Contacts of the helix formed by residues 205 - 217 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B ILE* 6.3 1.1 - - + -
203B HIS 4.8 4.3 - - - +
204B PRO* 1.3 75.5 - - - +
206B PRO* 1.3 71.0 - - + +
207B ILE* 3.4 5.1 - - - +
208B GLN* 2.6 39.3 + - - +
209B ILE* 2.8 26.1 + - - +
228B GLY 5.7 0.4 - - - +
229B SER 2.9 29.8 + - - +
230B GLY* 4.5 1.8 - - - -
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Residues in contact with PRO 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 3.4 39.3 - - + +
169B ILE* 3.2 35.2 - - + +
204B PRO 4.6 0.9 - - - +
205B THR* 1.3 86.5 - - - +
207B ILE* 1.3 62.8 + - - +
209B ILE* 3.3 9.2 + - + -
210B GLN* 3.3 12.8 + - - +
398B VAL* 3.7 15.5 - - + -
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B THR* 3.4 3.1 - - - +
206B PRO* 1.3 78.3 - - - +
208B GLN* 1.3 56.2 + - - +
211B GLY* 2.6 38.0 + - - +
221B MET* 3.8 17.3 - - + -
223B GLY* 4.6 1.3 - - - -
225B ALA* 4.0 19.5 - - + -
229B SER* 3.4 28.9 + - - +
230B GLY 3.9 1.6 - - - -
231B LYS* 3.7 19.7 - - - +
234B VAL* 3.9 11.1 - - + +
374B PHE* 4.5 8.1 - - + -
396B ILE* 3.5 34.3 - - + +
398B VAL* 3.5 20.5 - - + +
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PHE* 3.6 11.9 - - + -
186B MET* 3.6 4.7 - - - +
201B ILE* 5.0 4.5 - - - +
203B HIS 4.4 0.5 - - - +
204B PRO* 3.2 15.2 - - + +
205B THR* 2.6 44.5 + - - +
207B ILE* 1.3 76.9 - - - +
209B ILE* 1.3 64.3 + - - +
212B ILE* 3.0 43.5 + - + +
230B GLY* 2.8 38.6 + - - +
233B LEU* 3.6 22.5 - - + +
234B VAL* 3.7 14.6 - - + -
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 4.3 10.3 - - + -
167B TYR* 4.1 29.8 - - + -
169B ILE* 4.1 10.8 - - + -
179B PRO* 3.7 20.2 - - + -
180B ILE 3.0 49.1 + - - +
181B LYS* 4.4 5.4 - - + +
186B MET* 3.9 2.2 - - - -
204B PRO* 3.1 36.3 - - + +
205B THR 2.8 21.9 + - - +
206B PRO* 3.3 12.8 + - + +
208B GLN* 1.3 72.9 - - - +
210B GLN* 1.3 57.7 + - - +
213B PRO* 3.5 10.4 - - - +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 3.1 32.1 + - - +
169B ILE* 4.1 20.2 - - + -
171B VAL* 3.9 15.5 - - + -
176B ILE* 3.4 15.5 - - - +
177B PRO* 2.8 26.2 + - - +
178B PRO 4.6 0.6 + - - -
179B PRO* 3.5 15.8 - - + +
206B PRO 3.3 5.7 + - - +
208B GLN 3.3 0.2 - - - -
209B ILE* 1.3 79.0 - - + +
211B GLY* 1.3 58.4 + - - +
212B ILE 3.6 0.4 - - - -
213B PRO* 3.7 3.6 - - - +
214B THR* 2.7 39.8 + - - -
396B ILE* 3.6 19.5 - - + -
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE 2.6 25.0 + - - -
210B GLN* 1.3 71.2 - - - +
212B ILE* 1.3 64.1 + - - +
214B THR* 3.1 5.0 + - - -
215B ILE* 3.0 25.1 + - - +
221B MET* 4.1 5.6 - - - -
234B VAL* 3.6 15.7 - - - -
396B ILE* 3.8 15.4 - - - +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PHE* 4.4 5.6 - - + -
186B MET* 4.0 18.2 - - + -
188B PHE* 3.5 38.8 - - + -
208B GLN* 3.0 33.5 + - + +
211B GLY* 1.3 74.8 - - - +
213B PRO* 1.4 69.8 - - + +
215B ILE* 3.2 4.6 + - - +
216B LEU* 2.9 40.1 + - + +
233B LEU* 4.5 10.8 - - + +
234B VAL* 4.0 22.4 - - + +
237B LEU* 4.7 4.0 - - + -
238B PRO* 4.4 5.6 - - + -
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Residues in contact with PRO 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 4.2 12.1 - - + +
178B PRO* 3.8 16.4 - - + +
180B ILE* 3.8 32.3 - - + -
186B MET* 4.6 4.7 - - + -
208B GLN 3.7 1.6 - - - +
209B ILE 3.5 25.8 - - - +
210B GLN 3.7 7.0 - - - +
212B ILE* 1.4 94.6 - - + +
214B THR* 1.3 60.3 + - - +
216B LEU* 3.9 9.9 - - + +
217B SER* 3.1 26.2 + - - -
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 4.0 10.5 - - + +
210B GLN* 2.7 31.6 + - - -
211B GLY 3.1 11.1 + - - -
213B PRO* 1.3 79.1 - - - +
215B ILE* 1.3 60.9 + - + +
217B SER* 2.7 22.3 + - - -
219B ARG* 3.6 16.8 + - + +
221B MET* 4.3 20.0 - - + -
394B VAL* 3.9 34.0 - - + +
396B ILE* 3.7 8.0 - - + +
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLY 3.0 18.4 + - - +
212B ILE 3.2 0.6 + - - +
214B THR* 1.3 73.7 - - - +
216B LEU* 1.3 55.9 + - - +
217B SER 3.1 1.8 - - - -
218B GLY* 2.8 14.7 + - - -
219B ARG 4.2 4.0 - - - +
221B MET* 3.4 36.1 - - + -
234B VAL* 4.0 12.3 - - + +
238B PRO* 3.5 30.1 - - + -
242B PHE* 3.6 5.3 - - + -
340B TYR* 3.9 21.3 - - + +
370B GLN* 2.8 30.2 + - - +
372B LEU* 3.5 29.2 - - + -
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 6.5 0.4 - - + -
186B MET* 4.9 9.0 - - + -
187B LYS 5.1 5.4 - - - +
188B PHE* 4.5 4.0 - - + -
212B ILE* 2.9 41.1 + - + +
213B PRO* 3.9 8.3 - - + +
215B ILE* 1.3 75.6 - - - +
217B SER* 1.3 60.9 + - - +
218B GLY* 3.2 1.0 + - - -
238B PRO* 3.9 21.8 - - + +
241B MET* 3.6 33.4 - - + -
242B PHE* 3.8 26.4 - - + -
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 3.6 21.3 - - - +
213B PRO 3.1 16.0 + - - -
214B THR 2.7 20.1 + - - -
215B ILE 3.1 0.4 - - - -
216B LEU* 1.3 75.2 - - - +
218B GLY* 1.3 57.5 + - - +
219B ARG* 3.6 13.4 + - - +
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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
------------------------------------------------------------
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