Contacts of the helix formed by residues 209 - 219 (chain B) in PDB entry 1H5Y
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 ARG 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B GLY* 1.3 79.7 - - - +
210B VAL* 1.3 67.2 + - - +
211B GLU* 3.0 39.1 + - - +
212B HIS* 3.0 46.2 + - + +
213B PHE* 4.1 4.7 - - - -
229B LEU* 3.6 9.5 - - - +
234B VAL* 5.5 1.3 - - - -
235B LEU* 4.6 2.9 - - - -
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Residues in contact with VAL 210 (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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209B ARG* 1.3 75.7 - - - +
211B GLU* 1.3 76.7 + - - +
213B PHE* 3.1 24.0 + - + +
214B TYR 3.8 2.4 + - - -
235B LEU* 3.6 30.0 - - + +
239B GLN 4.6 1.3 - - - +
240B VAL* 4.0 19.3 - - + +
243B TYR* 3.5 55.5 - - + -
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Residues in contact with GLU 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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209B ARG* 3.0 50.3 + - + +
210B VAL* 1.3 85.1 + - - +
212B HIS* 1.3 64.2 + - + +
214B TYR* 3.0 5.3 + - - +
215B GLU* 2.9 43.5 + - - +
243B TYR* 3.4 26.9 - - + +
247B ARG* 5.1 2.7 - - - +
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Residues in contact with HIS 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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182B GLY 3.5 10.1 + - - -
183B LEU 3.5 8.2 - - - -
184B GLY* 3.3 34.0 + - - -
185B TYR* 3.4 27.9 - - + +
187B VAL* 5.7 0.2 - - - +
207B ALA* 4.4 4.5 - - + -
208B GLY 2.9 28.9 - - - -
209B ARG* 3.0 40.1 + - + +
211B GLU* 1.3 80.0 - - + +
213B PHE* 1.3 57.9 + - - +
215B GLU* 3.4 19.1 + - - +
216B ALA 3.0 22.9 + - - -
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Residues in contact with PHE 213 (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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5B LEU* 3.6 9.7 - - - +
185B TYR* 3.4 24.5 - + - -
207B ALA* 3.7 19.3 - - + -
209B ARG 4.1 3.4 - - - -
210B VAL* 3.1 23.8 + - + +
212B HIS* 1.3 79.2 - - - +
214B TYR* 1.3 62.0 + - - +
216B ALA* 3.3 4.7 + - - +
217B ALA 3.1 16.1 + - - -
224B VAL* 3.4 30.1 - - + -
226B ALA* 4.3 7.6 - - + -
229B LEU* 3.8 23.6 - - + -
230B PHE* 4.0 20.0 - + - -
240B VAL* 3.6 34.8 - - + -
244B LEU* 4.1 20.0 - - + -
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Residues in contact with TYR 214 (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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3B MET* 3.5 28.0 - - + +
210B VAL 3.8 0.4 + - - -
211B GLU 3.0 8.9 + - - +
213B PHE* 1.3 78.2 - - - +
215B GLU* 1.3 70.1 + - + +
217B ALA* 3.0 6.6 + - - +
218B ALA* 2.9 38.2 + - + +
243B TYR* 4.1 7.6 - - + -
244B LEU* 3.7 16.1 - - + +
247B ARG* 3.4 70.2 + - + +
249B VAL* 3.7 21.5 - - + -
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Residues in contact with GLU 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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187B VAL* 3.9 19.1 - - + +
211B GLU* 2.9 37.8 + - - +
212B HIS* 3.8 25.2 + - - +
213B PHE 3.2 0.2 - - - -
214B TYR* 1.3 88.8 - - + +
216B ALA* 1.3 58.9 + - - +
218B ALA* 3.5 5.6 + - - +
219B ALA* 3.1 23.4 + - - +
247B ARG* 5.4 2.3 + - - -
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Residues in contact with ALA 216 (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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185B TYR* 3.7 17.0 - - + -
187B VAL* 4.6 2.6 - - - +
190B ILE* 4.1 14.3 - - + +
203B ALA* 4.3 1.1 - - + -
212B HIS 3.0 13.7 + - - +
213B PHE 3.6 2.7 - - - +
214B TYR 3.2 0.2 - - - -
215B GLU* 1.3 75.9 - - - +
217B ALA* 1.3 61.9 + - - +
219B ALA* 3.2 5.2 + - - +
220B GLY 3.2 5.5 + - - -
221B ALA* 3.0 32.3 + - + +
224B VAL* 3.6 28.7 - - + -
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Residues in contact with ALA 217 (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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3B MET* 3.5 31.8 - - + +
4B ALA 5.1 0.4 - - - +
5B LEU* 3.8 27.5 - - + +
213B PHE 3.1 9.0 + - - +
214B TYR* 3.0 11.9 + - - +
216B ALA* 1.3 77.0 - - - +
218B ALA* 1.3 57.3 + - - +
220B GLY* 2.8 22.7 + - - -
221B ALA* 3.9 12.4 + - - +
249B VAL* 4.6 4.9 - - + -
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Residues in contact with ALA 218 (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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3B MET* 3.4 15.6 - - + -
214B TYR* 2.9 37.1 + - + +
215B GLU* 3.9 7.0 - - - +
217B ALA* 1.3 71.8 - - - +
219B ALA* 1.3 58.7 + - - +
220B GLY 3.2 0.6 + - - -
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Residues in contact with ALA 219 (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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187B VAL* 3.6 35.2 - - + +
190B ILE* 3.7 11.0 - - + +
191B ARG* 3.3 31.4 + - + +
194B ALA* 4.1 2.9 - - - +
195B ASP* 5.4 1.2 - - - +
215B GLU 3.1 17.2 + - - +
216B ALA 3.6 6.3 - - - +
217B ALA 3.1 0.6 - - - -
218B ALA* 1.3 76.1 - - - +
220B GLY* 1.3 57.5 + - - +
221B ALA 3.7 0.4 - - - -
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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
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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