Contacts of the helix formed by residues 26 - 49 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222 ASN 4.5 2.5 - - - +
232 ALA 3.1 15.2 + - - +
242 PHE 3.0 1.2 + - - -
252 SER* 1.3 78.2 + - - +
272 PRO* 1.4 66.5 - - - +
282 THR* 2.9 23.6 + - - -
292 VAL* 2.7 37.7 + - + -
302 ALA* 2.8 12.1 + - - -
323 THR* 4.0 19.3 + - + +
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Residues in contact with PRO 27 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 PRO* 3.5 33.4 - - + +
281 THR* 5.5 1.1 - - + -
311 SER* 3.5 19.1 - - - +
252 SER 3.2 7.1 - - - +
262 ASN* 1.4 92.1 - - - +
282 THR* 1.3 62.2 + - - +
302 ALA* 4.0 2.0 - - + +
312 SER* 2.8 29.3 + - - -
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Residues in contact with THR 28 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 PRO* 5.7 0.4 - - - -
262 ASN* 2.8 13.8 + - - -
272 PRO* 1.3 75.2 - - - +
292 VAL* 1.3 60.5 + - + +
312 SER* 3.1 5.1 + - - +
322 THR* 2.5 47.4 + - - +
263 ASN* 4.8 4.3 - - - +
283 THR* 3.1 33.5 - - + +
293 VAL* 4.6 0.2 - - + -
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Residues in contact with VAL 29 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 ALA 3.3 29.4 - - - +
242 PHE* 3.8 10.3 - - - +
262 ASN* 2.7 14.5 + - + +
282 THR* 1.3 70.7 - - - +
302 ALA* 1.3 65.4 + - - +
322 THR* 3.7 0.3 - - - -
332 ILE* 3.1 43.6 + - + +
283 THR* 4.3 1.3 - - - +
293 VAL* 3.9 29.2 - - + +
323 THR* 3.8 30.3 - - + +
333 ILE* 4.9 7.0 - - + -
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Residues in contact with ALA 30 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301 ALA* 3.6 29.4 - - + -
341 LEU* 4.6 2.7 - - + -
242 PHE* 3.3 35.4 + - + +
252 SER 4.9 0.7 - - - -
262 ASN 2.8 12.4 + - - +
272 PRO* 4.0 4.3 - - + +
292 VAL* 1.3 77.6 - - - +
312 SER* 1.3 57.5 + - - +
332 ILE* 4.0 0.7 - - - +
342 LEU* 2.9 37.5 + - + +
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Residues in contact with SER 31 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 SER 3.5 24.5 - - - -
271 PRO* 3.5 24.4 - - - +
272 PRO 2.8 21.3 + - - -
282 THR* 3.1 8.1 + - - +
302 ALA* 1.3 76.1 - - - +
322 THR* 1.3 57.8 + - - +
342 LEU* 4.6 0.2 - - - -
352 SER* 2.6 42.6 + - - -
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Residues in contact with THR 32 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 THR* 2.5 35.4 + - - +
292 VAL 3.7 3.1 - - - -
312 SER* 1.3 78.4 + - - +
332 ILE* 1.3 65.1 + - - +
352 SER* 3.2 3.3 + - - -
362 ASN* 3.1 35.0 + - - +
223 ASN 5.2 0.2 - - - +
233 ALA* 3.6 34.1 - - + +
263 ASN* 4.0 15.0 + - + +
293 VAL* 3.7 15.3 - - + +
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Residues in contact with ILE 33 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 PHE* 4.2 15.0 - - + -
292 VAL* 3.1 33.9 + - + +
302 ALA 4.0 1.6 - - - +
322 THR* 1.3 77.9 - - - +
342 LEU* 1.3 59.1 + - - +
362 ASN* 3.1 2.8 + - - +
372 VAL* 3.0 29.6 + - + +
203 LYS* 4.0 23.3 - - + -
233 ALA* 3.8 21.5 - - + -
293 VAL* 4.9 7.4 - - + -
333 ILE* 5.3 5.2 - - + -
187 T 5.7 2.2 - - - +
3228 T 3.7 38.4 - - - +
3238 A 4.7 6.7 - - - +
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Residues in contact with LEU 34 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211 PHE* 4.1 21.8 - - + -
