Contacts of the helix formed by residues 278 - 293 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER 4.8 0.2 + - - -
144A SER* 3.7 18.8 - - - +
172A ASP* 2.6 31.5 + - - +
175A ARG* 4.0 12.9 - - - +
176A THR* 3.8 19.9 + - - -
277A GLY* 1.3 67.2 - - - -
279A SER* 1.3 66.5 + - - +
280A CYS 3.0 3.0 + - - -
281A GLU* 3.2 8.9 + - - +
329A ARG* 4.2 4.7 + - - -
478A THR* 2.9 37.3 + - - -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 4.5 0.8 + - - -
275A SER* 2.9 17.4 + - - -
276A MET 3.7 4.3 + - - -
277A GLY 3.1 0.2 + - - -
278A SER* 1.3 75.5 + - - +
280A CYS* 1.3 63.9 + - - +
282A THR* 3.0 6.9 + - - -
283A ILE* 2.8 24.4 + - - +
329A ARG* 4.6 2.7 + - - +
363A TYR* 2.4 36.7 + - - -
370A PHE* 3.3 34.5 - - - -
478A THR* 4.8 1.1 - - - -
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Residues in contact with CYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER* 4.3 6.7 - - - +
275A SER* 3.7 27.6 - - - -
276A MET* 3.9 2.2 - - - -
277A GLY 3.7 15.7 - - - +
279A SER* 1.3 78.4 - - - +
281A GLU* 1.3 54.4 + - - +
283A ILE* 3.6 7.7 - - - +
284A GLU* 2.7 37.4 + - - +
299A LEU* 3.7 5.4 - - + +
301A LYS* 3.5 53.4 - - + +
302A VAL 4.7 0.4 - - - -
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER* 2.9 42.3 + - - +
145A SER* 4.1 13.9 + - - -
148A GLU* 4.4 4.4 - - - +
278A SER 3.2 3.5 + - - +
279A SER 3.1 0.2 + - - -
280A CYS* 1.3 74.9 - - - +
282A THR* 1.3 59.7 + - - +
284A GLU* 3.1 3.3 + - - +
285A GLU* 2.9 25.3 + - - +
301A LYS* 3.2 20.4 + - - -
476A GLN* 3.0 56.9 + - - +
478A THR* 3.7 19.5 - - + -
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A SER* 3.0 8.1 + - - -
281A GLU* 1.3 78.4 - - - +
283A ILE* 1.3 64.7 + - - +
285A GLU* 3.3 5.1 + - - +
286A VAL* 3.2 20.4 + - - +
370A PHE* 3.4 23.3 - - - +
371A SER 4.0 14.4 - - - +
372A PRO* 4.1 4.0 - - + -
375A VAL* 4.2 7.2 - - + -
476A GLN 3.6 4.9 - - - -
478A THR* 3.0 24.9 + - - -
479A TYR* 3.1 33.8 - - + -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 4.3 11.9 - - + -
275A SER* 3.4 36.3 - - - +
279A SER 2.8 23.2 + - - +
280A CYS* 3.6 6.3 - - - +
282A THR* 1.3 76.2 - - - +
284A GLU* 1.3 58.2 + - - +
286A VAL* 3.0 4.7 + - - +
287A ILE* 2.9 32.6 + - + +
299A LEU* 3.7 21.3 - - + -
327A LEU* 4.7 0.4 - - + -
370A PHE* 3.4 29.4 - - + -
375A VAL* 4.2 19.5 - - + +
379A TYR* 3.9 20.9 - - - +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A VAL* 3.1 34.9 - - + +
280A CYS 2.7 19.7 + - - +
281A GLU 3.4 4.5 - - - +
283A ILE* 1.3 72.4 - - - +
285A GLU* 1.3 64.2 + - - +
287A ILE* 3.1 11.4 + - - +
288A ASN* 3.0 30.9 + - - +
299A LEU* 4.1 6.5 - - + +
301A LYS* 2.8 27.6 + - - -
476A GLN* 3.0 28.9 + - - +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU 2.9 11.8 + - - +
282A THR* 3.5 10.3 - - - +
284A GLU* 1.3 80.0 - - - +
286A VAL* 1.3 58.2 + - - +
