Contacts of the helix formed by residues 325 - 335 (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 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A LEU* 4.9 0.2 - - - +
194B LEU* 4.3 15.1 - - + +
225B LYS* 5.3 13.3 + - - +
305B ILE* 4.4 0.2 - - - -
307B ILE* 4.2 7.7 - - + +
324B ALA* 1.3 73.1 - - - +
326B ALA* 1.3 62.3 + - - +
327B GLN* 3.5 12.4 + - - +
328B LYS* 3.1 52.5 + - + +
329B THR* 2.7 31.5 + - - -
1615B FAD 2.9 31.9 + - - -
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Residues in contact with ALA 326 (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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222B GLY 3.5 24.2 - - - +
223B ALA* 3.9 12.1 - - + -
283B VAL* 3.6 23.8 - - + -
305B ILE* 4.0 9.2 - - - -
325B ASP* 1.3 72.8 - - - +
327B GLN* 1.3 59.3 + - - +
329B THR* 3.3 2.3 + - - -
330B LEU* 2.8 36.5 + - + +
1615B FAD 2.9 19.2 + - + +
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Residues in contact with GLN 327 (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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225B LYS* 3.3 53.3 + - + +
226B ALA* 3.7 15.7 - - + -
229B GLU* 3.6 24.3 + - - +
325B ASP* 3.5 10.8 + - - +
326B ALA* 1.3 78.9 - - - +
328B LYS* 1.3 70.6 + - - +
330B LEU* 3.3 1.3 + - - +
331B ALA* 2.8 32.3 + - - +
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Residues in contact with LYS 328 (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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194B LEU* 3.7 33.9 + - - +
195B PRO 3.4 20.0 - - - -
196B GLU* 3.2 29.8 + - - +
197B PRO* 3.7 17.9 - - + +
325B ASP* 3.1 33.5 + - + +
327B GLN* 1.3 86.4 + - - +
329B THR* 1.3 57.0 + - - +
331B ALA* 3.7 6.3 + - - +
332B ALA* 3.0 25.3 + - - +
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Residues in contact with THR 329 (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 PRO* 3.5 9.2 - - + +
202B VAL* 3.7 27.6 - - + -
205B LEU* 6.0 0.9 - - + -
305B ILE* 3.6 32.5 - - + +
322B VAL* 4.6 4.5 - - + -
324B ALA* 3.3 20.6 - - - +
325B ASP 2.7 22.5 + - - -
326B ALA 3.7 2.7 - - - -
328B LYS* 1.3 73.2 - - - +
330B LEU* 1.3 62.7 + - - +
332B ALA* 3.1 4.0 + - - +
333B ILE* 2.8 33.6 + - + +
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Residues in contact with LEU 330 (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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217B ILE* 5.2 1.6 - - + -
223B ALA* 4.8 0.7 - - + -
226B ALA* 3.7 20.4 - - + -
229B GLU* 4.0 13.2 - - + -
230B LEU* 3.7 33.0 - - + -
233B LEU* 3.5 22.0 - - + +
281B LEU* 4.2 24.5 - - + -
283B VAL* 4.2 14.4 - - + -
305B ILE* 4.3 12.3 - - + -
326B ALA* 2.8 23.6 + - + +
327B GLN 3.9 2.7 - - - +
329B THR* 1.3 74.8 - - - +
331B ALA* 1.3 57.2 + - - +
333B ILE* 3.4 7.4 + - + +
334B LEU* 3.0 29.1 + - - +
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Residues in contact with ALA 331 (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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229B GLU* 4.0 22.1 - - + +
327B GLN* 2.8 21.4 + - + +
328B LYS* 3.7 7.9 - - - +
330B LEU* 1.3 77.2 - - - +
332B ALA* 1.3 56.2 + - - +
334B LEU* 3.4 6.6 + - - +
335B ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 332 (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 PRO* 4.6 11.0 - - + -
202B VAL* 4.3 13.0 - - + -
328B LYS 3.0 17.4 + - - +
329B THR* 3.1 11.8 + - - +
331B ALA* 1.3 73.3 - - - +
333B ILE* 1.3 65.3 + - - +
335B ALA* 3.5 14.7 + - - +
336B GLN* 3.6 18.1 + - - +
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Residues in contact with ILE 333 (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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202B VAL* 3.8 10.8 - - + -
205B LEU* 3.7 25.6 - - + -
206B THR* 3.5 29.4 - - + +
209B LEU* 5.3 6.7 - - + -
233B LEU* 3.7 20.6 - - + -
237B LEU* 5.0 3.6 - - + -
281B LEU* 4.4 5.6 - - + -
305B ILE* 4.2 18.4 - - + -
329B THR* 2.8 22.1 + - + +
330B LEU* 3.6 15.5 - - + +
332B ALA* 1.3 73.5 - - - +
334B LEU* 1.3 60.6 + - - +
336B GLN* 2.9 30.6 + - - +
337B VAL* 3.3 11.6 + - + +
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Residues in contact with LEU 334 (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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229B GLU* 4.4 25.8 - - + +
232B GLN* 4.1 29.6 - - + +
233B LEU* 3.8 34.8 - - + +
236B THR* 4.5 7.4 - - + +
330B LEU 3.0 17.9 + - - +
331B ALA* 3.6 5.2 - - - +
333B ILE* 1.3 76.1 - - - +
335B ALA* 1.3 61.7 + - - +
336B GLN 3.2 1.4 + - - -
337B VAL* 3.4 28.9 + - + +
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Residues in contact with ALA 335 (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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331B ALA 3.0 16.6 + - - +
332B ALA* 3.7 10.3 - - - +
333B ILE 3.2 0.6 - - - -
334B LEU* 1.3 75.1 - - - +
336B GLN* 1.3 59.5 + - - +
337B VAL 4.8 1.3 - - - +
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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