Contacts of the helix formed by residues 26 - 49 (chain 6) 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 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226 ASN 4.5 2.0 - - - +
236 ALA* 3.1 16.4 + - - +
246 PHE 3.0 1.0 + - - -
256 SER* 1.3 79.2 + - - +
276 PRO* 1.4 68.1 - - - +
286 THR* 2.9 23.6 + - - -
296 VAL* 2.7 39.2 + - + +
306 ALA* 2.8 11.5 + - - -
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Residues in contact with PRO 27 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275 PRO* 3.5 32.6 - - + +
285 THR* 5.5 1.3 - - + -
315 SER* 3.5 18.8 - - - +
256 SER 3.2 7.3 - - - +
266 ASN* 1.4 91.9 - - - +
286 THR* 1.3 60.1 + - - +
306 ALA* 4.0 2.2 - - + +
316 SER* 2.8 30.0 + - - -
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Residues in contact with THR 28 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266 ASN* 2.8 13.9 + - - -
276 PRO* 1.3 74.4 - - - +
296 VAL* 1.3 62.0 + - + +
316 SER* 3.1 5.3 + - - -
326 THR* 2.5 47.6 + - - +
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Residues in contact with VAL 29 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236 ALA* 3.3 33.7 - - + +
246 PHE* 3.8 10.1 - - - +
266 ASN* 2.7 21.3 + - + +
286 THR* 1.3 73.2 - - + +
306 ALA* 1.3 66.6 + - - +
326 THR* 3.7 3.8 - - - -
336 ILE* 3.1 43.7 + - + +
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Residues in contact with ALA 30 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305 ALA* 3.6 29.2 - - + -
345 LEU* 4.6 2.2 - - + -
246 PHE* 3.3 35.6 + - + +
256 SER 4.9 0.9 - - - +
266 ASN 2.8 11.9 + - - +
276 PRO* 4.0 4.5 - - + +
296 VAL* 1.3 77.7 - - - +
316 SER* 1.3 57.9 + - - +
336 ILE* 4.0 0.7 - - - +
346 LEU* 2.9 36.6 + - + +
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Residues in contact with SER 31 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255 SER 3.5 24.0 - - - -
275 PRO* 3.5 25.1 - - - +
276 PRO 2.8 20.4 + - - -
286 THR* 3.1 8.1 + - - +
306 ALA* 1.3 77.2 - - - +
326 THR* 1.3 58.1 + - - +
346 LEU* 4.5 0.4 - - - +
356 SER* 2.6 42.2 + - - -
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Residues in contact with THR 32 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286 THR* 2.5 37.3 + - - +
296 VAL* 3.7 5.8 - - - -
316 SER* 1.3 78.1 + - - +
336 ILE* 1.3 68.3 + - + +
356 SER* 3.2 3.2 + - - -
366 ASN* 3.1 44.5 + - - +
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Residues in contact with ILE 33 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246 PHE* 4.2 15.0 - - + -
296 VAL* 3.1 34.0 + - + +
306 ALA 4.0 1.8 - - - +
326 THR* 1.3 81.5 - - + +
346 LEU* 1.3 59.1 + - - +
366 ASN* 3.1 6.3 + - - +
376 VAL* 3.0 32.7 + - + +
3468 T 3.7 44.6 - - - +
3478 A 4.7 5.8 - - - +
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Residues in contact with LEU 34 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215 PHE* 4.1 21.8 - - + -
245 PHE* 3.4 41.5 - - + +
255 SER* 3.9 24.9 - - - -
305 ALA* 4.5 0.2 - - + -
246 PHE* 4.0 23.1 - - + -
306 ALA* 2.9 27.7 + - + +
316 SER 4.3 0.4 - - - +
336 ILE* 1.3 77.4 - - - +
356 SER* 1.3 53.0 + - - +
376 VAL* 3.4 9.1 + - + +
386 SER* 2.6 36.9 + - - -
3458 A 4.9 7.4 - - + +
3468 T 4.6 13.7 - - - +
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Residues in contact with SER 35 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255 SER* 4.6 8.4 - - - -
316 SER* 2.6 27.2 + - - -
326 THR* 3.2 6.4 + - - -
346 LEU* 1.3 77.7 - - - +
366 ASN* 1.3 69.9 + - - +
386 SER* 3.4 20.0 + - - -
396 PRO* 4.1 3.6 - - - +
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Residues in contact with ASN 36 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326 THR* 3.1 33.3 + - - +
336 ILE* 3.1 6.9 + - - +
356 SER* 1.3 86.7 + - - +
376 VAL* 1.3 62.4 + - + +
386 SER 3.3 1.0 + - - -
396 PRO* 3.6 12.5 - - - +
406 VAL* 4.3 6.6 - - - +
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Residues in contact with VAL 37 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215 PHE* 4.6 9.0 - - + -
336 ILE* 3.0 25.4 + - + +
346 LEU* 3.5 17.3 - - + +
366 ASN* 1.3 79.9 - - + +
386 SER* 1.3 66.0 + - - +
396 PRO* 3.5 1.3 - - - -
406 VAL* 3.3 14.7 + - + +
416 ALA* 2.8 23.1 + - + +
3458 A 4.1 21.1 - - - +
3468 T 3.9 16.6 - - - +
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Residues in contact with SER 38 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215 PHE* 3.6 22.0 - - - -
225 ASN* 5.5 2.7 + - - -
255 SER* 4.6 5.4 + - - -
