Contacts of the helix formed by residues 338 - 351 (chain D) in PDB entry 3AP3
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 338 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243D LEU 3.1 18.3 + - - +
244D HIS* 3.2 38.8 + - - +
245D PRO* 3.3 8.7 - - + +
246D ARG* 4.3 9.9 + - - +
247D ARG* 5.0 0.7 + - - +
336D ASN 3.8 0.4 + - - +
337D PRO* 1.3 73.0 - - - +
339D PRO* 1.3 65.6 - - + +
340D PHE* 4.1 9.9 - - + +
341D VAL* 2.6 34.0 + - + +
342D ILE* 3.0 9.4 + - - +
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Residues in contact with PRO 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D PRO 3.6 5.8 - - - +
338D ASP* 1.3 85.6 - - + +
340D PHE* 1.3 53.1 + - - +
342D ILE* 3.2 16.0 + - + +
343D ASN* 2.7 46.1 + - - +
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Residues in contact with PHE 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D PRO* 3.5 33.4 - - + -
246D ARG* 6.1 1.8 - - + -
265D LEU* 3.5 45.8 - - + -
266D HIS* 4.9 14.1 - + - -
268D GLU* 5.8 0.7 - - - -
293D VAL* 5.1 5.4 - - + -
338D ASP* 4.1 8.9 - - + +
339D PRO* 1.3 78.9 - - - +
341D VAL* 1.3 56.2 + - + +
343D ASN* 3.4 5.4 + - + +
344D ASN* 2.9 66.9 + - - +
347D ARG* 5.3 0.7 - - - -
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Residues in contact with VAL 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D VAL 3.0 23.1 - - - +
243D LEU 3.2 27.4 - - - +
245D PRO* 3.6 15.0 - - + -
293D VAL* 3.6 21.3 - - + +
294D ASN* 4.4 0.7 - - - -
295D LEU* 3.5 26.0 - - + -
338D ASP* 2.6 24.3 + - + +
340D PHE* 1.3 70.1 - - + +
342D ILE* 1.3 58.9 + - - +
344D ASN* 3.1 7.1 + - - +
345D THR* 2.4 34.2 + - - +
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Residues in contact with ILE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D LEU* 4.1 6.5 - - + +
337D PRO* 3.5 43.7 - - + +
338D ASP 3.0 4.6 + - - +
339D PRO* 3.5 21.1 - - + +
341D VAL* 1.3 75.2 - - - +
343D ASN* 1.3 62.6 + - - +
345D THR* 2.9 26.0 + - - -
346D GLN* 3.0 27.7 + - + +
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Residues in contact with ASN 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D PRO* 2.7 27.3 + - - +
340D PHE* 3.7 6.5 - - + +
342D ILE* 1.3 76.1 - - - +
344D ASN* 1.3 64.3 + - - +
346D GLN* 3.5 11.9 + - - +
347D ARG* 3.2 33.3 + - - +
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Residues in contact with ASN 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D PRO* 4.0 14.4 - - + +
293D VAL 3.6 21.9 + - - +
340D PHE* 2.9 62.7 + - - +
341D VAL 3.1 6.7 + - - +
343D ASN* 1.3 74.1 - - - +
345D THR* 1.3 65.8 + - - +
347D ARG* 2.3 52.7 + - - +
348D VAL* 2.9 26.0 + - - +
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Residues in contact with THR 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D ASN* 4.2 10.0 - - + +
295D LEU* 3.4 38.5 + - + +
296D GLU* 4.2 20.0 - - + +
341D VAL 2.4 28.6 + - - -
342D ILE* 3.0 11.9 + - - -
344D ASN* 1.3 74.7 - - - +
346D GLN* 1.3 62.4 + - - +
348D VAL* 2.9 7.2 + - - +
349D LEU* 2.9 33.2 + - + +
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Residues in contact with GLN 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ILE* 3.0 30.1 + - + +
343D ASN* 3.7 12.3 - - - +
345D THR* 1.3 75.1 - - - +
347D ARG* 1.3 51.3 + - - +
349D LEU* 2.6 45.6 + - - +
350D LYS* 2.7 42.6 + - - +
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Residues in contact with ARG 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D GLU* 4.1 8.7 + - - +
292D PRO* 3.2 31.1 - - + +
340D PHE* 5.3 2.0 - - - -
343D ASN* 3.2 18.4 + - - +
344D ASN* 2.3 49.3 + - - +
346D GLN* 1.3 79.1 - - + +
348D VAL* 1.3 61.2 + - + +
350D LYS* 3.2 25.1 + - + +
351D GLY 3.2 9.7 + - - -
352D ASP* 3.3 38.0 + - + +
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Residues in contact with VAL 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D LYS* 3.7 47.6 - - + +
292D PRO* 4.2 12.8 - - + -
294D ASN* 4.2 17.3 - - + +
296D GLU* 3.4 24.5 - - - +
344D ASN 2.9 16.4 + - - +
345D THR* 2.9 11.0 + - - +
347D ARG* 1.3 76.2 - - + +
349D LEU* 1.3 59.7 + - - +
350D LYS 3.4 0.5 + - - -
351D GLY* 3.4 11.8 + - - -
352D ASP* 4.6 3.3 + - - +
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D GLU* 3.8 29.4 - - + +
345D THR* 2.9 26.2 + - + +
346D GLN* 2.6 37.7 + - - +
348D VAL* 1.3 73.6 - - + +
350D LYS* 1.3 58.2 + - + -
351D GLY* 3.5 0.7 + - - -
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Residues in contact with LYS 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D GLN* 2.7 40.4 + - - +
347D ARG* 3.6 18.6 - - + +
348D VAL 3.2 0.6 - - - -
349D LEU* 1.3 74.1 - - + +
351D GLY* 1.3 59.3 + - - +
352D ASP* 4.3 7.4 - - - +
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Residues in contact with GLY 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D ARG 3.2 2.0 + - - -
348D VAL 3.4 7.1 + - - -
349D LEU 3.3 4.2 - - - -
350D LYS* 1.3 80.8 - - - +
352D ASP* 1.4 65.8 + - - +
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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