Contacts of the helix formed by residues 199 - 209 (chain B) in PDB entry 2ABQ
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 ALA 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B HIS* 6.3 0.2 - - + -
185B LEU* 3.9 25.1 - - + +
193B ILE* 4.0 11.9 - - + -
195B SER 3.9 0.4 + - - -
196B ILE 4.7 1.6 - - - +
197B GLU 2.9 0.6 - - - -
198B ASP* 1.3 82.2 - - - +
200B ILE* 1.3 62.4 + - - +
201B PRO* 3.4 3.6 - - - -
202B HIS* 3.2 8.2 + - - +
203B VAL* 2.8 29.4 + - + +
216B VAL* 5.4 2.7 - - + -
218B PHE* 4.5 19.3 - - + -
224B LEU* 4.8 7.4 - - + -
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Residues in contact with ILE 200 (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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196B ILE 3.8 6.7 + - - +
197B GLU* 2.9 49.8 - - + +
199B ALA* 1.3 76.9 - - - +
201B PRO* 1.3 71.2 - - + +
203B VAL* 3.3 6.7 - - - +
204B GLN* 2.8 29.2 + - - +
224B LEU* 3.6 22.9 - - + -
231B MSE 3.7 20.0 - - - -
305B GLU* 3.8 18.2 - - + -
306B GLY* 4.6 17.7 - - - +
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Residues in contact with PRO 201 (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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197B GLU 3.0 19.7 - - - +
198B ASP* 4.3 0.4 - - - -
199B ALA* 3.4 5.8 - - - +
200B ILE* 1.3 96.1 - - + +
202B HIS* 1.3 71.1 + - + +
204B GLN* 3.3 7.7 - - + +
205B ARG* 3.2 24.9 + - - +
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Residues in contact with HIS 202 (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 LEU* 5.1 4.5 - - + -
189B VAL* 2.9 45.7 - - + +
191B LYS* 5.2 11.4 - - + +
193B ILE* 5.6 4.0 - - + -
198B ASP* 3.8 25.9 + - - -
199B ALA* 3.7 6.5 - - - +
200B ILE 3.1 0.6 - - - -
201B PRO* 1.3 91.7 - - + +
203B VAL* 1.3 62.5 + - - +
204B GLN 3.1 1.6 - - - -
205B ARG* 3.5 13.8 + - - +
206B LEU* 3.0 31.3 + - + +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 5.4 4.5 - - + +
199B ALA* 2.8 16.8 + - + +
200B ILE* 3.3 18.8 - - - +
202B HIS* 1.3 74.1 - - - +
204B GLN* 1.3 64.2 + - - +
206B LEU* 3.6 6.6 + - + -
207B ILE* 3.1 31.4 + - - +
214B ILE* 3.4 42.2 - - + +
216B VAL* 4.7 7.6 - - + -
224B LEU* 4.6 10.8 - - + +
226B ALA* 3.7 24.2 - - + -
231B MSE 3.8 13.5 - - + -
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Residues in contact with GLN 204 (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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200B ILE* 2.8 16.5 + - - +
201B PRO* 3.3 10.8 - - + +
203B VAL* 1.3 77.4 - - - +
205B ARG* 1.3 66.2 + - - +
207B ILE* 3.3 13.6 + - - +
208B GLY* 3.0 18.5 + - - -
227B SER 5.4 1.6 + - - -
230B GLY* 6.0 1.4 - - - -
231B MSE 2.9 38.0 - - - +
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Residues in contact with ARG 205 (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 LEU* 5.5 3.2 - - - +
189B VAL* 3.9 35.8 - - - +
201B PRO 3.2 11.6 + - - +
202B HIS* 3.5 11.9 + - - +
204B GLN* 1.3 78.5 - - - +
206B LEU* 1.3 77.7 + - - +
208B GLY* 3.0 12.2 + - - -
209B GLU* 3.1 50.6 + - + +
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Residues in contact with LEU 206 (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 LEU* 3.9 27.8 - - + -
178B ILE* 5.0 4.9 - - + -
180B PRO* 6.1 0.2 - - + -
185B LEU* 4.3 21.3 - - + -
188B LEU* 4.6 8.5 - - + -
189B VAL* 5.0 3.6 - - + -
202B HIS 3.0 24.0 + - - +
203B VAL* 3.7 7.9 - - + +
204B GLN 3.2 0.4 - - - -
205B ARG* 1.3 85.7 - - - +
207B ILE* 1.3 66.2 + - - +
209B GLU* 3.1 32.0 + - - +
211B ILE* 3.5 30.0 + - + +
214B ILE* 3.4 22.7 - - + -
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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
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203B VAL 3.1 13.5 + - - +
204B GLN* 3.6 12.3 - - - +
206B LEU* 1.3 76.6 - - - +
208B GLY* 1.3 64.7 + - - +
210B GLY* 3.1 13.2 + - - -
211B ILE* 3.5 21.4 - - - +
212B GLU 5.2 0.4 - - - +
214B ILE* 3.8 12.3 - - + -
226B ALA* 3.1 47.6 - - + +
227B SER* 3.5 8.5 - - - +
228B ALA* 4.1 25.8 - - + +
231B MSE 3.8 10.5 - - + -
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Residues in contact with GLY 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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204B GLN 3.0 14.3 + - - -
205B ARG* 3.0 6.9 + - - -
207B ILE* 1.3 78.9 - - - +
209B GLU* 1.3 59.1 + - - +
210B GLY 3.2 1.0 + - - -
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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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171B LEU* 5.3 13.0 - - - +
172B ALA* 5.8 1.9 - - - -
174B LYS* 3.2 32.2 + - + +
205B ARG* 3.1 47.9 + - + +
206B LEU* 3.1 22.2 + - - +
208B GLY* 1.3 76.9 - - - +
210B GLY* 1.3 57.4 + - - +
211B ILE* 3.7 5.8 - - + +
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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