Contacts of the helix formed by residues 191 - 208 (chain C) in PDB entry 2YWB
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 THR 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A LEU 3.6 15.7 - - - +
368A LEU 3.6 9.8 + - - +
369A LEU 4.6 0.4 - - - -
370A GLY* 3.9 16.8 - - - +
23C ARG* 5.0 1.3 - - + -
188C ARG 4.0 13.5 - - - +
189C ASP 3.0 5.6 + - - +
190C TRP* 1.3 78.9 - - - +
192C PRO* 1.3 72.8 - - - +
193C GLU* 2.8 28.6 + - - -
194C HIS* 3.6 12.1 - - - +
195C VAL* 3.1 23.7 + - - +
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Residues in contact with PRO 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 3.6 46.9 - - + +
368A LEU* 4.4 5.2 - - + -
190C TRP 4.8 0.2 - - - +
191C THR* 1.3 88.0 - - - +
193C GLU* 1.3 58.9 + - - +
195C VAL* 3.5 2.6 + - + -
196C LEU* 3.0 29.1 + - - +
364C GLU* 4.2 22.2 - - + +
365C LEU* 3.4 11.0 - - + +
368C LEU* 3.4 26.0 - - + +
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Residues in contact with GLU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 4.9 14.1 - - + -
196A LEU* 3.7 13.6 - - + +
368A LEU* 2.9 43.4 - - + +
369A LEU* 5.8 0.2 - - - +
191C THR* 2.8 30.3 + - - +
192C PRO* 1.3 75.5 - - - +
194C HIS* 1.3 69.2 + - + +
196C LEU* 3.3 2.8 + - - +
197C GLU* 3.1 40.4 + - - +
368C LEU* 3.5 15.4 - - + +
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Residues in contact with HIS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ASP* 3.3 27.1 - - + +
190C TRP* 5.4 3.8 - + - -
191C THR* 3.3 18.7 + - - +
193C GLU* 1.3 84.0 - - + +
195C VAL* 1.3 73.6 + - + +
197C GLU* 3.4 10.9 + - - +
198C GLU* 3.1 48.8 + - + +
201C ARG* 5.8 2.4 + - - -
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TRP* 3.5 54.5 - - + -
191C THR 3.1 20.5 + - - +
192C PRO* 3.8 5.2 - - + +
194C HIS* 1.3 82.9 - - + +
196C LEU* 1.3 63.0 + - - +
198C GLU* 3.3 7.8 + - + +
199C LEU* 3.0 41.9 + - + +
357C LEU* 4.6 7.4 - - + -
365C LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 196 (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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193A GLU* 4.0 12.8 - - - +
192C PRO 3.0 19.3 + - - +
193C GLU* 3.6 5.4 - - - +
195C VAL* 1.3 75.8 - - - +
197C GLU* 1.3 58.9 + - + +
199C LEU* 3.1 5.6 + - - -
200C LEU* 2.8 48.1 + - + +
228C LEU* 3.6 25.6 - - + -
231C LYS* 6.3 1.3 - - - -
365C LEU* 3.9 17.7 - - + +
368C LEU* 3.9 31.2 - - + -
369C LEU* 4.2 27.8 - - + -
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Residues in contact with GLU 197 (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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197A GLU* 5.7 1.2 - - - +
193C GLU* 3.1 33.0 + - - +
194C HIS* 3.7 9.8 + - - +
196C LEU* 1.3 80.1 - - + +
198C GLU* 1.3 64.1 + - - +
200C LEU* 3.3 12.8 + - + +
201C ARG* 3.1 37.0 + - + +
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Residues in contact with GLU 198 (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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190C TRP* 5.8 3.6 - - - -
194C HIS* 3.1 46.2 + - + +
195C VAL* 3.6 8.1 - - - +
196C LEU 3.2 0.2 - - - -
197C GLU* 1.3 77.7 - - - +
199C LEU* 1.3 58.6 + - + +
201C ARG* 3.0 34.7 + - - +
202C GLU* 3.1 49.4 + - - +
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Residues in contact with LEU 199 (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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195C VAL* 3.0 29.2 + - + +
196C LEU 3.6 3.6 - - - +
198C GLU* 1.3 75.2 - - + +
200C LEU* 1.3 66.2 + - - +
202C GLU* 4.0 20.6 - - + +
203C VAL* 3.0 31.8 + - - +
228C LEU* 4.1 13.9 - - + -
353C PRO* 3.3 34.3 - - + +
354C PHE* 3.9 13.5 - - + -
357C LEU* 4.3 6.5 - - + -
