Contacts of the helix formed by residues 200 - 217 (chain C) in PDB entry 4WNP
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 GLY 200 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ILE* 3.8 24.4 - - - +
172C LEU* 4.5 1.6 - - - +
199C ASP* 1.3 79.9 + - - +
201C LYS* 1.3 59.3 + - - +
202C ALA 3.0 2.2 + - - -
203C ASP* 3.1 16.4 + - - +
204C LEU 3.8 0.7 + - - -
269C PHE* 3.4 34.9 - - - -
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Residues in contact with LYS 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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199C ASP* 2.7 25.7 + - - +
200C GLY* 1.3 67.9 - - - -
202C ALA* 1.3 63.1 + - - +
203C ASP 3.3 0.2 - - - -
204C LEU* 3.2 24.0 + - + +
205C TRP 3.3 5.4 + - - -
263C HIS* 3.1 33.0 + - + +
264C LYS* 3.7 11.1 + - - +
266C ARG* 2.7 54.2 + - + +
267C MET 3.6 13.2 - - - +
268C ASP* 3.5 28.5 + - + +
269C PHE* 4.2 3.5 - - + -
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Residues in contact with ALA 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 6.3 2.5 - - + -
189C ALA* 3.8 16.0 + - + +
191C GLU* 4.1 5.0 + - - +
192C VAL* 3.9 17.9 - - + -
198C TYR* 3.8 21.1 - - + -
199C ASP* 3.1 15.0 + - - +
200C GLY 3.0 0.4 - - - -
201C LYS* 1.3 74.5 - - - +
203C ASP* 1.3 66.6 + - - +
204C LEU 3.0 2.5 + - - -
205C TRP* 3.2 12.6 + - - +
206C SER* 3.2 14.9 + - - -
266C ARG* 3.9 1.7 - - - +
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Residues in contact with ASP 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C MET* 3.9 19.9 - - + +
135C ILE* 3.7 12.7 - - - +
136C HIS* 2.9 24.7 + - - +
137C ARG* 2.9 31.6 + - - +
139C LEU* 3.7 22.4 - - + +
200C GLY* 3.1 12.2 + - - +
202C ALA* 1.3 79.5 - - - +
204C LEU* 1.3 57.5 + - + +
206C SER* 3.3 9.7 + - - -
207C ILE* 2.9 32.3 + - - +
269C PHE* 5.0 1.4 - - + -
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Residues in contact with LEU 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 GLY 4.2 0.4 - - - +
201C LYS* 3.3 20.0 - - - +
202C ALA 3.0 0.8 - - - -
203C ASP* 1.3 76.4 - - - +
205C TRP* 1.3 65.1 + - - +
207C ILE* 3.4 11.4 + - + +
208C GLY* 3.0 17.8 + - - -
258C LEU* 3.5 24.7 - - + +
266C ARG* 4.3 5.8 - - - -
267C MET 3.3 23.3 - - - +
268C ASP* 3.7 21.8 - - - +
269C PHE* 3.8 35.2 - - + +
272C PHE* 4.0 32.8 - - + -
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Residues in contact with TRP 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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186C MET 4.9 1.0 + - - -
187C TYR* 3.6 6.7 + - - +
188C MET 3.0 17.0 + - - -
189C ALA* 3.3 29.8 - - + -
190C PRO* 3.4 29.6 - - + -
201C LYS 3.3 3.0 + - - -
202C ALA 3.2 9.5 + - - +
204C LEU* 1.3 75.4 - - - +
206C SER* 1.3 67.8 + - - +
208C GLY* 3.0 3.8 + - - -
209C THR* 2.9 35.5 + - + +
221C PHE* 3.6 29.4 - + - -
233C TYR* 3.5 22.2 + - - -
239C LEU* 4.0 9.2 - - + -
258C LEU 3.7 11.2 - - - -
259C LEU* 3.4 42.4 - - + +
260C GLN 3.6 20.0 - - - -
261C ARG 4.1 0.4 - - - -
266C ARG* 4.0 9.5 - - - +
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Residues in contact with SER 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG 5.8 2.3 - - - -
139C LEU* 3.6 31.6 + - - +
187C TYR 2.8 25.9 + - - -
188C MET* 4.7 2.6 - - - -
189C ALA 4.7 0.5 + - - -
202C ALA 3.2 10.9 + - - -
203C ASP* 3.4 13.0 + - - -
204C LEU 3.3 0.2 - - - -
205C TRP* 1.3 77.0 - - - +
207C ILE* 1.3 62.6 - - - +
209C THR* 2.4 22.5 + - - -
210C ILE* 2.9 12.4 + - - +
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Residues in contact with ILE 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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119C LEU* 3.5 31.2 - - + -
122C ILE* 4.0 16.6 - - + -
126C MET* 3.8 30.1 - - + -
139C LEU* 3.9 17.3 - - + -
203C ASP 2.9 22.2 + - - +
204C LEU* 3.8 15.9 - - + +
205C TRP 3.3 0.2 - - - -
206C SER* 1.3 74.2 - - - +
208C GLY* 1.3 58.2 + - - +
210C ILE* 3.0 15.6 + - + +
211C VAL* 2.8 29.6 + - + +
258C LEU* 4.7 2.2 - - + -
272C PHE* 4.1 20.9 - - + -
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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 LEU 3.0 11.5 + - - -
205C TRP 3.0 7.8 + - - -
207C ILE* 1.3 77.4 - - - +
209C THR* 1.3 61.1 + - - +
211C VAL* 3.5 3.5 + - - -
212C TYR* 3.0 24.9 + - - +
255C LEU* 3.6 9.2 - - - +
258C LEU* 3.9 25.1 - - - +
259C LEU* 3.9 9.9 - - - +