241 PHE* 3.4 40.8 - - + +
251 SER* 3.9 25.8 - - - -
301 ALA* 4.5 0.2 - - + -
242 PHE* 4.0 23.1 - - + -
302 ALA* 2.9 27.5 + - + +
312 SER 4.3 0.7 - - - +
332 ILE* 1.3 77.8 - - - +
352 SER* 1.3 52.2 + - - +
372 VAL* 3.4 8.3 + - + +
382 SER* 2.6 36.9 + - - -
3218 A 4.9 7.0 - - + -
3228 T 4.6 14.1 - - - +
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Residues in contact with SER 35 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 SER* 4.6 8.7 - - - -
312 SER* 2.6 26.8 + - - -
322 THR* 3.2 6.6 + - - -
342 LEU* 1.3 78.4 - - - +
362 ASN* 1.3 69.7 + - - +
382 SER* 3.4 20.1 + - - -
392 PRO* 4.1 3.3 - - - +
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Residues in contact with ASN 36 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322 THR* 3.1 23.5 + - - +
332 ILE 3.1 5.8 + - - +
352 SER* 1.3 85.7 + - - +
372 VAL* 1.3 59.2 + - - +
382 SER 3.3 1.1 + - - -
392 PRO* 3.6 12.0 - - - +
402 VAL* 4.3 1.9 - - - +
193 ALA* 3.4 30.2 + - + +
223 ASN* 4.0 10.4 - - - +
233 ALA* 3.4 31.7 - - + +
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Residues in contact with VAL 37 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211 PHE* 4.6 9.4 - - + -
332 ILE* 3.0 20.4 + - + +
342 LEU* 3.5 17.0 - - + +
362 ASN* 1.3 76.2 - - - +
382 SER* 1.3 65.8 + - - +
392 PRO* 3.5 1.3 - - - -
402 VAL* 3.9 7.6 - - + -
412 ALA* 2.8 24.0 + - + +
163 LYS* 4.9 8.3 - - + -
193 ALA* 3.7 22.9 - - + -
203 LYS* 3.7 27.1 - - + -
3218 A 4.1 20.9 - - - +
3228 T 3.9 6.1 - - - +
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Residues in contact with SER 38 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211 PHE* 3.6 21.6 - - - -
221 ASN* 5.5 2.5 + - - -
251 SER* 4.6 5.2 + - - -
342 LEU 2.6 21.7 + - - -
352 SER* 3.4 16.0 - - - -
372 VAL* 1.3 81.3 - - - +
392 PRO* 1.4 72.7 - - - +
412 ALA* 2.9 10.9 + - - +
422 GLN* 3.0 25.4 + - - +
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Residues in contact with PRO 39 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 SER 4.1 3.6 - - - +
362 ASN 3.6 12.3 - - - +
372 VAL 3.5 1.6 - - - -
382 SER* 1.4 97.9 - - - +
402 VAL* 1.3 67.6 + - + +
422 GLN* 3.4 19.8 + - + +
432 GLN* 3.1 21.5 + - - +
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Residues in contact with VAL 40 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 ASN 4.3 5.4 - - - +
372 VAL* 3.5 11.7 - - + +
382 SER 3.0 0.6 - - - -
392 PRO* 1.3 78.7 - - + +
412 ALA* 1.3 67.2 + - - +
432 GLN* 3.1 9.7 + - - +
442 ASN* 3.1 33.5 + - - +
123 GLN* 5.2 1.3 - - - +
153 ALA* 4.0 29.4 - - + +
163 LYS* 3.9 33.0 - - + +
193 ALA* 4.3 14.4 - - + -
3218 A 4.8 1.6 - - - +
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Residues in contact with ALA 41 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171 TRP* 4.1 17.0 - - + -
211 PHE* 4.3 12.1 - - + -
372 VAL 2.8 14.2 + - - +
382 SER 3.3 8.7 - - - +
402 VAL* 1.3 76.2 - - - +
422 GLN* 1.3 58.0 + - - +
442 ASN* 3.1 2.1 + - - +
452 PHE* 2.8 31.7 + - - +
3208 T 4.2 2.6 - - - +
3218 A 3.7 35.4 - - - -
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Residues in contact with GLN 42 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141 TYR* 3.7 12.2 + - - +