288A ASN* 3.7 9.3 + - - +
289A HIS* 3.6 14.0 + - - +
412A THR* 3.1 36.4 + - - +
413A THR* 3.9 4.6 + - - -
414A PRO* 4.5 8.3 - - + +
476A GLN* 3.3 16.9 + - + +
477A SER* 2.7 32.3 + - - -
479A TYR* 2.6 38.3 + - - -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A THR 3.3 14.6 - - - +
283A ILE 3.0 7.4 + - - +
285A GLU* 1.3 74.8 - - - +
287A ILE* 1.3 69.6 + - + +
288A ASN 3.1 0.2 - - - -
289A HIS* 3.1 5.3 + - - +
290A LEU* 2.9 47.4 + - + +
372A PRO* 3.6 36.8 - - + +
375A VAL* 4.3 20.0 - - + -
376A LYS 4.9 1.3 - - - +
379A TYR* 5.1 1.6 - - + -
409A PHE* 3.9 18.4 - - + -
412A THR* 4.2 6.5 - - - +
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A VAL* 4.0 7.6 - - + +
265A GLY* 3.8 23.3 - - - +
283A ILE* 2.9 19.3 + - + +
284A GLU* 3.2 11.0 - - - +
286A VAL* 1.3 76.7 - - - +
288A ASN* 1.3 62.5 + - - +
290A LEU* 3.7 0.5 - - - +
291A ALA* 2.7 41.3 + - + +
297A ILE* 4.1 15.8 - - + +
298A GLY* 3.4 25.6 - - - -
299A LEU* 3.5 18.6 - - + +
379A TYR* 3.4 31.6 - - + +
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Residues in contact with ASN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL* 5.4 2.6 - - - +
284A GLU* 3.0 24.2 + - - +
285A GLU* 3.8 9.5 - - - +
286A VAL 3.1 0.2 - - - -
287A ILE* 1.3 83.1 - - - +
289A HIS* 1.3 67.0 + - - +
291A ALA* 3.8 4.2 - - - +
292A ALA* 2.9 23.5 + - - +
476A GLN* 4.3 11.4 - - - +
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Residues in contact with HIS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU 3.6 9.5 + - - +
286A VAL* 3.1 7.1 + - - +
288A ASN* 1.3 80.8 - - - +
290A LEU* 1.3 90.6 + - + +
292A ALA* 3.0 17.4 + - - +
293A LYS* 3.0 37.3 + - - +
409A PHE* 4.2 13.3 - + - -
410A ALA* 4.0 22.3 - - + +
411A ASP 4.0 8.9 + - - -
412A THR* 3.8 28.9 - - + +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A VAL* 2.9 31.6 + - + +
289A HIS* 1.3 99.2 - - + +
291A ALA* 1.3 57.4 + - - +
293A LYS* 2.9 33.0 + - + +
295A GLU* 3.0 34.8 + - - +
297A ILE* 3.4 28.3 - - + -
376A LYS* 3.9 23.6 - - + -
379A TYR* 4.5 9.0 - - + -
409A PHE* 3.8 18.4 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLY* 6.1 0.2 - - - -
266A ALA* 5.6 9.6 - - + +
287A ILE* 2.7 30.4 + - + +
288A ASN* 3.8 4.7 - - - +
290A LEU* 1.3 68.4 - - - +
292A ALA* 1.3 57.4 + - - +
293A LYS 2.8 5.6 - - - -
294A GLY* 2.8 20.8 + - - -
295A GLU 3.9 18.2 + - - +
297A ILE* 4.6 3.8 - - + +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ASN 2.9 13.6 + - - +
289A HIS* 3.0 14.1 + - - +
291A ALA* 1.3 75.5 - - - +
293A LYS* 1.3 57.9 + - + +
294A GLY 3.4 1.0 + - - -
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A HIS* 3.0 45.9 + - + +
290A LEU* 2.9 18.8 + - + +
291A ALA 2.8 0.4 - - - -
292A ALA* 1.3 80.3 - - + +
294A GLY* 1.3 57.6 + - - +
295A 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