Contacts of the helix formed by residues 25 - 40 (chain 9) in PDB entry 2J28
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 25 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229 LEU* 5.3 11.4 - - + +
239 THR* 4.8 1.6 - - - +
249 GLU* 1.0 92.0 - - - +
269 ASN* 1.3 68.1 + - - +
279 VAL 2.7 5.5 + - - -
289 LYS* 3.2 15.8 + - + +
299 ASP* 3.0 38.5 + - - +
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Residues in contact with ASN 26 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119 ARG 5.2 2.1 - - - +
129 THR* 3.9 35.1 + - - +
149 ARG 5.2 4.6 + - - -
179 SER* 5.3 10.9 + - - +
239 THR* 2.8 23.5 + - - +
259 ASP* 1.3 76.0 - - - +
279 VAL* 1.3 61.7 + - + +
299 ASP* 3.6 6.5 + - - +
309 THR* 2.6 37.9 + - - -
339 GLU* 4.4 0.2 - - - +
749 PHE* 6.4 0.2 - - - -
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Residues in contact with VAL 27 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239 THR 5.4 0.4 - - - +
249 GLU* 4.0 14.1 - - - +
259 ASP 2.7 3.0 + - - -
269 ASN* 1.3 75.6 - - + +
289 LYS* 1.3 73.5 + - - +
309 THR* 2.6 22.6 + - - -
319 LEU* 2.7 14.2 + - + -
569 LYS* 6.3 0.4 - - - +
749 PHE* 3.5 43.3 - - + -
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Residues in contact with LYS 28 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249 GLU 4.7 0.6 + - - +
259 ASP* 3.2 19.0 + - - +
279 VAL* 1.3 79.9 - - - +
299 ASP* 1.3 75.3 + - - +
319 LEU* 2.7 21.4 - - + +
329 ARG* 2.5 29.4 + - + +
569 LYS* 5.2 15.5 - - - +
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Residues in contact with ASP 29 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259 ASP* 3.0 30.8 + - - +
269 ASN* 3.6 5.9 + - - +
279 VAL 2.8 2.8 + - - -
289 LYS* 1.3 87.6 - - - +
309 THR* 1.3 52.5 + - - +
329 ARG* 2.5 7.5 + - - +
339 GLU* 2.4 56.9 + - + +
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Residues in contact with THR 30 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89 ARG* 4.3 15.0 - - + +
129 THR* 4.2 15.4 + - - +
269 ASN* 2.6 25.7 + - - -
279 VAL* 2.6 16.5 + - - -
299 ASP* 1.3 77.1 - - - +
319 LEU* 1.3 52.1 + - - +
339 GLU* 2.8 18.1 + - - -
349 VAL* 2.4 56.2 + - + +
749 PHE* 4.9 15.6 - - + -
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Residues in contact with LEU 31 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279 VAL* 2.7 14.6 + - + +
289 LYS* 2.7 32.3 - - + +
299 ASP 2.6 3.0 + - - -
309 THR* 1.3 73.9 - - - +
329 ARG* 1.3 50.3 + - - +
349 VAL* 3.4 3.8 - - - +
359 ARG* 2.3 40.9 + - - +
519 PHE* 5.2 3.4 - - + -
529 ILE* 3.3 48.5 - - + +
559 VAL* 4.3 25.8 - - + -
569 LYS* 4.4 20.0 - - - -
749 PHE* 5.5 6.5 - - + -
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Residues in contact with ARG 32 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289 LYS* 2.5 20.1 + - + +
299 ASP* 2.5 14.7 + - - +
319 LEU* 1.3 74.2 - - + +
339 GLU* 1.3 52.2 + - + +
359 ARG* 2.8 21.4 - - + +
369 MET* 2.2 63.2 + - + +
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Residues in contact with GLU 33 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59 LEU* 3.6 5.9 - - - +
