Contacts of the helix formed by residues 208 - 217 (chain B) in PDB entry 2Q9Q
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 TYR 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA* 4.0 10.5 - - + -
41B PRO* 3.4 44.4 - - + -
42B GLU* 2.6 34.0 + - - -
44B LEU* 3.5 17.2 - - - +
167B LEU* 3.7 16.8 + - + +
169B SER 2.8 21.7 + - - +
171B VAL* 3.9 16.6 - - + +
206B ILE 3.5 1.8 + - - -
207B ARG* 1.3 72.0 - - - +
209B LYS* 1.3 68.2 + - - +
211B ILE* 2.9 14.9 + - + +
212B ALA* 2.9 44.3 + - + +
215B VAL* 4.1 20.7 - - + +
222B LEU* 4.2 9.4 - - + -
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Residues in contact with LYS 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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167B LEU* 2.9 43.7 + - + +
168B ASP* 3.7 21.3 + - - +
207B ARG* 3.3 17.4 - - - +
208B TYR* 1.3 80.1 - - - +
210B THR* 1.3 59.9 + - - +
211B ILE 3.5 0.3 + - - -
212B ALA* 3.9 12.3 + - + +
213B PRO* 4.5 4.0 - - - +
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Residues in contact with THR 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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182B ILE* 4.2 15.6 - - + +
183B LEU 3.2 27.5 + - - +
184B VAL* 4.9 0.2 - - - -
185B GLU* 4.7 7.1 + - - -
206B ILE* 3.9 23.8 - - + +
207B ARG* 3.2 36.9 + - - +
208B TYR 3.1 1.0 - - - -
209B LYS* 1.3 79.6 - - - +
211B ILE* 1.3 58.8 + - + +
212B ALA 3.7 0.2 - - - -
213B PRO* 4.6 5.0 - - - +
214B LEU* 5.5 1.4 - - - +
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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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171B VAL* 4.4 2.9 - - + -
173B LEU* 3.8 25.8 - - + -
182B ILE* 4.6 5.6 - - + -
198B LEU* 4.6 8.3 - - + -
206B ILE* 4.2 16.6 - - + -
207B ARG 4.0 8.3 - - - +
208B TYR* 2.9 26.9 + - + +
210B THR* 1.3 87.4 - - + +
212B ALA* 1.3 66.9 + - - +
213B PRO* 3.3 3.8 - - - -
214B LEU* 2.9 37.7 + - + +
215B VAL* 3.2 26.5 + - + -
220B VAL* 4.6 0.7 - - + -
222B LEU* 4.2 12.6 - - + -
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Residues in contact with ALA 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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42B GLU* 4.4 4.0 - - - +
167B LEU* 6.3 1.3 - - + -
208B TYR* 2.9 47.0 + - + +
209B LYS* 4.1 7.6 - - - +
210B THR 3.7 0.4 - - - -
211B ILE* 1.3 76.9 - - - +
213B PRO* 1.3 66.9 - - + +
215B VAL* 2.9 22.5 + - - +
216B ALA* 3.2 11.7 + - - +
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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
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209B LYS 4.5 6.1 - - - +
210B THR 4.6 3.6 - - - +
211B ILE* 3.5 5.8 - - - -
212B ALA* 1.3 97.2 - - + +
214B LEU* 1.3 60.3 + - + +
216B ALA* 3.5 8.7 + - + +
217B SER* 3.1 28.6 + - - -
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Residues in contact with LEU 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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179B GLN* 3.2 37.0 - - + +
182B ILE* 4.3 13.9 - - + -
198B LEU* 3.8 29.2 - - + -
210B THR 5.5 0.9 - - - +
211B ILE* 2.9 28.3 + - + +
213B PRO* 1.3 80.8 - - + +
215B VAL* 1.3 63.6 + - - +
217B SER* 3.3 5.8 + - - +
218B GLY 3.1 2.3 + - - -
219B ALA* 3.0 32.6 + - + -
220B VAL* 3.3 20.3 + - + -
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Residues in contact with VAL 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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32B GLN* 5.3 0.2 - - - +
36B ASN* 3.5 39.0 + - + +
44B LEU* 4.4 16.6 - - + -
208B TYR* 4.1 12.1 - - + +
211B ILE* 3.4 35.0 - - + +
212B ALA* 2.9 8.0 + - - +
214B LEU* 1.3 77.7 - - - +
216B ALA* 1.3 62.8 - - - +
218B GLY* 3.2 12.8 + - - -
220B VAL* 3.9 17.7 - - + +
222B LEU* 4.0 15.9 - - + -
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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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44B LEU* 6.2 2.7 - - + +
45B GLU* 3.9 25.0 - - - +
47B LYS* 4.7 13.1 + - - +
212B ALA 3.2 7.9 + - - +
213B PRO* 3.7 11.2 - - + +
214B LEU 3.3 0.2 - - - -
215B VAL* 1.3 83.4 - - - +
217B SER* 1.3 59.3 + - - +
218B GLY* 3.3 1.0 + - - -
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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
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177B GLU* 4.7 4.0 - - - +
213B PRO 3.1 17.9 + - - -
214B LEU* 3.3 15.4 + - - +
216B ALA* 1.3 77.0 - - - +
218B GLY* 1.3 58.9 + - - +
219B ALA* 3.5 11.8 + - - +
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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