171 TRP* 4.3 10.8 - - + -
181 GLN* 3.2 39.8 - - - +
211 PHE* 5.8 0.7 - - + -
221 ASN* 4.7 2.4 + - - -
382 SER* 3.0 20.3 + - - +
392 PRO* 3.5 29.1 - - - +
412 ALA* 1.3 76.8 - - - +
432 GLN* 1.3 58.0 + - - +
452 PHE* 3.7 0.9 - - - +
462 GLN* 2.9 43.2 + - - +
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Residues in contact with GLN 43 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392 PRO 3.1 9.4 + - - +
402 VAL* 3.1 11.8 + - - +
422 GLN* 1.3 79.9 - - - +
442 ASN* 1.3 60.0 + - - +
462 GLN* 3.4 15.3 + - - +
472 THR* 2.6 61.7 + - - +
123 GLN* 5.3 8.5 - - + +
11X SER* 5.2 5.9 + - - -
12X GLN* 6.2 2.2 - - - +
43Y GLN* 3.1 41.5 - - - +
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Residues in contact with ASN 44 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402 VAL* 3.1 23.4 + - - +
412 ALA 3.1 3.3 + - - +
432 GLN* 1.3 75.1 - - - +
452 PHE* 1.3 65.3 + - - +
472 THR* 3.4 4.5 + - - -
482 ASN* 3.1 22.5 + - - +
83 ARG* 3.6 24.3 - - - +
123 GLN* 2.9 33.7 + - - +
163 LYS* 5.0 4.8 - - - +
207 T 5.5 0.4 + - - -
3208 T 3.5 29.8 - - - +
3218 A 3.0 21.6 + - - -
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Residues in contact with PHE 45 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 TYR* 4.1 2.2 - + - -
131 ARG* 4.5 6.7 - - + -
141 TYR* 3.4 42.6 - + + -
171 TRP* 3.5 60.8 - + + -
412 ALA 2.8 16.2 + - - +
422 GLN 3.7 3.1 - - - +
442 ASN* 1.3 77.2 - - - +
462 GLN* 1.3 64.8 + - - +
492 VAL* 3.0 64.4 + - + +
317 A 5.2 4.9 - - - -
3198 A 4.6 10.3 - + - -
3208 T 3.6 23.0 - - - -
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Residues in contact with GLN 46 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 TYR* 3.3 20.2 + - - +
141 TYR* 2.9 38.9 + - + -
422 GLN* 2.9 33.5 + - - +
432 GLN* 3.7 14.8 + - - +
452 PHE* 1.3 78.1 - - - +
472 THR* 1.3 63.2 + - - +
502 PRO* 3.1 21.5 - - - +
11X SER* 4.3 28.0 - - - +
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Residues in contact with THR 47 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432 GLN* 2.6 41.9 + - - +
442 ASN* 3.7 6.7 - - - -
452 PHE 3.2 0.2 - - - -
462 GLN* 1.3 80.5 - - - +
482 ASN* 1.3 74.1 + - - +
502 PRO* 3.7 6.4 - - - +
512 LYS* 3.4 23.2 - - - +
123 GLN* 4.6 13.9 + - - +
9X SER* 6.0 1.3 - - - -
11X SER* 5.0 5.2 - - - -
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Residues in contact with ASN 48 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442 ASN 3.1 10.6 + - - +
472 THR* 1.3 87.1 - - - +
492 VAL* 1.3 62.2 + - - +
502 PRO* 3.4 1.3 - - - -
512 LYS* 3.0 34.2 + - + +
522 PHE* 3.1 27.5 - - + -
882 ASN* 4.9 5.0 + - - +
73 SER 3.9 13.6 + - - +
83 ARG* 3.4 15.6 - - - +
123 GLN* 5.2 2.4 - - - +
3198 A 3.8 19.9 - - - +
3208 T 3.1 20.0 + - - -
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Residues in contact with VAL 49 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 TYR* 3.8 9.6 - - + -
131 ARG* 3.7 27.1 + - - +
452 PHE* 3.0 64.5 + - + +
482 ASN* 1.3 70.8 - - - +
502 PRO* 1.4 60.9 - - + +
512 LYS 3.0 4.3 - - - -
522 PHE* 2.8 30.8 + - - +
532 THR 3.2 6.4 + - - -
3198 A 3.9 28.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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