89 ARG* 2.5 59.4 + - - +
299 ASP* 2.4 55.6 + - + +
309 THR* 2.8 19.1 + - - +
329 ARG* 1.3 65.7 - - + +
349 VAL* 1.3 68.5 + - - +
369 MET* 2.7 19.3 + - - +
379 ALA* 3.0 9.9 + - - +
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Residues in contact with VAL 34 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29 PHE* 4.6 5.6 - - + -
59 LEU* 2.7 41.0 - - + +
89 ARG* 4.3 5.8 - - + -
309 THR* 2.4 47.7 + - + +
319 LEU* 3.5 3.4 - - - +
339 GLU* 1.3 72.8 - - - +
359 ARG* 1.3 58.0 + - - +
369 MET 2.7 0.7 + - - -
379 ALA* 2.8 6.2 + - - +
389 LEU* 2.6 34.1 - - + +
519 PHE* 6.4 1.6 - - + -
829 LEU* 6.2 4.5 - - + -
2959 LEU* 5.5 6.1 - - + -
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Residues in contact with ARG 35 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319 LEU* 2.3 33.0 + - - +
329 ARG* 2.8 28.3 - - + +
349 VAL* 1.3 69.0 - - - +
369 MET* 1.3 57.4 + - - +
389 LEU* 2.8 32.6 - - + +
399 LEU* 4.1 5.4 + - - +
459 LEU* 5.4 3.2 - - + +
489 VAL* 4.2 12.6 - - + +
499 ARG* 5.5 7.1 - - - +
529 ILE* 3.5 50.9 - - + +
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Residues in contact with MET 36 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329 ARG* 2.2 49.8 + - + +
339 GLU* 3.1 13.5 - - - +
349 VAL 2.7 3.4 + - - -
359 ARG* 1.3 67.1 - - - +
379 ALA* 1.3 54.9 + - - +
389 LEU 2.3 20.0 + - - -
399 LEU* 3.2 11.7 + - - +
409 GLU* 3.4 28.9 + - + +
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Residues in contact with ALA 37 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29 PHE* 4.1 17.0 + - - +
49 ASN 4.9 3.6 - - - +
59 LEU* 3.2 46.7 - - + -
339 GLU 3.0 1.7 + - - +
349 VAL 2.8 3.2 + - - +
369 MET* 1.3 74.0 - - - +
389 LEU* 1.3 55.2 + - - +
409 GLU* 4.2 12.8 - - - +
419 ALA* 3.1 26.4 + - - +
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Residues in contact with LEU 38 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29 PHE* 4.2 12.1 - - + -
59 LEU* 3.6 15.9 - - + -
349 VAL* 2.6 31.2 - - + +
359 ARG* 2.8 38.1 - - + +
369 MET 2.3 12.5 + - - -
379 ALA* 1.3 66.7 - - - +
399 LEU* 1.3 58.6 + - - +
409 GLU 3.0 0.7 - - - -
419 ALA* 2.4 41.2 + - - +
439 VAL* 3.1 25.8 - - + -
459 LEU* 5.8 0.4 - - + -
489 VAL* 5.2 12.3 - - + -
519 PHE* 6.3 2.7 - - + -
529 ILE* 5.6 2.5 - - + -
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Residues in contact with LEU 39 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359 ARG 4.1 2.2 + - - +
369 MET* 3.2 4.3 + - - +
389 LEU* 1.3 78.7 - - - +
409 GLU* 1.3 66.2 + - - +
429 ASP* 2.2 33.8 + - - +
439 VAL* 2.7 31.7 - - - +
449 ALA* 4.3 1.6 - - - -
459 LEU* 2.3 65.5 - - + +
2279 GLN* 4.7 2.7 - - - +
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Residues in contact with GLU 40 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369 MET* 3.4 36.4 + - + +
379 ALA* 4.2 11.8 - - - +
389 LEU 3.0 0.2 - - - -
399 LEU* 1.3 80.1 - - - +
419 ALA* 1.3 57.2 + - + +
429 ASP 3.2 4.5 + - - -
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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