Contacts of the helix formed by residues 26 - 37 (chain 1) in PDB entry 3J9X
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 ASN 26 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221 ASN 3.6 2.2 + - - +
231 ALA 3.1 15.1 + - - +
241 PHE 3.0 1.4 + - - +
251 SER* 1.3 77.2 + - - +
271 PRO* 1.4 68.2 - - - +
281 THR* 2.7 32.4 + - - +
291 VAL* 2.7 34.7 + - + -
301 ALA* 2.9 11.5 + - - -
28z THR* 4.9 3.4 - - - +
32z THR* 4.0 19.0 + - + +
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Residues in contact with PRO 27 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 SER 3.2 6.2 - - - +
261 ASN* 1.4 92.3 - - - +
281 THR* 1.3 63.2 + - + +
301 ALA* 4.1 1.5 - - + +
311 SER* 2.8 30.7 + - - -
272 PRO* 3.5 33.3 - - + +
312 SER* 3.5 20.4 - - - +
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Residues in contact with THR 28 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261 ASN* 2.7 20.0 + - - +
271 PRO* 1.3 80.3 - - + +
291 VAL* 1.3 58.3 + - - +
311 SER* 3.2 5.7 + - - -
321 THR* 2.4 40.1 + - - -
272 PRO* 5.5 1.6 - - + -
28z THR* 3.1 30.0 - - + +
29z VAL* 4.8 0.9 - - - -
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Residues in contact with VAL 29 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231 ALA 3.5 19.7 - - - +
241 PHE* 4.0 8.3 - - - -
261 ASN* 2.7 30.6 + - + +
281 THR* 1.3 74.9 - - - +
301 ALA* 1.3 66.4 + - - +
321 THR* 3.7 0.5 - - - -
331 ILE* 3.0 43.8 + - + +
28z THR 4.5 0.2 - - - +
29z VAL* 3.9 27.6 - - + -
32z THR* 3.7 25.1 - - - +
33z ILE* 4.9 7.4 - - + -
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Residues in contact with ALA 30 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241 PHE* 3.3 40.2 + - + +
251 SER 5.0 0.7 - - - -
261 ASN 2.9 10.4 + - - +
271 PRO* 4.1 2.7 - - + +
291 VAL* 1.3 79.6 - - - +
311 SER* 1.3 56.9 + - - +
331 ILE* 3.9 0.5 - - - +
341 LEU* 2.9 37.7 + - + +
302 ALA* 3.6 27.8 - - + -
342 LEU* 4.5 3.1 - - + -
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Residues in contact with SER 31 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 PRO 2.8 21.6 + - - -
281 THR* 3.2 9.2 + - - -
301 ALA* 1.3 76.1 - - - +
321 THR* 1.3 59.8 + - - +
341 LEU 4.5 0.2 - - - +
351 SER* 2.6 40.4 + - - -
252 SER 3.4 24.2 + - - -
272 PRO* 3.5 24.5 - - - +
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Residues in contact with THR 32 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281 THR* 2.4 26.5 + - - -
291 VAL 3.7 3.6 - - - -
311 SER* 1.3 78.0 + - - +
331 ILE* 1.3 63.2 + - - +
351 SER* 3.2 3.6 + - - -
361 ASN* 3.0 36.0 + - - +
23z ALA* 3.6 34.3 - - + +
26z ASN* 4.0 18.8 + - + +
29z VAL* 3.8 12.7 - - + +
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Residues in contact with ILE 33 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241 PHE* 4.3 14.4 - - + -
291 VAL* 3.0 33.7 + - + +
301 ALA 3.9 2.2 - - - +
321 THR* 1.3 77.4 - - - +
341 LEU* 1.3 60.4 + - + +
361 ASN* 3.1 2.8 + - - +
371 VAL* 3.0 29.4 + - + +
297 A 3.6 42.0 - - - +
307 T 4.7 8.5 - - - +
3118 A 5.4 2.0 - - - +
20z LYS* 3.9 17.7 - - + -
23z ALA* 3.8 22.4 - - + -
29z VAL* 4.9 7.4 - - + -
33z ILE* 5.3 6.1 - - + -
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Residues in contact with LEU 34 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241 PHE* 4.0 13.9 - - + -
301 ALA* 2.9 29.5 + - + +
311 SER 4.3 0.4 - - - +
331 ILE* 1.3 78.7 - - - +
351 SER* 1.3 52.6 + - - +
371 VAL* 3.4 6.7 + - + +
381 SER* 2.6 36.9 + - - -
212 PHE* 3.9 24.4 - - + -
242 PHE* 3.5 38.8 - - + +
252 SER* 3.8 25.8 - - - -
302 ALA* 4.6 0.2 - - + -
287 T 4.6 6.3 - - + -
297 A 4.2 24.0 - - - +
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Residues in contact with SER 35 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311 SER* 2.6 26.5 + - - -
321 THR* 3.2 6.2 + - - -
341 LEU* 1.3 77.4 - - - +
361 ASN* 1.3 69.2 + - - +
381 SER* 3.3 20.1 + - - -
391 PRO* 4.0 3.5 - - - +
252 SER* 4.5 9.3 - - - -
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Residues in contact with ASN 36 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321 THR* 3.0 26.6 + - - +
331 ILE* 3.1 4.7 + - - +
351 SER* 1.3 90.1 + - - +
371 VAL* 1.3 58.6 + - - +
381 SER 3.3 0.8 + - - -
391 PRO* 3.6 11.6 - - - +
401 VAL* 4.3 2.1 - - - +
19z ALA* 3.4 30.7 + - + +
22z ASN* 4.0 10.1 - - - +
23z ALA* 3.5 31.1 - - - +
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Residues in contact with VAL 37 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 ILE 3.0 21.3 + - - +
341 LEU* 3.5 15.3 - - + +
361 ASN* 1.3 76.5 - - - +
381 SER* 1.3 69.5 + - - +
391 PRO* 3.5 1.3 - - - -
401 VAL* 3.3 9.4 + - + +
411 ALA* 2.9 20.2 + - + +
212 PHE* 4.5 9.0 - - + -
287 T 3.9 21.8 - - - +
297 A 3.9 4.7 - - - +
16z LYS* 4.7 10.5 - - + -
19z ALA* 3.7 18.6 - - + -
20z LYS* 3.6 30.5 - - + -
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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