Contacts of the helix formed by residues 9 - 26 (chain 3) 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 SER 9 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 ARG* 1.3 75.1 - - - +
103 TYR* 1.3 59.4 + - - +
113 SER* 3.6 9.8 + - - -
123 GLN* 2.8 36.0 + - - +
133 ARG* 2.8 27.1 + - - +
534 THR* 4.3 3.6 - - - -
47Y THR* 5.5 12.7 - - - +
51Y LYS* 6.0 5.2 - - - -
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Residues in contact with TYR 10 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 SER* 1.3 73.1 - - - +
113 SER* 1.3 70.1 + - - +
133 ARG* 3.0 4.9 + - + -
143 TYR* 2.9 46.3 + + + +
454 PHE* 4.1 0.8 - + - -
464 GLN* 3.3 35.9 + - - +
494 VAL* 3.8 17.5 - - + -
504 PRO* 3.5 39.5 - - + -
534 THR* 3.5 32.0 - - + +
50Y PRO* 4.9 12.1 - - + -
10Z TYR* 2.8 44.1 + + - -
11Z SER* 5.5 0.2 - - - -
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Residues in contact with SER 11 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 SER* 3.2 10.1 + - - -
103 TYR* 1.3 86.6 - - - +
123 GLN* 1.3 60.0 + - - +
143 TYR* 4.1 3.2 - - - +
153 ALA* 3.0 30.7 + - - +
43Y GLN* 5.1 8.5 - - - -
46Y GLN* 2.8 49.1 + - - +
47Y THR* 4.1 5.5 - - - -
50Y PRO* 4.8 0.5 - - - +
10Z TYR* 5.0 1.8 + - - -
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Residues in contact with GLN 12 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402 VAL* 5.2 2.0 - - - +
432 GLN* 5.3 9.3 - - + +
442 ASN* 2.9 34.4 + - - +
472 THR* 4.6 18.9 + - - +
482 ASN* 5.2 1.8 - - - +
73 SER 4.2 5.3 + - - +
83 ARG* 3.6 28.6 - - - +
93 SER* 2.8 39.1 + - - +
113 SER* 1.3 77.6 - - - +
133 ARG* 1.3 65.9 + - - +
153 ALA* 3.7 5.2 - - - +
163 LYS* 3.2 23.9 + - - +
207 T 4.5 3.4 + - - -
43Y GLN* 6.1 2.5 - - - +
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Residues in contact with ARG 13 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 ARG* 4.1 6.5 - - + +
93 SER 2.8 23.2 + - - +
103 TYR* 3.0 9.6 + - + +
123 GLN* 1.3 72.8 - - - +
143 TYR* 1.3 63.8 + - - +
163 LYS 3.7 0.2 + - - -
173 TRP* 3.1 22.6 + - - +
454 PHE* 4.6 7.2 - - + -
494 VAL* 3.7 21.0 + - - +
524 PHE* 4.6 4.8 - - - +
534 THR* 2.8 44.2 + - - +
564 ASN* 4.3 10.6 - - - +
197 A 3.4 54.5 + - + +
207 T 3.6 40.4 + - - -
3308 T 4.1 7.7 + - - -
3318 A 5.3 5.5 + - - -
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Residues in contact with TYR 14 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 TYR* 2.9 36.2 + + + +
113 SER* 4.1 3.1 - - - +
133 ARG* 1.3 76.3 - - - +
153 ALA* 1.3 68.7 + - - +
173 TRP* 3.1 16.4 + + - +
183 GLN* 2.7 58.1 + - + +
424 GLN* 3.7 9.0 + - - +
454 PHE* 3.4 35.7 - + + -
464 GLN* 2.9 36.2 + - + -
46Y GLN* 6.2 2.0 - - - -
10Z TYR* 5.5 1.6 - - - -
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Residues in contact with ALA 15 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402 VAL* 4.0 21.7 - - + +
113 SER 3.0 20.7 + - - +
123 GLN* 3.4 7.8 + - - +
143 TYR* 1.3 81.9 - - - +
163 LYS* 1.3 63.1 + - - +
183 GLN* 3.3 6.7 + - - +
193 ALA* 3.2 19.6 + - - +
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Residues in contact with LYS 16 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 VAL* 4.9 8.1 - - + -
402 VAL* 3.9 19.3 - - + -
442 ASN* 5.0 2.7 - - - +
83 ARG* 6.0 0.2 - - - +
123 GLN 3.2 13.2 + - - +
153 ALA* 1.3 77.2 - - - +
173 TRP* 1.3 66.9 + - - +
193 ALA* 3.1 4.4 + - - +
203 LYS* 3.0 25.1 + - + +
197 A 3.3 41.6 + - - +
207 T 4.3 15.0 + - - +
3218 A 3.8 37.2 + - - +
3228 T 2.8 36.1 + - - +
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Residues in contact with TRP 17 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 ARG 3.1 19.1 + - - +
143 TYR* 3.1 22.3 + + - +
163 LYS* 1.3 76.3 - - - +
183 GLN* 1.3 93.4 + - - +
203 LYS* 3.4 1.6 + - - +
213 PHE* 2.9 52.1 + + + +
414 ALA* 4.1 21.3 - - + -
424 GLN* 4.3 5.8 - - + -
454 PHE* 3.5 44.9 - + + -
177 A 5.3 0.2 - - - -
187 T 3.6 19.2 + - + +
197 A 3.5 28.4 - - - +
