Residues in contact with LEU 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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245C SER* 3.5 11.2 - - - +
246C GLU* 1.3 77.7 - - - +
248C ALA* 1.3 68.3 + - - +
250C ASP* 3.4 5.7 - - + +
251C PHE 3.2 12.1 + - - -
272C HIS* 3.3 17.5 - - + +
273C PRO* 3.8 17.0 - - + +
274C TRP* 3.3 43.6 - - + +
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Residues in contact with ALA 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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113C GLU* 3.6 2.7 - - - +
207C THR* 6.3 0.2 - - - -
211C LEU* 3.6 13.5 - - + -
244C THR* 3.4 16.8 - - + -
245C SER* 2.8 22.4 + - - +
247C LEU* 1.3 72.4 - - - +
249C LYS* 1.3 70.1 + - - +
251C PHE* 2.6 24.7 + - - +
252C ILE* 3.2 7.6 + - - +
274C TRP* 3.4 29.8 - - + +
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Residues in contact with LYS 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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211C LEU* 6.0 0.2 - - - -
236C PHE* 3.7 24.4 - - + -
238C GLU* 5.0 5.5 + - - -
241C PHE* 3.8 29.1 + - + -
244C THR* 3.1 37.8 + - + +
245C SER 3.4 5.8 - - - +
246C GLU* 3.3 39.9 + - - +
248C ALA* 1.3 77.5 - - - +
250C ASP* 1.3 65.0 + - - +
252C ILE* 3.0 15.5 - - - +
253C ARG* 2.9 48.1 + - - +
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Residues in contact with ASP 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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246C GLU 2.7 21.4 + - - +
247C LEU* 3.4 11.9 - - + +
248C ALA 2.8 2.8 + - - -
249C LYS* 1.3 71.1 - - - +
251C PHE* 1.3 64.0 + - - +
253C ARG* 2.8 29.6 + - - +
254C LYS* 2.6 46.5 + - - +
272C HIS* 3.0 19.1 + - + +
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Residues in contact with PHE 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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120C ILE* 4.0 22.2 - - + -
124C LEU* 4.3 13.0 - - + -
203C ILE* 4.8 1.8 - - + -
207C THR* 4.1 15.3 - - + -
247C LEU 3.2 7.9 + - - +
248C ALA 2.6 15.3 + - - +
250C ASP* 1.3 76.1 + - - +
252C ILE* 1.3 64.6 + - + +
254C LYS* 3.4 9.6 + - - +
255C LEU* 3.4 39.5 + - + +
264C LEU* 4.5 4.3 - - + -
269C ALA* 3.4 37.7 - - + -
272C HIS* 3.7 30.0 + + + -
274C TRP* 3.5 26.7 - + + -
275C ILE* 4.0 13.9 - - + -
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Residues in contact with ILE 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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204C GLY* 4.0 5.6 - - - +
207C THR* 3.4 39.9 - - + -
208C TYR* 3.6 21.5 - - + +
211C LEU* 4.9 5.8 - - + -
234C TYR* 4.2 0.7 - - + -
236C PHE* 3.5 25.8 - - + -
241C PHE* 5.7 2.0 - - + -
248C ALA 3.7 10.8 - - - +
249C LYS* 3.0 17.3 - - - +
251C PHE* 1.3 75.9 - - + +
253C ARG* 1.3 59.3 + - - +
255C LEU* 2.8 10.3 + - - +
256C LEU* 2.8 59.7 + - + +
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Residues in contact with ARG 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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234C TYR* 3.5 15.8 + - - +
236C PHE* 3.4 38.8 - - + +
246C GLU* 4.5 10.5 + - - +
249C LYS* 2.9 40.4 + - - +
250C ASP* 2.8 20.3 + - - +
252C ILE* 1.3 75.8 - - - +
254C LYS* 1.3 58.6 + - + +
255C LEU 3.4 0.2 + - - -
256C LEU 3.5 6.8 - - - +
257C VAL* 3.1 21.5 - - - +
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Residues in contact with LYS 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 ASP* 2.6 51.5 + - - +
251C PHE 3.8 3.8 - - - +
252C ILE 3.2 0.2 - - - -
253C ARG* 1.3 78.5 - - + +
255C LEU* 1.3 57.8 + - - +
257C VAL* 3.5 14.3 - - - +
262C LYS 4.7 1.0 - - - +
263C ARG* 3.6 1.4 - - - +
264C LEU* 3.2 60.6 + - + -
272C HIS* 4.2 9.2 - - + -
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Residues in contact with LEU 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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200C MET* 3.8 46.4 - - + +
201C TRP* 4.0 6.1 - - - -
203C ILE* 4.1 7.0 - - + -
204C GLY* 3.6 30.7 - - - +
251C PHE* 3.4 42.4 - - + +
252C ILE 2.8 5.9 + - - +
254C LYS* 1.3 75.9 - - - +
256C LEU* 1.3 59.3 + - - +
257C VAL 2.7 15.9 + - - -
263C ARG* 2.9 22.8 + - - -
264C LEU* 3.8 23.6 - - + +
269C ALA* 4.4 2.7 - - + -
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Residues in contact with LEU 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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201C TRP* 3.7 38.8 - - + +
204C GLY* 4.1 2.9 - - - -
205C VAL* 3.8 22.9 - - + +
208C TYR* 4.5 3.4 - - + -
216C PRO* 4.4 10.5 - - + -
217C PHE* 4.3 13.0 - - + -
232C VAL* 4.4 6.3 - - - +
234C TYR* 3.5 45.8 + - + +
252C ILE* 2.8 41.8 + - + +
253C ARG 3.5 4.7 - - - +
255C LEU* 1.3 74.0 - - - +
257C VAL* 1.3 63.5 + - - +
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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