365C LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 200 (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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196C LEU* 2.8 39.6 + - + +
197C GLU* 3.3 11.4 + - + +
199C LEU* 1.3 72.7 - - - +
201C ARG* 1.3 66.1 + - + +
203C VAL* 3.3 4.3 + - - +
204C ARG* 3.0 32.4 + - - +
228C LEU* 3.4 40.8 - - + +
231C LYS* 4.0 25.6 - - + +
232C ALA* 3.8 19.5 - - + +
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Residues in contact with ARG 201 (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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194C HIS* 5.2 3.0 + - - -
197C GLU* 3.1 23.6 + - + +
198C GLU* 3.0 62.0 + - - +
199C LEU 3.3 0.2 - - - -
200C LEU* 1.3 76.0 - - + +
202C GLU* 1.3 67.7 + - + +
204C ARG* 2.9 23.7 + - - +
205C GLU* 3.1 32.1 + - - +
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Residues in contact with GLU 202 (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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198C GLU* 3.1 42.0 + - + +
199C LEU* 4.0 19.6 - - + +
201C ARG* 1.3 83.1 - - + +
203C VAL* 1.3 64.3 + - + +
205C GLU* 4.1 6.5 - - - +
206C ARG* 3.0 35.9 + - + +
351C LEU* 6.2 0.2 - - - -
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Residues in contact with VAL 203 (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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199C LEU 3.0 24.1 + - - +
200C LEU* 3.7 3.6 - - - +
202C GLU* 1.3 76.3 - - + +
204C ARG* 1.3 65.1 + - - +
206C ARG* 4.7 2.9 - - - -
207C ALA* 3.1 24.7 + - + +
228C LEU* 3.5 24.0 - - + -
229C LEU* 3.4 23.3 - - + -
232C ALA* 4.1 9.2 - - + -
234C VAL* 3.4 23.3 - - + -
351C LEU* 4.6 12.1 - - + -
353C PRO* 4.2 18.8 - - + -
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Residues in contact with ARG 204 (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 LEU* 3.0 22.7 + - - +
201C ARG* 2.9 12.2 + - - +
203C VAL* 1.3 76.1 - - - +
205C GLU* 1.3 56.3 + - + +
207C ALA* 4.3 0.2 - - - +
208C GLY* 2.6 39.6 + - - +
231C LYS 4.1 6.3 + - - -
232C ALA* 2.8 46.4 + - + +
233C GLY* 4.4 4.6 - - - +
234C VAL* 4.3 7.0 - - - -
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Residues in contact with GLU 205 (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 ARG* 3.1 33.4 + - - +
202C GLU* 4.1 5.3 + - - +
204C ARG* 1.3 80.1 - - + +
206C ARG* 1.3 68.7 + - + +
208C GLY* 2.8 16.7 + - - -
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Residues in contact with ARG 206 (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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202C GLU* 3.0 24.1 + - + +
203C VAL* 4.1 3.1 - - - +
205C GLU* 1.3 78.8 - - + +
207C ALA* 1.3 60.3 + - - +
310C ARG* 4.3 6.2 + - - -
311C PHE* 2.9 28.9 - - + -
349C GLU* 3.2 31.8 + - - +
350C LEU 2.7 30.3 + - - -
351C LEU* 4.3 20.0 - - + +
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Residues in contact with ALA 207 (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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203C VAL 3.1 16.2 + - - +
204C ARG 4.3 0.2 - - - +
206C ARG* 1.3 78.7 - - - +
208C GLY* 1.3 66.9 + - - +
209C LYS 3.0 0.3 + - - -
210C ASP* 2.9 31.9 + - - +
212C VAL* 3.8 28.3 - - + -
234C VAL* 4.3 15.0 - - + -
310C ARG* 5.6 0.2 - - - -
311C PHE* 3.2 11.4 - - + -
351C LEU* 4.6 7.3 - - + +
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Residues in contact with GLY 208 (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 ARG* 2.6 25.0 + - - +
205C GLU* 2.8 10.5 + - - -
207C ALA* 1.3 74.6 - - - +
209C LYS* 1.3 66.8 + - - +
210C ASP 4.9 0.9 - - - +
234C VAL* 5.2 9.9 - - - +
235C ASP 5.6 0.3 + - - -
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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