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Residues in contact with THR 209 (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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186C MET 4.1 10.3 - - - +
187C TYR* 3.1 28.7 - - - +
205C TRP* 2.9 40.5 + - + +
206C SER* 2.4 22.9 + - - -
208C GLY* 1.3 75.1 - - - +
210C ILE* 1.3 57.2 + - - +
212C TYR* 3.5 2.0 + - - +
213C GLN* 3.0 29.6 + - - +
220C PRO* 4.0 29.1 - - + +
221C PHE* 5.7 0.4 - - + -
259C LEU* 3.9 10.3 - - + -
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Residues in contact with ILE 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 4.0 27.1 - - + -
104C LEU* 5.1 0.2 - - - +
122C ILE* 5.1 12.6 - - + -
139C LEU* 3.8 11.9 - - + -
140C LYS* 3.7 39.5 - - - +
141C PRO* 4.1 12.1 - - + -
144C ILE* 4.7 10.5 - - + -
187C TYR* 4.4 3.6 - - + -
206C SER 2.9 17.5 + - - +
207C ILE* 3.3 18.2 - - + +
209C THR* 1.3 78.4 + - - +
211C VAL* 1.3 68.2 + - + +
213C GLN* 3.4 6.0 + - - +
214C CYS* 3.0 26.0 + - - -
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Residues in contact with VAL 211 (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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115C ILE* 3.7 26.0 - - + +
119C LEU* 3.6 37.7 - - + -
122C ILE* 6.3 0.7 - - + -
207C ILE* 2.8 25.9 + - + +
208C GLY* 4.0 4.9 - - - +
210C ILE* 1.3 76.6 - - + +
212C TYR* 1.3 62.9 + - - +
214C CYS* 3.1 10.7 + - - +
215C LEU* 3.0 20.1 + - - +
251C LEU* 3.9 17.7 - - + -
254C LEU* 5.6 2.0 - - + -
255C LEU* 3.9 16.6 - - + -
258C LEU* 5.5 3.6 - - + -
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Residues in contact with TYR 212 (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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208C GLY 3.0 19.1 + - - +
209C THR* 3.7 6.7 - - - +
211C VAL* 1.3 76.9 - - - +
213C GLN* 1.3 57.0 + - - +
215C LEU* 3.0 8.0 + - + +
216C THR* 2.8 61.1 + - + +
218C LYS* 3.1 25.1 - - + -
219C ALA 3.8 2.6 + - - -
220C PRO* 3.4 35.7 + - + +
241C PRO* 3.8 20.6 - - + -
242C THR* 2.6 38.0 + - - -
243C ILE* 4.2 7.0 - - + -
244C PRO* 5.2 0.2 - - + -
255C LEU* 3.7 22.1 - - + +
259C LEU* 4.4 7.0 - - + -
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Residues in contact with GLN 213 (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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101C ALA* 5.3 5.3 + - - +
104C LEU* 3.9 22.9 - - + +
105C HIS* 5.4 8.7 + - - -
141C PRO* 3.7 12.9 - - + +
142C GLN* 5.9 1.0 - - - +
187C TYR* 2.4 37.5 + - - -
209C THR 3.0 17.9 + - - +
210C ILE* 3.8 5.4 - - - +
212C TYR* 1.3 76.4 - - - +
214C CYS* 1.3 58.1 + - - +
217C GLY* 2.6 37.6 + - - -
218C LYS* 3.1 31.0 - - - +
219C ALA* 4.6 5.2 + - - +
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Residues in contact with CYS 214 (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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100C LEU* 4.1 17.9 - - - -
104C LEU* 3.8 25.1 - - - -
109C THR* 3.6 5.4 - - - -
110C LEU* 3.0 46.3 + - + +
115C ILE* 3.9 20.9 - - + -
118C PHE* 5.6 2.9 - - - -
210C ILE* 3.0 25.7 + - - -
211C VAL* 3.3 11.4 - - - +
213C GLN* 1.3 77.9 - - - +
215C LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 215 (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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109C THR* 3.6 15.8 - - - +
110C LEU 4.6 5.2 - - - +
112C GLU* 4.3 14.4 - - + +
115C ILE* 3.8 14.8 - - + +
211C VAL 3.0 12.3 + - - +
212C TYR* 3.0 8.7 + - + +
214C CYS* 1.3 80.0 - - - +
216C THR* 1.3 64.7 + - + +
243C ILE* 4.7 0.4 - - + -
244C PRO* 4.6 13.3 - - + +
247C THR* 3.7 33.9 - - + +
251C LEU* 3.8 24.2 - - + -
255C LEU* 3.9 17.5 - - + -
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Residues in contact with THR 216 (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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109C THR* 3.6 13.1 - - - +
212C TYR* 2.8 40.1 + - + +
215C LEU* 1.3 80.4 - - + +
217C GLY* 1.3 59.7 + - - +
218C LYS* 3.0 42.3 + - - +
244C PRO* 3.8 35.2 - - + -
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Residues in contact with GLY 217 (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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104C LEU* 6.0 2.0 - - - -
108C ARG 3.6 20.2 - - - -
109C THR* 4.0 0.8 - - - +
213C GLN* 2.6 33.7 + - - +
215C LEU 3.7 0.8 - - - -
216C THR* 1.3 72.0 - - - +
218C LYS* 1.3 63.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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