Contacts of the helix formed by residues 32 - 38 (chain 4) in PDB entry 1G6Q
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 ILE 32 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314 GLY* 1.4 70.8 - - - +
334 HIS* 1.3 63.3 + - + +
344 GLU* 3.1 7.3 - - - +
354 GLU* 2.9 47.1 + - - +
364 MET* 3.7 10.6 + - + -
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Residues in contact with HIS 33 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1863 TRP* 4.4 2.9 - - - -
1973 PHE* 4.6 12.3 - - + -
314 GLY 2.6 16.3 + - - +
324 ILE* 1.3 73.6 - - + +
344 GLU* 1.3 64.9 + - - +
364 MET* 3.4 21.6 + - + +
374 LEU* 3.1 24.9 + - - +
674 CYS 5.1 0.2 - - - -
684 GLY* 2.8 41.7 + - - -
694 THR* 3.9 15.1 - - + +
884 ASP* 5.1 3.8 - - - -
904 SER* 5.4 1.4 + - - -
924 ILE* 3.5 38.8 - - + +
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Residues in contact with GLU 34 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1783 TYR* 5.5 1.6 + - - -
1813 GLU* 3.0 29.2 - - - +
1823 LYS* 3.6 28.4 - - - +
1853 TYR* 3.9 18.9 + - + -
1863 TRP* 3.9 24.0 - - + -
2013 VAL* 6.1 0.3 - - - +
314 GLY 4.3 3.2 + - - +
324 ILE* 2.9 5.5 + - - +
334 HIS* 1.3 76.2 - - - +
354 GLU* 1.3 55.3 + - - +
364 MET 3.0 1.4 + - - -
374 LEU* 3.8 0.3 - - - -
384 GLN* 2.8 51.7 + - - +
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Residues in contact with GLU 35 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324 ILE* 2.9 31.8 + - + +
344 GLU* 1.3 73.6 - - - +
364 MET* 1.3 63.9 + - + +
384 GLN* 4.3 9.8 - - - +
394 ASP* 3.7 16.6 + - - +
1364 TYR* 4.6 9.9 + - - -
2814 TYR* 6.2 0.2 - - - +
2834 HIS* 4.1 30.9 - - + +
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Residues in contact with MET 36 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324 ILE* 3.7 11.6 + - + +
334 HIS* 3.4 30.2 + - + +
344 GLU 3.0 1.6 + - - -
354 GLU* 1.3 79.8 - - + +
374 LEU* 1.3 64.0 + - + +
394 ASP* 3.2 10.3 + - - +
424 ARG* 3.1 38.6 + - - +
684 GLY* 5.3 11.9 - - - +
1324 GLU* 4.0 28.7 - - + +
1434 MET* 5.0 15.9 - - + -
2834 HIS* 4.0 24.7 - - + -
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Residues in contact with LEU 37 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1853 TYR* 3.1 12.1 - - - +
1863 TRP* 3.6 20.6 - - + -
1893 VAL* 3.9 15.7 - - + -
1903 TYR* 2.9 20.6 - - + -
1943 TYR* 3.5 31.4 - - + -
334 HIS 3.1 13.7 + - - +
344 GLU 3.1 2.2 + - - +
364 MET* 1.3 74.3 - - + +
384 GLN* 1.3 55.9 + - - +
394 ASP 3.2 1.3 - - - -
424 ARG* 3.6 26.7 - - - +
434 THR* 2.8 17.8 + - + +
684 GLY 4.0 6.5 - - - +
694 THR* 3.4 21.1 - - + +
714 ILE* 3.8 13.0 - - + -
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Residues in contact with GLN 38 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813 GLU* 4.7 9.1 + - - +
1853 TYR* 3.1 16.5 + - + +
1903 TYR* 3.6 15.1 + - - +
344 GLU* 2.8 41.6 + - - +
354 GLU* 4.3 7.9 + - - +
374 LEU* 1.3 73.9 - - - +
394 ASP* 1.3 59.3 + - - +
404 THR* 2.8 15.0 + - - +
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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
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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