Contacts of the helix formed by residues 223 - 236 (chain U) in PDB entry 5GJQ
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 223 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445P LEU* 6.3 0.2 - - + -
449P GLU* 2.3 41.3 + - - +
453P HIS* 5.1 8.9 + - - -
211U TYR* 2.5 18.5 + - - +
221U PRO* 4.7 12.7 - - - +
222U ILE* 1.3 82.7 - - - +
224U HIS* 1.3 53.0 + - - +
225U GLN* 2.3 23.9 + - + -
226U ILE* 2.4 33.9 + - + +
227U ILE 3.5 2.4 + - - -
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Residues in contact with HIS 224 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214O GLY* 5.0 8.1 + - - -
215O GLU* 6.3 0.6 - - - -
218O MET* 4.7 25.3 - - + +
340O VAL* 4.8 17.1 - - + +
341O LEU 5.9 1.5 + - - -
222U ILE* 3.2 28.2 - - + +
223U ASN* 1.3 75.1 - - - +
225U GLN* 1.3 55.1 - - + +
226U ILE 3.4 0.2 - - - -
227U ILE* 4.1 13.5 - - - +
228U TYR* 1.7 60.6 + - + +
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Residues in contact with GLN 225 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445P LEU* 4.5 19.4 - - + +
223U ASN* 2.3 15.9 + - + +
224U HIS* 1.3 72.9 - - + +
226U ILE* 1.3 61.7 + - - +
228U TYR* 3.6 11.5 - - + +
229U GLN* 3.4 25.7 + - - +
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Residues in contact with ILE 226 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442P THR* 4.2 14.8 - - - +
445P LEU* 3.8 35.4 - - + -
446P ILE* 4.3 17.7 - - + +
449P GLU* 2.5 40.6 - - + +
211U TYR* 4.0 11.2 - - + +
212U LEU* 5.4 0.4 - - + -
223U ASN* 2.4 30.1 + - + +
225U GLN* 1.3 71.6 - - - +
227U ILE* 1.3 60.0 + - + +
229U GLN* 2.7 30.9 + - - +
230U LEU* 2.9 27.7 + - + +
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Residues in contact with ILE 227 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339O ARG 4.8 5.8 - - - +
340O VAL* 5.0 0.7 - - - -
341O LEU* 3.8 47.3 - - + +
342O ASP 6.1 0.2 - - - -
346O ILE* 5.4 13.9 - - + -
349O MET* 5.0 7.9 - - + -
212U LEU* 5.6 5.8 - - + -
215U VAL* 6.0 3.1 - - + -
222U ILE* 3.8 25.8 - - - +
223U ASN 3.5 1.2 + - - +
224U HIS* 4.2 14.1 - - - +
226U ILE* 1.3 79.8 - - + +
228U TYR* 1.3 63.7 + - + +
230U LEU* 3.0 17.3 + - + +
231U GLN* 3.0 34.4 + - + +
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Residues in contact with TYR 228 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338O PRO* 3.2 33.6 - - + +
339O ARG* 3.9 16.3 + - + +
340O VAL* 4.6 9.1 - - + +
224U HIS* 1.7 57.1 + - + +
225U GLN* 3.6 16.4 - - + +
227U ILE* 1.3 79.4 - - - +
229U GLN* 1.3 58.9 + - + +
231U GLN* 3.3 13.6 + - - +
232U ASP* 2.9 36.2 + - - +
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Residues in contact with GLN 229 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438P LEU* 4.6 19.8 - - + +
441P LYS* 4.0 25.2 - - - +
442P THR* 3.4 38.7 + - - +
445P LEU* 4.9 11.2 - - - +
225U GLN 3.4 16.3 + - - +
226U ILE* 2.7 19.5 + - - +
228U TYR* 1.3 75.5 - - + +
230U LEU* 1.3 58.2 + - - +
232U ASP* 3.3 12.9 + - - +
233U VAL* 2.9 32.4 + - - +
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Residues in contact with LEU 230 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349O MET* 4.9 21.5 - - + -
