Contacts of the helix formed by residues 229 - 246 (chain 3) in PDB entry 3EXG
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 229 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 ILE* 3.8 10.4 - - - +
103 LYS 4.5 0.9 + - - -
2263 ASP* 3.4 23.0 + - - +
2283 MET* 1.3 79.0 - - - +
2303 ILE* 1.3 65.4 + - - +
2313 LEU* 2.6 26.7 + - - +
2323 CYS* 3.3 30.2 + - - -
2333 VAL* 3.4 14.3 + - - +
2903 LEU* 4.8 12.5 - - + +
2943 ARG* 2.7 42.7 + - - -
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Residues in contact with ILE 230 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353 TYR* 4.6 26.2 - - + -
393 MET* 4.3 17.9 - - + -
703 ALA* 3.8 15.0 - - - +
733 VAL* 3.8 15.9 - - + +
743 GLY* 3.5 33.7 - - - +
773 ALA* 5.6 0.7 - - + -
2283 MET 3.1 5.3 + - - -
2293 ASP* 1.3 74.5 - - - +
2313 LEU* 1.3 65.4 + - + +
2333 VAL* 3.5 3.5 + - - +
2343 ARG* 3.0 27.5 + - + +
2873 PRO 4.8 2.7 - - - +
2903 LEU* 6.4 0.2 - - + -
2913 LEU* 4.1 39.5 - - + +
2943 ARG* 5.3 1.1 - - - +
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Residues in contact with LEU 231 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73 PHE* 3.6 32.8 - - + -
93 ILE* 3.7 12.6 - - + +
253 THR* 4.2 9.6 - - + +
273 LEU* 3.9 22.4 - - + -
353 TYR* 5.0 4.5 - - + -
2293 ASP* 2.6 18.1 + - - +
2303 ILE* 1.3 85.1 - - + +
2323 CYS* 1.3 61.2 + - - +
2343 ARG* 3.8 31.8 + - - +
2353 GLU* 3.2 28.6 + - - +
2913 LEU* 5.3 2.0 - - + -
2943 ARG* 3.0 28.5 - - - +
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Residues in contact with CYS 232 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 ILE* 4.0 17.5 - - + -
103 LYS* 4.0 15.7 - - - +
123 CYS* 5.8 2.9 - - - -
2253 VAL* 3.5 21.3 - - + -
2263 ASP* 3.7 19.1 - - - +
2293 ASP* 3.3 33.0 + - - -
2313 LEU* 1.3 73.7 - - - +
2333 VAL* 1.3 59.6 + - - +
2353 GLU* 2.9 5.4 + - - -
2363 ALA* 2.5 36.8 + - + +
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Residues in contact with VAL 233 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703 ALA* 4.0 15.9 - - + +
713 CYS* 4.3 4.0 - - - +
743 GLY* 3.6 15.7 - - - -
753 LEU* 3.1 33.2 - - + +
2253 VAL* 4.6 7.6 - - + -
2263 ASP 3.9 11.9 - - - +
2273 GLY* 4.1 13.7 - - - -
2293 ASP 3.4 14.6 + - - +
2303 ILE 3.5 8.7 - - - +
2323 CYS* 1.3 76.5 - - - +
2343 ARG* 1.3 63.5 + - - +
2363 ALA* 4.0 1.8 - - - +
2373 THR* 2.8 30.0 + - - -
2533 MET* 5.0 0.2 - - - +
2553 LEU* 4.8 9.9 - - + -
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Residues in contact with ARG 234 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253 THR* 3.1 19.2 + - - +
263 VAL 2.9 29.7 + - - -
273 LEU* 4.3 4.2 - - - +
313 ASP* 4.4 10.5 + - - -
353 TYR* 3.2 35.7 + - - -
743 GLY* 3.4 10.9 + - - +
773 ALA* 3.4 23.3 - - + -
783 GLY 4.1 0.2 - - - +
2303 ILE* 3.0 19.6 + - + +
2313 LEU* 3.8 24.2 + - + +
2333 VAL* 1.3 76.4 - - - +
2353 GLU* 1.3 60.9 + - - +
2373 THR* 3.3 1.8 + - - -
2383 ARG* 2.9 75.3 + - - +
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Residues in contact with GLU 235 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 ILE* 3.6 24.9 - - + -
213 PRO* 4.3 9.5 - - + +
223 PRO* 3.3 24.7 - - + +
253 THR* 3.3 25.8 + - - +
2313 LEU 3.2 21.4 + - - +
2323 CYS* 2.9 5.9 + - - +
2343 ARG* 1.3 84.6 + - - +
2363 ALA* 1.3 66.2 + - - +
2373 THR 3.2 0.2 + - - -
2383 ARG* 3.3 22.3 + - - +
2393 PHE* 3.0 23.4 + - - +
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Residues in contact with ALA 236 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123 CYS* 4.7 0.9 - - - -
213 PRO* 4.2 16.4 - - + +
2233 LEU* 3.9 12.3 - - + -
2253 VAL* 3.6 33.4 - - + -
2323 CYS* 2.5 19.3 + - + +
2333 VAL* 4.2 2.5 - - - +
2353 GLU* 1.3 72.6 - - - +
2373 THR* 1.3 57.1 + - - +
2393 PHE* 3.3 4.8 + - - +
2403 ALA* 2.8 29.8 + - - +
2533 MET* 4.2 9.1 - - + +
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Residues in contact with THR 237 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753 LEU* 3.2 32.0 - - - +
783 GLY* 3.5 29.2 - - - +
793 ILE* 3.6 15.9 - - + -
1623 LEU* 4.6 8.3 - - + -