3328 T 2.9 37.6 + - + -
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Residues in contact with GLN 18 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143 TYR* 2.7 54.8 + - + +
153 ALA* 3.5 7.2 - - - +
173 TRP* 1.3 87.8 - - - +
193 ALA* 1.3 62.9 + - - +
213 PHE* 3.2 6.5 + - - +
223 ASN* 2.9 63.3 + - - +
424 GLN* 3.2 35.6 - - - +
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Residues in contact with ALA 19 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 ASN* 3.4 34.4 - - - +
372 VAL* 3.7 17.0 - - + -
402 VAL* 4.3 6.7 - - + -
153 ALA 3.2 9.0 + - - +
163 LYS* 3.1 9.7 + - - +
183 GLN* 1.3 80.1 - - - +
203 LYS* 1.3 58.8 + - - +
223 ASN* 3.5 9.4 + - - +
233 ALA* 3.1 26.7 + - - +
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Residues in contact with LYS 20 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332 ILE* 4.0 21.5 - - + -
372 VAL* 3.7 15.3 - - + -
163 LYS* 3.0 17.4 + - + +
173 TRP 3.9 2.9 - - - +
193 ALA* 1.3 73.7 - - - +
213 PHE* 1.3 66.7 + - - +
233 ALA* 3.3 4.0 + - - +
243 PHE* 3.0 23.7 + - - +
187 T 3.5 40.5 + - + +
197 A 3.1 30.7 + - - +
3228 T 2.8 31.8 + - - +
3238 A 3.2 26.9 + - - -
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Residues in contact with PHE 21 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173 TRP* 2.9 46.5 + + + +
183 GLN* 3.6 10.5 - - - +
203 LYS* 1.3 76.6 - - - +
223 ASN* 1.3 73.6 + - - +
243 PHE* 3.3 11.7 + + - +
253 SER* 3.1 23.3 + - - -
344 LEU* 4.1 31.2 - - + -
374 VAL* 4.6 4.3 - - + -
384 SER* 3.6 37.2 - - - -
414 ALA* 4.3 12.1 - - + -
177 A 6.1 3.8 - + - -
187 T 5.6 2.8 - - - +
3328 T 5.8 0.4 - - - -
3338 A 4.5 24.5 - - - -
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Residues in contact with ASN 22 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 ASN* 4.0 13.0 + - - +
183 GLN* 2.9 51.4 + - - +
193 ALA* 3.6 7.7 - - - +
213 PHE* 1.3 80.7 - - - +
233 ALA* 1.3 63.0 + - - +
253 SER* 2.6 25.6 + - - -
263 ASN* 3.6 3.3 + - - +
384 SER* 5.5 2.4 + - - -
424 GLN* 4.7 3.1 + - - -
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Residues in contact with ALA 23 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322 THR* 3.6 15.7 - - + +
332 ILE* 3.8 27.6 - - + -
362 ASN* 3.4 16.1 - - - +
193 ALA 3.1 12.9 + - - +
203 LYS* 3.5 11.0 - - - +
223 ASN* 1.3 78.1 - - - +
243 PHE* 1.3 64.6 + - - +
263 ASN* 3.1 22.0 + - - +
293 VAL* 3.5 10.0 - - - +
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Residues in contact with PHE 24 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203 LYS 3.0 15.9 + - - +
213 PHE* 3.3 12.8 + + - +
233 ALA* 1.3 76.9 - - - +
253 SER* 1.3 63.0 + - - +
263 ASN 3.0 1.4 + - - -
293 VAL* 4.0 5.6 - - - -
303 ALA* 3.3 45.3 + - + +
333 ILE* 4.3 14.4 - - + -
343 LEU* 4.0 22.2 - - + -
244 PHE* 4.4 9.4 - + - -
344 LEU* 3.4 31.4 - - + -
177 A 3.7 52.7 - - + -
187 T 4.6 8.5 - - - +
3338 A 6.3 0.2 - - - -
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Residues in contact with SER 25 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213 PHE* 3.1 15.5 + - - -
223 ASN* 2.6 23.4 + - - -
243 PHE* 1.3 76.5 - - - +
263 ASN* 1.3 61.6 + - - +
273 PRO* 3.2 4.5 - - - +
303 ALA* 5.0 0.4 - - - -
314 SER* 3.5 21.5 + - - +
344 LEU* 3.9 35.2 - - - -
354 SER* 4.6 5.8 - - - -
384 SER* 4.6 8.6 + - - -
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Residues in contact with ASN 26 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 THR* 4.9 3.4 - - - +
322 THR* 4.0 19.0 + - + +
223 ASN 3.6 2.2 + - - +
233 ALA 3.1 15.6 + - - +
243 PHE 3.0 0.6 + - - -
253 SER* 1.3 78.8 + - - +
273 PRO* 1.4 67.4 - - - +
283 THR* 2.7 32.0 + - - +
293 VAL* 2.7 33.8 + - + -
303 ALA* 2.9 12.2 + - - -
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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) + - + + + + + -
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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