Contacts of the helix formed by residues 205 - 217 (chain A) in PDB entry 5H1Y
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A HIS 4.5 5.4 - - - +
204A PRO* 1.3 74.3 - - - +
206A PRO* 1.4 70.9 - - - +
207A ILE* 3.4 8.3 - - - +
208A GLN* 2.8 33.8 + - - +
209A ILE* 2.8 27.7 + - - +
228A GLY 5.7 0.9 - - - +
229A SER 2.7 31.5 + - - +
230A GLY* 4.4 2.0 - - - -
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Residues in contact with PRO 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TYR* 3.6 39.3 - - + +
169A ILE* 3.6 18.3 - - + +
204A PRO 4.8 0.4 - - - +
205A THR* 1.4 86.7 - - - +
207A ILE* 1.3 62.9 + - - +
209A ILE* 3.2 18.0 + - + +
210A GLN* 3.3 11.4 + - - +
229A SER 5.1 0.9 - - - +
398A VAL* 3.8 20.2 - - + -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A THR* 3.4 2.5 - - - +
206A PRO* 1.3 79.4 - - - +
208A GLN* 1.3 55.9 + - - +
211A GLY* 2.7 35.0 + - - -
221A MET* 3.8 18.2 - - + -
223A GLY* 4.7 2.0 - - - -
225A ALA* 3.9 22.7 - - + -
229A SER* 3.3 29.4 + - - +
230A GLY 3.7 2.2 - - - -
231A LYS* 3.7 20.4 - - + +
234A VAL* 3.8 11.0 - - + +
374A PHE* 4.5 4.5 - - + -
396A ILE* 3.6 35.0 - - + +
398A VAL* 3.6 18.4 - - + +
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Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PHE* 3.5 13.8 - - + -
186A MET* 3.6 4.9 - - - +
201A ILE* 5.2 2.8 - - - +
203A HIS 4.3 0.5 - - - +
204A PRO* 3.1 16.6 - - + +
205A THR* 2.8 34.7 + - - +
207A ILE* 1.3 76.0 - - - +
209A ILE* 1.3 66.3 + - - +
212A ILE* 3.1 43.6 + - + +
213A PRO* 3.6 0.9 - - - +
230A GLY* 2.8 40.4 + - - +
233A LEU* 3.7 23.2 - - + +
234A VAL* 3.8 11.2 - - + -
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 4.4 7.2 - - + -
167A TYR* 3.7 41.1 - - + -
169A ILE* 3.8 11.9 - - + -
179A PRO* 3.4 22.1 - - + +
180A ILE 2.9 46.8 + - - +
181A LYS* 4.3 9.4 - - + +
186A MET* 4.1 1.3 - - - +
204A PRO* 3.9 22.9 - - + +
205A THR 2.8 16.8 + - - +
206A PRO* 3.2 8.9 + - + +
208A GLN* 1.3 76.0 - - - +
210A GLN* 1.3 57.6 + - - +
213A PRO* 3.3 11.4 - - - +
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Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ARG* 2.9 30.7 + - - +
169A ILE* 3.9 22.4 - - + -
171A VAL* 3.8 21.1 - - + -
176A ILE* 3.5 12.6 - - + +
177A PRO* 2.9 25.4 + - - +
178A PRO 4.2 1.6 + - - -
179A PRO* 3.4 20.0 - - + +
206A PRO 3.3 3.5 + - - +
209A ILE* 1.3 79.3 - - - +
211A GLY* 1.3 59.6 + - - +
213A PRO* 3.3 7.5 - - - +
214A THR* 2.6 32.2 + - - +
396A ILE* 3.8 17.3 - - + -
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Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE 2.7 25.4 + - - -
210A GLN* 1.3 70.9 - - - +
212A ILE* 1.3 64.5 + - - +
214A THR* 3.1 4.2 + - - -
215A ILE* 2.9 26.3 + - - +
221A MET* 4.0 2.9 - - - -
234A VAL* 3.6 15.5 - - - -
396A ILE* 3.6 16.7 - - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PHE* 4.5 8.1 - - + -
186A MET* 3.8 24.5 - - + -
188A PHE* 3.6 26.5 - - + -
208A GLN* 3.1 31.6 + - + +
211A GLY* 1.3 74.4 - - - +
213A PRO* 1.4 60.8 - - + +
215A ILE* 3.1 5.5 + - - +
216A LEU* 2.9 54.7 + - + +
233A LEU 4.2 13.9 - - - +
234A VAL* 3.8 21.5 - - - +
237A LEU* 4.5 4.5 - - + -
238A PRO* 4.4 6.1 - - + -
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Residues in contact with PRO 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 4.1 10.7 - - + +
178A PRO 3.6 23.8 - - - +
180A ILE* 3.9 26.5 - - + -
186A MET* 4.8 3.1 - - + -
208A GLN 3.6 1.3 - - - +
209A ILE 3.3 22.9 - - - +
210A GLN* 3.3 13.2 - - - +
212A ILE* 1.4 95.4 - - + +
214A THR* 1.3 60.9 + - - +
216A LEU* 3.8 11.1 - - + +
217A SER* 3.1 25.3 + - - -
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Residues in contact with THR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 4.0 14.0 - - + +
210A GLN* 2.6 30.6 + - - -
211A GLY 3.1 10.3 + - - -
213A PRO* 1.3 79.1 - - - +
215A ILE* 1.3 61.8 + - - +
217A SER* 3.0 18.0 + - - -
219A ARG* 3.4 20.1 + - + +
221A MET* 4.2 17.3 - - + -
394A VAL* 3.7 36.2 - - + +
396A ILE* 3.7 10.2 - - + +
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLY 2.9 19.8 + - - +
212A ILE 3.1 4.7 + - - +
214A THR* 1.3 75.7 - - - +
216A LEU* 1.3 56.4 + - - +
218A GLY* 2.8 23.0 + - - -
219A ARG 4.4 1.8 - - - +
221A MET* 3.5 31.4 - - + -
234A VAL* 3.8 18.6 - - + +
238A PRO* 3.6 27.1 - - + -
242A PHE* 3.7 6.8 - - + -
340A TYR* 3.7 26.2 - - + +
370A GLN* 3.0 17.3 + - - +
372A LEU* 3.5 28.7 - - + -
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 6.3 0.9 - - + -
186A MET* 4.6 15.9 - - + -
187A LYS 5.1 4.7 - - - +
188A PHE* 4.9 5.4 - - + -
212A ILE* 2.9 41.9 + - + +
213A PRO* 3.8 9.4 - - + +
215A ILE* 1.3 75.0 - - - +
217A SER* 1.3 57.5 + - - +
218A GLY 3.2 1.3 + - - -
238A PRO* 4.0 24.9 - - + +
241A MET* 5.0 10.1 - - + -
242A PHE* 4.0 26.7 - - + -
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Residues in contact with SER 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PRO* 3.6 18.1 - - - +
213A PRO 3.1 12.4 + - - -
214A THR 3.0 15.6 + - - -
215A ILE 3.1 0.2 - - - -
216A LEU* 1.3 74.6 - - - +
218A GLY* 1.3 57.6 + - - +
219A ARG* 3.5 18.9 + - - +
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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