353O LEU* 5.4 5.8 - - + -
442P THR* 4.5 9.4 - - + +
208U ILE* 3.5 35.7 - - + -
212U LEU* 3.7 39.7 - - + -
226U ILE* 2.9 25.7 + - + +
227U ILE* 3.0 14.6 + - + +
229U GLN* 1.3 73.7 - - - +
231U GLN* 1.3 58.5 + - + +
233U VAL* 2.7 34.5 + - + +
234U PHE* 3.0 18.8 + - + -
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Residues in contact with GLN 231 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282O PHE* 5.2 16.0 - - + -
338O PRO* 2.8 38.9 - - + +
339O ARG 3.6 7.3 + - - +
340O VAL 3.9 21.4 + - - +
341O LEU* 3.9 19.6 - - - +
349O MET* 5.2 10.8 - - + -
227U ILE* 3.0 18.2 + - + +
228U TYR* 3.4 15.8 + - - +
230U LEU* 1.3 76.0 - - - +
232U ASP* 1.3 53.8 + - - +
234U PHE* 2.7 33.5 + - + +
235U ASN* 2.9 19.1 + - - +
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Residues in contact with ASP 232 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335O TRP* 5.4 3.7 - - - -
338O PRO* 2.9 28.5 - - - +
438P LEU* 3.5 22.0 - - + +
228U TYR* 2.9 17.8 + - - +
229U GLN* 3.5 14.5 - - - +
231U GLN* 1.3 74.1 - - - +
233U VAL* 1.3 60.6 + - - +
235U ASN* 3.9 13.0 + - - +
236U LEU* 3.3 29.2 + - + +
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Residues in contact with VAL 233 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353O LEU* 5.9 3.1 - - + -
356O TRP* 4.5 19.1 - - + -
435P LEU* 4.0 16.5 - - + +
438P LEU* 4.0 26.0 - - + +
439P VAL* 4.3 14.4 - - + -
442P THR* 5.6 1.6 - - + -
208U ILE* 6.3 1.1 - - + -
229U GLN 2.9 17.6 + - - +
230U LEU* 2.7 29.0 + - + +
232U ASP* 1.3 71.9 - - - +
234U PHE* 1.3 73.9 + - + +
236U LEU* 3.4 5.4 + - - +
237U LEU* 3.3 22.3 + - + +
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Residues in contact with PHE 234 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289O ARG* 6.3 0.2 - - - +
349O MET* 3.1 55.9 - - + -
352O ARG* 3.9 33.9 - - + -
353O LEU* 4.7 15.0 - - + -
356O TRP* 6.3 1.6 - + - -
230U LEU* 3.0 17.2 + - + -
231U GLN* 2.7 18.9 + - + +
233U VAL* 1.3 81.0 - - + +
235U ASN* 1.3 59.3 + - - +
236U LEU 3.0 1.8 - - - -
237U LEU* 2.8 52.3 + - + +
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Residues in contact with ASN 235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289O ARG* 3.2 36.7 + - - +
334O THR 4.8 3.6 - - - +
335O TRP* 3.9 28.8 - - + +
336O VAL 2.9 27.7 + - - -
338O PRO* 4.4 5.9 - - - +
231U GLN* 2.9 24.5 + - - +
232U ASP* 4.0 15.9 + - - +
234U PHE* 1.3 78.9 - - - +
236U LEU* 1.3 63.1 + - + +
237U LEU 3.7 2.5 + - - +
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Residues in contact with LEU 236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335O TRP* 5.7 9.0 - - + +
431P LYS* 3.9 34.5 - - + +
434P SER* 3.8 12.3 - - - -
435P LEU* 3.4 47.9 - - + +
438P LEU* 3.6 15.5 - - + -
232U ASP 3.3 17.5 + - - +
233U VAL 3.8 5.6 - - - +
234U PHE 3.0 1.0 - - - -
235U ASN* 1.3 81.7 - - + +
237U LEU* 1.3 64.1 - - - +
238U PRO* 3.1 8.4 - - - +
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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