346 LEU 2.6 21.5 + - - -
356 SER* 3.4 15.0 - - - -
376 VAL* 1.3 81.6 - - - +
396 PRO* 1.4 73.0 - - - +
416 ALA* 2.9 10.7 + - - +
426 GLN* 3.0 24.7 + - - +
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Residues in contact with PRO 39 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356 SER 4.1 4.5 - - - +
366 ASN 3.6 12.8 - - - +
376 VAL 3.5 1.3 - - - -
386 SER* 1.4 96.5 - - - +
406 VAL* 1.3 69.2 + - + +
426 GLN* 3.4 20.2 + - + +
436 GLN* 3.1 21.3 + - - +
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Residues in contact with VAL 40 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366 ASN 4.3 13.9 - - - +
376 VAL* 3.5 15.9 - - + +
386 SER 3.0 0.4 - - - -
396 PRO* 1.3 78.3 - - + +
416 ALA* 1.3 67.3 + - - +
436 GLN* 3.1 9.1 + - + +
446 ASN* 3.1 35.1 + - - +
3458 A 4.8 2.9 - - - +
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Residues in contact with ALA 41 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175 TRP* 4.1 16.8 - - + -
215 PHE* 4.3 11.4 - - + -
376 VAL 2.8 13.5 + - - +
386 SER 3.3 8.5 - - - +
406 VAL* 1.3 76.4 - - - +
426 GLN* 1.3 57.8 + - - +
446 ASN* 3.1 1.9 + - - +
456 PHE* 2.8 32.1 + - - +
3448 T 4.2 2.5 - - - +
3458 A 3.7 35.2 - - - -
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Residues in contact with GLN 42 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145 TYR* 3.7 12.3 + - - +
175 TRP* 4.3 10.5 - - + -
185 GLN* 3.2 40.5 - - - +
215 PHE* 5.8 0.7 - - + -
225 ASN* 4.7 2.4 + - - -
386 SER* 3.0 19.9 + - - +
396 PRO* 3.5 29.6 - - - +
416 ALA* 1.3 76.6 - - - +
436 GLN* 1.3 56.3 + - - +
456 PHE* 3.7 0.7 - - - +
466 GLN* 2.9 44.4 + - - +
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Residues in contact with GLN 43 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396 PRO 3.1 9.6 + - - +
406 VAL* 3.1 12.4 + - - +
426 GLN* 1.3 79.7 - - - +
446 ASN* 1.3 59.5 + - - +
466 GLN* 3.4 14.2 + - - +
476 THR* 2.6 60.8 + - - +
11b SER* 5.2 5.9 + - - -
12b GLN* 6.2 1.8 - - - +
43c GLN* 3.1 41.8 - - - +
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Residues in contact with ASN 44 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406 VAL* 3.1 23.4 + - - +
416 ALA 3.1 3.1 + - - +
436 GLN* 1.3 80.2 - - - +
456 PHE* 1.3 65.4 + - - +
476 THR* 3.4 5.6 + - - -
486 ASN* 3.1 23.8 + - - +
3448 T 3.5 32.1 - - - +
3458 A 3.0 23.6 + - - +
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Residues in contact with PHE 45 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 TYR* 4.1 2.5 - + - -
135 ARG* 4.5 6.5 - - + -
145 TYR* 3.4 43.3 - + + -
175 TRP* 3.5 60.3 - + + -
416 ALA 2.8 16.8 + - - +
426 GLN 3.7 3.1 - - - +
446 ASN* 1.3 76.9 - - - +
466 GLN* 1.3 64.2 + - - +
496 VAL* 3.0 64.0 + - + +
77 A 5.2 5.2 - - - -
3438 A 4.6 10.3 - + - -
3448 T 3.6 23.9 - - - -
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Residues in contact with GLN 46 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 TYR* 3.3 21.5 + - - +
145 TYR* 2.9 38.5 + - + -
426 GLN* 2.9 34.7 + - - +
436 GLN* 3.7 15.0 + - - +
456 PHE* 1.3 77.5 - - - +
476 THR* 1.3 62.9 + - - +
506 PRO* 3.1 21.8 - - - +
11b SER* 4.3 26.6 - - - +
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Residues in contact with THR 47 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436 GLN* 2.6 41.9 + - - +
446 ASN* 3.7 7.1 + - - -
456 PHE 3.2 0.4 - - - -
466 GLN* 1.3 80.5 - - - +
486 ASN* 1.3 73.6 + - - +
506 PRO* 3.7 6.4 - - - +
516 LYS* 3.4 23.2 - - - +
9b SER* 5.8 4.7 - - - -
11b SER* 5.0 5.9 + - - -
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Residues in contact with ASN 48 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446 ASN* 3.1 12.4 + - - +
476 THR* 1.3 86.4 - - - +
496 VAL* 1.3 62.2 + - - +
506 PRO* 3.4 2.0 - - - -
516 LYS* 3.0 33.0 + - + +
526 PHE* 3.1 26.9 - - + -
886 ASN* 4.9 4.3 + - - -
3438 A 3.8 20.4 - - - +
3448 T 3.1 21.0 + - - -
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Residues in contact with VAL 49 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 TYR* 3.8 10.1 - - + -
135 ARG* 3.7 27.6 - - + +
456 PHE* 3.0 62.5 + - + +
486 ASN* 1.3 71.7 - - - +
506 PRO* 1.4 60.8 - - + +
516 LYS 3.0 4.0 - - - -
526 PHE* 2.8 30.7 + - - +
536 THR 3.2 6.6 + - - -
3438 A 3.9 27.8 - - + +
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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
------------------------------------------------------------
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