Contacts of the helix formed by residues 201 - 215 (chain C) in PDB entry 5MLE
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 ASN 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ASP* 3.1 18.4 + - - +
238A ARG* 4.3 2.2 - - - +
168C MET 4.2 0.4 - - - -
200C GLU* 1.3 69.4 - - - +
202C GLY* 1.3 61.4 - - - +
203C ASP* 3.3 11.4 + - - +
204C ILE* 3.2 43.4 + - + +
205C ILE* 3.3 24.7 + - - +
231C VAL* 3.4 19.2 + - + +
234C GLU* 2.8 31.4 + - - +
235C ALA* 3.6 0.8 - - - +
238C ARG* 3.0 16.9 - - - +
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Residues in contact with GLY 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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168C MET 3.0 17.2 + - - -
169C ALA* 3.8 12.6 - - - -
170C PHE 4.4 5.6 - - - -
171C LYS* 4.2 8.2 + - - +
175C GLN* 3.5 14.6 + - - -
200C GLU 3.2 1.2 + - - -
201C ASN* 1.3 69.1 + - - +
203C ASP* 1.3 64.5 + - - +
205C ILE* 3.4 6.7 + - - +
206C ALA* 3.0 25.8 + - - +
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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
----------------------------------------------------------
177A THR* 4.0 8.0 - - - +
178A ASP* 3.5 32.3 + - + +
179A CYS* 3.3 34.5 + - + +
171C LYS* 3.6 17.8 + - - +
175C GLN* 3.4 25.1 + - - +
201C ASN* 3.3 4.3 + - - +
202C GLY* 1.3 74.8 - - - +
204C ILE* 1.3 61.4 + - - +
206C ALA* 3.5 6.5 + - - +
207C GLU* 3.4 24.4 + - - +
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Residues in contact with ILE 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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178A ASP* 5.0 3.4 - - + +
182A TYR* 4.4 16.8 - - + -
241A THR* 4.3 21.1 - - + -
242A ILE* 3.8 31.9 - - + -
245A GLN* 4.3 13.2 - - + -
201C ASN* 3.2 39.0 + - + +
203C ASP* 1.3 75.6 - - + +
205C ILE* 1.3 68.0 + - - +
207C GLU* 3.1 6.8 + - - +
208C GLU* 2.9 36.7 + - + +
231C VAL* 4.1 19.3 - - + -
234C GLU* 5.1 0.4 - - + +
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Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ALA* 4.4 6.3 - - + -
170C PHE 5.7 0.4 - - - +
200C GLU* 3.8 24.5 - - + +
201C ASN 3.3 19.3 + - - +
202C GLY* 3.7 6.3 - - - +
204C ILE* 1.3 76.5 - - - +
206C ALA* 1.3 56.2 + - - +
208C GLU* 2.9 2.3 + - - +
209C GLN* 2.7 59.5 + - + +
226C SER 3.9 20.1 - - - +
227C ARG* 3.6 44.9 - - + +
231C VAL* 4.3 13.0 - - + -
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LYS* 4.3 25.1 - - + +
202C GLY 3.0 17.0 + - - +
203C ASP 3.5 7.0 - - - +
204C ILE 3.2 0.2 - - - -
205C ILE* 1.3 78.6 - - - +
207C GLU* 1.3 62.4 - - + +
209C GLN* 3.4 16.7 + - - +
210C GLN* 3.4 18.2 + - - +
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Residues in contact with GLU 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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179A CYS* 3.4 29.3 - - - -
182A TYR* 3.8 46.3 + - + -
183A GLU* 4.0 21.4 - - - +
203C ASP 3.4 11.8 + - - +
204C ILE 3.1 7.3 + - - +
206C ALA* 1.3 79.4 - - + +
208C GLU* 1.3 63.5 + - - +
210C GLN* 3.3 7.6 + - - +
211C ARG* 3.1 21.1 + - - +
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Residues in contact with GLU 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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182A TYR* 3.2 17.2 + - - +
245A GLN* 2.9 39.0 - - - +
204C ILE* 2.9 31.5 + - + +
207C GLU* 1.3 77.9 - - - +
209C GLN* 1.3 56.2 + - - +
211C ARG* 2.6 43.8 + - - +
212C ILE* 2.9 34.9 + - + +
225C LEU 5.2 3.1 - - - +
226C SER* 3.7 27.8 - - - +
228C PRO* 5.5 3.1 - - + -
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Residues in contact with GLN 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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205C ILE* 2.7 41.4 + - + +
206C ALA* 3.5 15.8 + - - +
207C GLU 3.3 0.2 - - - -
208C GLU* 1.3 72.5 - - - +
210C GLN* 1.3 55.3 + - - +
212C ILE 3.7 0.2 + - - -
213C LEU* 3.2 35.1 + - + +
223C HIS* 6.0 0.2 + - - -
226C SER* 4.0 19.6 + - - +
227C ARG* 4.3 10.7 + - - -
348C PHE* 4.0 8.3 - - + -
349C THR* 3.8 32.3 - - + +
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Residues in contact with GLN 210 (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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206C ALA 3.4 7.5 + - - +
207C GLU* 3.3 11.0 + - - +
208C GLU 3.2 0.4 - - - -
209C GLN* 1.3 77.5 - - - +
211C ARG* 1.3 66.8 + - - +
213C LEU* 4.4 14.0 - - - +
214C ASP* 3.0 57.2 + - - +
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Residues in contact with ARG 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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182A TYR* 4.1 9.6 + - - +
245A GLN 5.8 1.0 + - - -
207C GLU 3.1 13.2 + - - +
208C GLU* 2.6 38.7 + - - +
210C GLN* 1.3 77.6 - - - +
212C ILE* 1.3 83.7 + - - +
214C ASP* 3.6 5.2 + - - +
215C LEU* 3.3 55.5 + - + +
225C LEU 5.3 2.8 + - - -
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Residues in contact with ILE 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 GLU* 2.9 20.5 + - + +
209C GLN 4.1 3.8 - - - +
211C ARG* 1.3 97.9 - - - +
213C LEU* 1.3 65.3 + - - +
215C LEU* 3.1 22.7 + - + +
217C ILE* 3.5 41.5 + - + +
222C GLY* 3.9 18.6 - - - -
225C LEU* 3.9 28.3 - - + +
226C SER* 4.3 17.5 - - - +
348C PHE* 3.9 6.1 - - + -
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Residues in contact with LEU 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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209C GLN* 3.2 23.1 + - + +
210C GLN* 4.0 17.0 - - - +
212C ILE* 1.3 79.0 - - - +
214C ASP* 1.3 59.3 + - - +
216C GLY* 2.9 22.3 + - - -
217C ILE 3.8 9.3 + - - +
218C THR* 4.3 17.2 - - + +
347C ASN* 3.6 34.8 - - + +
348C PHE* 3.7 20.9 - - + -
349C THR* 4.3 13.9 - - + +
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Residues in contact with ASP 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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210C GLN* 3.0 48.4 + - - +
211C ARG* 3.9 6.2 - - - +
213C LEU* 1.3 76.9 - - - +
215C LEU* 1.3 64.8 + - + +
216C GLY 3.2 1.2 + - - -
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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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211C ARG* 3.3 45.0 + - + +
212C ILE* 3.1 16.7 + - + +
214C ASP* 1.3 79.3 - - + +
216C GLY* 1.3 58.4 + - - +
217C ILE* 3.5 20.0 - - + +
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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