Contacts of the helix formed by residues 206 - 216 (chain B) in PDB entry 5H8N
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 SER 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B GLY 5.4 4.5 - - - -
177B VAL* 4.0 10.5 - - - -
204B TYR* 3.3 7.5 - - - +
205B GLU* 1.3 79.4 - - - +
207B ALA* 1.3 63.4 + - - +
208B ALA* 3.7 7.6 + - - +
209B GLU* 3.4 35.1 + - - +
210B ALA* 3.4 14.9 + - - +
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Residues in contact with ALA 207 (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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14B GLN* 3.5 35.4 - - - +
177B VAL* 3.7 13.3 - - + +
206B SER* 1.3 72.6 - - - +
208B ALA* 1.3 58.4 + - - +
210B ALA* 3.3 3.5 + - - +
211B ILE* 2.9 38.9 + - + +
222B PHE* 3.8 7.1 - - + -
224B TRP* 3.6 21.3 - - + +
228B VAL* 5.3 0.4 - - + -
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Residues in contact with ALA 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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13B HIS* 4.9 19.3 - - + +
206B SER* 3.3 7.9 + - - +
207B ALA* 1.3 77.9 - - - +
209B GLU* 1.4 51.8 + - + +
211B ILE* 3.3 10.9 + - - +
212B GLN* 2.9 34.4 + - - +
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Residues in contact with GLU 209 (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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51B THR* 5.0 11.3 - - - +
204B TYR* 3.9 19.8 - - + -
205B GLU* 3.7 28.7 + - - +
206B SER* 3.4 23.9 + - - +
208B ALA* 1.4 73.9 - - + +
210B ALA* 1.4 59.7 + - - +
212B GLN* 3.3 7.8 + - - +
213B ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 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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204B TYR* 3.9 23.0 - - + -
206B SER 3.4 8.3 + - - +
207B ALA 3.3 8.9 + - - +
209B GLU* 1.4 76.0 - - - +
211B ILE* 1.4 64.0 + - - +
213B ALA* 3.2 4.4 + - - +
214B VAL* 3.1 27.9 + - - +
219B LEU* 3.7 8.4 - - + +
222B PHE* 3.6 35.7 - - + -
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Residues in contact with ILE 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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150B LEU* 4.2 12.6 - - + -
207B ALA* 2.9 30.4 + - + +
208B ALA* 3.7 8.7 - - - +
210B ALA* 1.4 71.7 - - - +
212B GLN* 1.4 62.2 + - - +
214B VAL* 3.4 5.5 + - - +
215B ARG* 3.3 22.5 + - + +
222B PHE* 3.8 22.2 - - + -
228B VAL* 4.2 14.8 - - + -
229B LEU* 4.5 1.8 - - + -
232B GLU* 3.7 46.0 - - + +
236B LYS* 4.2 8.5 - - - +
239B LEU* 3.9 20.5 - - + +
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Residues in contact with GLN 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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208B ALA 2.9 17.2 + - - +
209B GLU* 3.5 10.1 - - - +
210B ALA 3.3 0.2 - - - -
211B ILE* 1.4 76.1 - - - +
213B ALA* 1.3 50.6 + - - +
215B ARG* 3.1 24.6 + - - +
216B ASP* 2.9 65.0 + - - +
236B LYS* 6.1 0.8 - - - +
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Residues in contact with ALA 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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204B TYR* 3.3 33.9 - - + +
209B GLU 2.9 18.2 + - - +
210B ALA 3.4 6.3 - - - +
212B GLN* 1.3 74.7 - - - +
214B VAL* 1.4 55.8 + - - +
216B ASP* 3.5 4.6 + - - -
217B ASN 3.1 6.4 + - - -
218B LYS* 2.8 39.2 + - + -
219B LEU* 3.1 11.4 + - + +
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Residues in contact with VAL 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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150B LEU* 4.2 7.2 - - + +
151B VAL* 3.7 11.0 - - - +
152B LYS* 3.6 40.2 - - + +
210B ALA 3.1 15.3 + - - +
211B ILE 3.7 7.2 - - - +
212B GLN 3.3 0.2 - - - -
213B ALA* 1.4 72.3 - - - +
215B ARG* 1.3 64.4 + - - +
217B ASN* 3.4 10.2 + - - -
219B LEU* 3.2 37.2 - - + +
220B HIS* 4.7 2.2 - - - +
221B ALA 4.5 0.2 - - - -
222B PHE* 3.8 20.9 - - + +
239B LEU* 3.7 13.9 - - + -
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Residues in contact with ARG 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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152B LYS* 2.8 31.5 + - - +
211B ILE* 3.3 16.7 + - - +
212B GLN* 3.1 29.2 + - - +
214B VAL* 1.3 76.0 - - - +
216B ASP* 1.3 59.5 + - - +
217B ASN* 3.3 8.2 + - - -
236B LYS* 3.5 41.2 - - - +
238B ASP* 2.8 40.7 + - - +
239B LEU* 3.8 18.6 - - + -
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Residues in contact with ASP 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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212B GLN* 2.9 45.2 + - - +
213B ALA* 3.5 2.5 + - - +
214B VAL 3.3 0.2 - - - -
215B ARG* 1.3 73.9 - - - +
217B ASN* 1.3 68.7 + - - +
218B LYS* 3.2 31.8 + - + +
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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