Contacts of the helix formed by residues 278 - 293 (chain B) in PDB entry 2PDA
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 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER 4.8 0.2 + - - -
144B SER* 3.7 18.4 - - - +
172B ASP* 2.6 31.3 + - - +
175B ARG* 4.0 13.1 - - - +
176B THR* 3.8 20.4 + - - -
277B GLY* 1.3 66.8 - - - -
279B SER* 1.3 66.8 + - - +
280B CYS 3.0 2.8 + - - -
281B GLU* 3.2 9.0 + - - +
329B ARG* 4.2 4.3 + - - -
478B THR* 2.9 35.9 + - - -
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ASP* 4.5 0.8 + - - -
275B SER* 2.9 18.5 + - - -
276B MET 3.7 4.3 + - - -
277B GLY 3.1 0.4 + - - -
278B SER* 1.3 76.2 + - - +
280B CYS* 1.3 64.3 + - - +
282B THR* 3.0 7.8 + - - -
283B ILE* 2.8 24.2 + - - +
329B ARG* 4.6 2.0 + - - +
363B TYR* 2.4 36.2 + - - -
370B PHE* 3.3 33.4 - - - -
478B THR* 4.8 1.3 - - - -
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Residues in contact with CYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B SER* 4.3 7.4 - - - +
275B SER* 3.7 28.0 - - - -
276B MET* 3.9 2.5 - - - -
277B GLY 3.7 15.5 - - - +
278B SER 3.0 0.4 - - - -
279B SER* 1.3 79.0 - - - +
281B GLU* 1.3 54.0 + - - +
283B ILE* 3.6 8.1 - - - +
284B GLU* 2.7 37.4 + - - +
299B LEU* 3.7 5.4 - - - +
301B LYS* 3.5 53.8 - - + +
302B VAL 5.6 0.2 - - - -
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B SER* 2.9 42.3 + - - +
145B SER* 4.1 13.5 + - - -
148B GLU* 4.4 4.8 - - - +
278B SER 3.2 2.6 + - - +
279B SER 3.1 0.2 + - - -
280B CYS* 1.3 75.6 - - - +
282B THR* 1.3 59.5 + - - +
284B GLU* 3.1 2.8 + - - +
285B GLU* 2.9 25.3 + - - +
301B LYS* 3.2 20.3 + - - -
476B GLN* 3.0 54.1 + - - +
478B THR* 3.7 20.2 - - + -
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B SER* 3.0 8.3 + - - -
281B GLU* 1.3 79.3 - - - +
283B ILE* 1.3 62.9 + - - +
285B GLU* 3.3 5.3 + - - +
286B VAL* 3.2 21.1 + - - +
370B PHE* 3.4 24.2 - - - +
371B SER 4.0 13.9 - - - +
372B PRO* 4.1 4.9 - - + -
375B VAL* 4.2 7.6 - - + -
476B GLN 3.3 5.1 + - - -
478B THR* 3.0 23.9 + - - -
479B TYR* 3.1 34.4 - - + -
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 4.3 12.6 - - + -
275B SER* 3.4 36.6 - - - +
279B SER 2.8 23.8 + - - +
280B CYS* 3.6 6.3 - - - +
282B THR* 1.3 75.7 - - - +
284B GLU* 1.3 57.5 + - - +
286B VAL* 3.0 5.0 + - - +
287B ILE* 2.9 33.0 + - + +
299B LEU* 3.7 21.3 - - + -
327B LEU* 4.7 0.7 - - + -
370B PHE* 3.4 27.6 - - + -
375B VAL* 4.2 19.5 - - + -
379B TYR* 3.9 20.4 - - - +
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 3.1 34.8 - - + +
280B CYS 2.7 21.2 + - - +
281B GLU 3.4 4.7 - - - +
283B ILE* 1.3 71.8 - - - +
285B GLU* 1.3 64.4 + - - +
287B ILE* 3.1 10.7 + - - +
288B ASN* 3.0 31.5 + - - +
299B LEU* 4.1 6.5 - - + +
301B LYS* 2.8 27.6 + - - -
476B GLN* 3.0 28.1 + - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLU 2.9 12.8 + - - +
282B THR 3.5 10.5 - - - +
283B ILE 3.2 0.2 - - - -
284B GLU* 1.3 77.8 - - - +
286B VAL* 1.3 57.7 + - - +
288B ASN* 3.7 9.2 + - - +
289B HIS* 3.6 13.9 + - - +
412B THR* 3.1 36.4 + - - +
413B THR* 3.9 4.2 + - - -
414B PRO* 4.5 8.1 - - + +
476B GLN* 3.3 16.2 + - + +
477B SER* 2.7 33.0 + - - -
