Contacts of the helix formed by residues 28 - 35 (chain 1) in PDB entry 6Q8O
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 THR 28 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 GLY* 2.4 38.2 + - - +
261 SER 3.9 1.7 - - - +
271 TRP* 1.3 87.6 - - + +
291 LEU* 1.3 65.9 + - - +
301 ASP* 4.1 10.1 - - - +
311 TYR* 2.8 31.2 + - - +
321 TYR* 3.4 4.2 + - - +
341 ARG* 5.6 1.4 + - - -
1121 HIS* 5.3 0.4 - - - -
1511 GLU* 5.7 2.0 - - - -
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Residues in contact with LEU 29 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 TRP 3.3 4.6 + - - -
281 THR* 1.3 70.6 - - - +
301 ASP* 1.3 60.2 + - - +
321 TYR* 3.2 4.8 + - + +
331 LEU* 2.9 37.5 + - + +
381 TYR* 3.4 35.4 - - + -
1121 HIS* 3.5 37.2 + - + +
1511 GLU* 5.0 16.8 + - + +
1521 ALA* 5.2 7.4 - - + +
1551 ARG* 3.3 40.8 - - - +
1571 TYR* 4.5 17.0 - - + -
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Residues in contact with ASP 30 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281 THR* 3.0 9.0 - - - +
291 LEU* 1.3 77.7 + - - +
311 TYR* 1.3 59.8 - - - +
331 LEU* 3.1 15.7 + - + +
341 ARG* 2.9 43.1 + - - +
1551 ARG* 3.2 32.3 + - - -
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Residues in contact with TYR 31 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 HIS* 3.4 34.9 - + + +
231 LYS* 3.1 42.8 - - + +
241 GLU 4.9 3.4 - - - -
251 GLY 3.2 16.6 - - - +
261 SER* 3.6 14.4 - - - -
281 THR* 2.8 26.9 + - - +
301 ASP* 1.3 77.2 - - - +
321 TYR* 1.3 63.5 + - - +
341 ARG* 3.1 32.4 + - - +
351 HIS* 2.8 55.5 + + - -
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Residues in contact with TYR 32 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 HIS* 4.3 23.6 - + - -
261 SER 4.8 4.5 + - - +
281 THR 3.4 3.6 + - - +
291 LEU* 3.2 11.1 + - + +
311 TYR* 1.3 84.5 - - + +
331 LEU* 1.3 57.7 + - - +
351 HIS* 3.5 8.1 + - - -
361 GLY 3.7 0.5 + - - -
371 GLY* 2.9 47.0 + - - -
381 TYR* 3.5 34.1 - + - -
1101 VAL* 5.2 7.6 - - + -
1121 HIS* 3.6 21.1 - - + -
1131 LEU* 3.7 36.2 - - + +
1161 GLU* 2.2 31.6 + - - -
2281 VAL* 4.3 2.9 - - - +
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Residues in contact with LEU 33 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291 LEU* 2.9 25.7 + - + +
301 ASP* 3.2 24.7 - - - +
311 TYR 3.0 0.4 - - - -
321 TYR* 1.3 72.8 - - - +
341 ARG* 1.3 62.9 + - + +
351 HIS 3.0 6.0 + - - -
361 GLY* 3.1 13.2 + - - -
371 GLY 3.9 10.4 + - - +
381 TYR* 4.2 25.8 - - + -
1551 ARG* 4.1 19.3 - - - +
1571 TYR* 5.1 15.7 - - + +
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Residues in contact with ARG 34 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281 THR* 5.6 1.0 + - - -
301 ASP* 2.9 23.0 + - - +
311 TYR* 3.1 36.9 + - - +
331 LEU* 1.3 75.7 - - + +
351 HIS* 1.3 69.1 + - + +
361 GLY 3.4 0.8 + - - -
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Residues in contact with HIS 35 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 HIS* 3.1 40.7 + + + +
311 TYR* 2.8 65.9 + + - +
321 TYR 3.5 2.9 + - - +
331 LEU 3.0 1.4 + - - -
341 ARG* 1.3 91.1 - - + +
361 GLY* 1.3 59.6 + - - +
371 GLY 3.6 1.1 - - - -
2321 GLU* 5.3 1.0 - - - +
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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
------------------------------------------------------------
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