Contacts of the helix formed by residues 198 - 212 (chain B) in PDB entry 2EZT
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 ASP 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B GLU 3.4 3.6 + - - -
197B PRO* 1.3 67.5 - - - +
199B VAL* 1.3 65.7 + - - +
200B GLN* 3.4 5.9 + - - +
201B ALA* 3.3 36.0 + - + +
202B VAL* 3.1 24.9 + - - +
322B VAL* 4.7 10.6 - - + +
323B LEU 5.2 5.2 + - - +
324B ALA* 5.1 1.2 - - - +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU* 5.8 4.5 - - + -
197B PRO 2.9 13.4 + - - +
198B ASP* 1.3 73.8 - - - +
200B GLN* 1.3 71.5 + - + +
202B VAL* 3.8 4.4 - - - +
203B THR* 2.9 34.6 + - - +
336B GLN* 5.1 0.6 - - - +
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Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP* 3.4 5.8 + - - +
199B VAL* 1.3 83.3 - - + +
201B ALA* 1.3 64.1 + - - +
203B THR* 3.6 6.5 + - - -
204B ARG* 3.2 45.9 + - - +
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Residues in contact with ALA 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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198B ASP* 3.3 27.0 + - + +
200B GLN* 1.3 76.9 - - - +
202B VAL* 1.3 58.1 + - - +
204B ARG* 3.4 22.8 + - - +
205B LEU* 2.9 30.7 + - - +
320B ILE* 4.0 8.9 - - + +
321B ALA 5.8 0.7 - - - +
322B VAL* 3.9 21.1 - - + -
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PRO* 3.9 15.7 - - + -
198B ASP 3.1 19.5 + - - +
199B VAL* 3.8 4.9 - - - +
200B GLN 3.3 0.2 - - - -
201B ALA* 1.3 74.1 - - - +
203B THR* 1.3 52.9 + - - +
205B LEU* 3.3 7.4 + - + +
206B THR* 2.8 39.8 + - - -
322B VAL* 4.1 12.8 - - + -
329B THR* 3.7 24.0 - - + -
332B ALA* 4.3 16.2 - - + -
333B ILE* 3.8 24.7 - - + +
336B GLN* 4.0 13.2 - - - +
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Residues in contact with THR 203 (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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199B VAL* 2.9 24.8 + - - +
200B GLN* 3.8 7.0 - - - -
202B VAL* 1.3 76.9 - - - +
204B ARG* 1.3 56.8 + - - +
206B THR* 3.3 2.9 + - - -
207B GLN* 3.0 27.6 + - + +
336B GLN* 3.4 30.7 + - - +
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP* 5.6 0.2 + - - -
200B GLN* 3.2 51.8 + - - +
201B ALA* 3.6 25.9 - - - +
202B VAL 3.3 0.2 - - - -
203B THR* 1.3 75.1 - - - +
205B LEU* 1.3 63.1 + - - +
207B GLN* 3.2 7.7 + - - +
208B THR* 3.2 26.3 + - - +
320B ILE* 3.7 22.8 - - + +
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Residues in contact with LEU 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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201B ALA 2.9 17.7 + - - +
202B VAL* 3.5 6.5 - - - +
204B ARG* 1.3 77.2 - - - +
206B THR* 1.3 63.6 + - - +
208B THR* 3.4 1.3 + - - -
209B LEU* 3.1 20.6 + - + +
281B LEU* 4.0 24.5 - - + -
303B LEU* 3.4 34.5 - - + +
304B GLN 4.0 11.4 - - - +
305B ILE* 4.2 4.5 - - + -
320B ILE* 3.7 18.7 - - + +
322B VAL* 3.8 21.8 - - + -
329B THR* 6.0 0.9 - - + -
333B ILE* 3.7 28.3 - - + -
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL 2.8 28.3 + - - -
203B THR 3.5 6.1 - - - -
204B ARG 3.3 0.2 - - - -
205B LEU* 1.3 74.4 - - - +
207B GLN* 1.3 65.6 + - - +
209B LEU* 3.3 5.1 + - - +
210B LEU* 3.0 33.5 + - + +
333B ILE* 3.5 26.5 - - + +
336B GLN* 3.9 20.9 - - + +
337B VAL* 3.5 32.3 - - + -
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Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B THR* 3.0 13.1 + - + +
204B ARG* 3.2 10.2 + - - +
206B THR* 1.3 77.1 - - - +
208B THR* 1.3 68.2 + - - +
210B LEU* 3.4 5.2 + - + +
211B ALA* 3.0 42.5 + - - +
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Residues in contact with THR 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 ARG* 3.2 13.7 + - - +
205B LEU* 3.8 7.2 - - - -
206B THR 3.3 0.2 - - - -
207B GLN* 1.3 86.0 + - - +
209B LEU* 1.3 63.0 + - - +
211B ALA* 3.5 5.1 + - - +
212B ALA* 3.5 18.0 + - - +
279B VAL* 4.1 4.3 - - + +
301B TYR* 3.8 42.1 - - + -
303B LEU* 3.8 20.2 - - + -
319B ASP* 5.9 0.7 - - + -
320B ILE* 4.1 9.2 - - + +
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Residues in contact with LEU 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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205B LEU* 3.1 19.5 + - + +
206B THR* 3.7 4.5 - - - +
207B GLN 3.3 0.4 - - - -
208B THR* 1.3 75.2 - - - +
210B LEU* 1.3 69.6 + - + +
212B ALA* 3.3 18.7 - - - +
215B PRO* 4.0 19.0 - - + +
216B LEU 4.4 7.6 - - - +
217B ILE* 4.6 7.0 - - + -
233B LEU* 6.0 0.9 - - + -
237B LEU* 4.7 5.6 - - + -
239B ILE* 3.8 29.2 - - + +
279B VAL* 4.2 13.7 - - + -
281B LEU* 3.9 39.7 - - + -
303B LEU* 3.8 8.7 - - + +
333B ILE* 5.3 9.6 - - + -
340B ARG* 4.7 1.0 + - - -
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Residues in contact with LEU 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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206B THR* 3.0 25.6 + - + +
207B GLN* 4.0 4.9 - - - +
209B LEU* 1.3 86.4 - - + +
211B ALA* 1.3 58.5 + - - +
212B ALA 3.4 3.5 + - - +
237B LEU* 3.8 39.3 - - + -
239B ILE* 5.0 0.2 - - + -
333B ILE* 5.8 0.2 - - + -
337B VAL* 4.1 24.9 - - + -
338B SER 5.7 1.3 - - - +
340B ARG* 2.8 41.8 + - + +
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN* 3.0 37.2 + - - +
208B THR* 3.5 6.5 + - - +
209B LEU 3.3 0.2 - - - -
210B LEU* 1.3 71.8 - - - +
212B ALA* 1.3 65.6 + - - +
213B GLU* 3.6 1.9 + - - +
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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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208B THR 3.5 3.4 + - - +
209B LEU 3.3 16.2 + - - +
210B LEU 3.2 9.4 - - - +
211B ALA* 1.3 79.9 - - - +
213B GLU* 1.3 62.1 + - - +
215B PRO* 3.9 16.6 - - + +
278B ASP* 3.4 20.2 - - - +
279B VAL* 3.5 28.0 - - + -
340B ARG* 4.8 4.0 + - - -
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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