479B TYR* 2.6 37.7 + - - -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR 3.3 14.4 - - - +
283B ILE 3.0 7.6 + - - +
285B GLU* 1.3 75.3 - - + +
287B ILE* 1.3 70.0 + - - +
288B ASN 3.1 0.2 - - - -
289B HIS* 3.1 5.8 + - - +
290B LEU* 2.9 47.2 + - + +
372B PRO* 3.6 37.5 - - + +
375B VAL* 4.3 19.1 - - + -
376B LYS 4.9 1.3 - - - +
379B TYR* 5.1 1.8 - - + -
409B PHE* 3.9 17.9 - - + -
412B THR* 4.2 5.8 - - - +
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Residues in contact with ILE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 4.0 7.6 - - + +
265B GLY* 3.8 23.1 - - - +
283B ILE* 2.9 18.4 + - + +
284B GLU* 3.2 11.4 - - - +
286B VAL* 1.3 77.1 - - - +
288B ASN* 1.3 63.7 + - - +
290B LEU* 3.9 0.5 - - - +
291B ALA* 2.7 41.7 + - + +
297B ILE* 4.1 15.6 - - + +
298B GLY* 3.4 26.2 - - - -
299B LEU* 3.5 19.3 - - + +
379B TYR* 3.4 31.6 - - + +
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Residues in contact with ASN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 5.4 2.8 - - - +
284B GLU* 3.0 23.4 + - - +
285B GLU* 3.8 8.6 - - - +
286B VAL 3.1 0.2 - - - -
287B ILE* 1.3 82.9 - - - +
289B HIS* 1.3 66.9 + - - +
291B ALA* 3.3 4.4 + - - +
292B ALA* 2.9 23.4 + - - +
476B GLN* 4.3 11.8 - - - +
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Residues in contact with HIS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU 3.6 10.5 + - - +
286B VAL* 3.1 7.5 + - - +
288B ASN* 1.3 81.7 - - - +
290B LEU* 1.3 91.2 + - + +
292B ALA* 3.0 17.7 + - - +
293B LYS* 3.0 36.9 + - - +
409B PHE* 4.2 13.1 - + - -
410B ALA* 4.0 21.8 - - + +
411B ASP 4.0 8.9 + - - -
412B THR* 3.8 28.5 - - + +
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Residues in contact with LEU 290 (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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286B VAL* 2.9 31.9 + - + +
289B HIS* 1.3 98.2 - - + +
291B ALA* 1.3 58.2 + - - +
293B LYS* 2.9 33.0 + - + +
295B GLU* 3.0 35.9 + - - +
297B ILE* 3.4 27.4 - - + -
376B LYS* 3.9 23.1 - - + -
379B TYR* 4.5 9.4 - - + -
409B PHE* 3.8 18.6 - - + -
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Residues in contact with ALA 291 (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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265B GLY* 6.1 0.4 - - - -
266B ALA* 5.6 9.0 - - + +
287B ILE* 2.7 31.3 + - + +
288B ASN* 3.8 5.2 - - - +
290B LEU* 1.3 68.1 - - - +
292B ALA* 1.3 59.2 + - - +
293B LYS 2.8 5.6 - - - -
294B GLY* 2.8 20.3 + - - -
295B GLU 3.9 20.5 + - - +
297B ILE* 4.6 3.8 - - + +
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Residues in contact with ALA 292 (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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288B ASN 2.9 13.4 + - - +
289B HIS* 3.0 13.9 + - - +
291B ALA* 1.3 75.7 - - - +
293B LYS* 1.3 58.3 + - + +
294B GLY 3.4 1.6 + - - -
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B HIS* 3.0 45.5 + - + +
290B LEU* 2.9 19.4 + - + +
291B ALA 2.8 0.8 - - - -
292B ALA* 1.3 81.2 - - + +
294B GLY* 1.3 57.8 + - - -
295B GLU* 3.5 7.0 + - + +
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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