1903 ILE* 5.7 2.9 - - + -
2333 VAL 2.8 23.3 + - - -
2343 ARG 3.6 3.6 - - - -
2353 GLU 3.2 0.2 - - - -
2363 ALA* 1.3 75.5 - - - +
2383 ARG* 1.3 55.1 + - - +
2403 ALA* 2.9 4.4 + - - +
2413 ALA* 2.8 32.9 + - + +
2533 MET* 3.5 12.5 - - + +
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Residues in contact with ARG 238 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263 VAL 5.2 1.8 + - - -
353 TYR* 4.8 2.2 + - - -
773 ALA 3.2 18.7 + - - -
783 GLY* 3.3 26.5 - - - -
2343 ARG* 2.9 61.7 + - - +
2353 GLU* 3.8 17.7 + - - +
2373 THR* 1.3 74.7 - - - +
2393 PHE* 1.3 61.1 + - - +
2413 ALA* 4.2 2.3 - - - +
2423 ALA* 3.2 23.2 + - - +
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Residues in contact with PHE 239 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173 LEU* 4.2 15.5 - - + -
193 GLU* 4.0 14.6 - - - -
203 GLY* 3.5 32.1 - - - -
213 PRO* 3.7 32.5 - - + -
223 PRO* 5.4 3.6 - - + -
2233 LEU* 3.9 15.0 - - + -
2353 GLU 3.0 13.4 + - - +
2363 ALA 3.3 10.8 - - - +
2383 ARG* 1.3 76.9 - - - +
2403 ALA* 1.3 63.3 + - + +
2423 ALA* 3.3 7.6 + - + +
2433 TYR* 2.9 32.4 + + + +
2513 ILE* 4.2 18.4 - - + -
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Residues in contact with ALA 240 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1903 ILE* 4.2 21.5 - - + -
2233 LEU* 5.3 0.9 - - + -
2363 ALA 2.8 19.8 + - - +
2373 THR* 2.9 4.3 + - - +
2393 PHE* 1.3 80.1 - - + +
2413 ALA* 1.3 64.4 + - - +
2433 TYR* 2.9 9.1 + - - +
2443 CYS* 2.8 25.6 + - - +
2513 ILE* 4.2 18.4 - - + -
2533 MET* 4.4 10.8 - - + -
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Residues in contact with ALA 241 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783 GLY 4.0 13.2 - - - +
793 ILE* 4.6 5.8 - - + -
1603 VAL* 4.3 12.6 - - + -
1903 ILE* 4.0 11.2 - - + +
2373 THR 2.8 17.7 + - - +
2383 ARG 4.2 3.1 - - - +
2403 ALA* 1.3 72.8 - - - +
2423 ALA* 1.3 57.7 + - - +
2443 CYS* 3.9 1.4 - - - +
2453 ARG* 2.8 62.6 + - - +
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Residues in contact with ALA 242 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2383 ARG 3.2 18.4 + - - +
2393 PHE* 3.4 8.1 - - - +
2413 ALA* 1.3 76.3 - - - +
2433 TYR* 1.3 65.8 + - - +
2453 ARG* 3.3 7.4 + - - +
2463 SER* 3.0 23.8 + - - -
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Residues in contact with TYR 243 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173 LEU* 3.9 27.4 - - + -
2213 PRO* 3.3 24.6 - - + +
2393 PHE* 2.9 21.7 + + + +
2403 ALA* 2.9 12.2 + - - +
2423 ALA* 1.3 77.7 - - - +
2443 CYS* 1.3 64.8 + - - +
2463 SER* 2.8 24.6 + - - -
2483 LYS* 3.3 53.3 + - + +
2493 GLY 3.3 20.6 - - - -
2503 PRO 3.7 8.9 + - - -
2513 ILE* 4.5 15.0 - - + -
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Residues in contact with CYS 244 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1603 VAL* 3.7 21.3 - - + -
1883 PRO* 3.8 17.3 - - + +
1893 CYS 3.7 21.8 - - - -
1903 ILE* 3.7 21.1 - - - -
2403 ALA 2.8 11.3 + - - +
2413 ALA* 3.9 1.6 - - - +
2433 TYR* 1.3 74.9 - - - +
2453 ARG* 1.3 59.5 + - - +
2463 SER 3.1 1.6 - - - -
2473 GLY* 3.0 19.8 + - - -
2493 GLY 3.1 24.9 + - - +
2513 ILE* 3.9 15.9 - - - -
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Residues in contact with ARG 245 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783 GLY 4.8 1.4 + - - -
793 ILE* 4.7 3.2 - - - +
803 ASN* 3.1 28.0 + - - +
833 ASP* 3.0 33.7 + - - -
1583 ASP* 3.1 54.5 + - - +
1603 VAL* 3.7 12.4 - - + +
1883 PRO* 5.5 0.4 - - - -
2413 ALA* 2.8 44.7 + - - +
2423 ALA* 3.9 6.4 - - - +
2443 CYS* 1.3 68.6 - - - +
2463 SER* 1.3 59.6 + - - +
2473 GLY 3.0 6.1 + - - -
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Residues in contact with SER 246 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2423 ALA 3.0 12.9 + - - -
2433 TYR* 2.8 21.2 + - - -
2443 CYS 3.1 0.6 - - - -
2453 ARG* 1.3 76.2 - - - +
2473 GLY* 1.3 59.4 + - - +
2483 LYS* 3.2 26.0 + - - +
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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