Contacts of the helix formed by residues 368 - 378 (chain F) in PDB entry 6O81
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 GLU 368 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F SER* 4.2 14.9 + - - +
337F GLY* 4.2 5.7 - - - -
338F CYS* 3.6 38.7 + - + +
362F ASP* 4.0 2.4 + - - +
363F SER 6.1 0.2 - - - +
366F TRP* 4.1 23.5 - - + +
367F LEU* 1.3 73.6 - - - +
369F GLY* 1.3 61.7 + - - +
370F ARG 3.2 3.1 - - - -
371F HIS* 3.0 46.7 + - + +
417F ARG* 3.3 48.0 + - - +
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Residues in contact with GLY 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337F GLY* 3.6 15.5 - - - -
360F VAL* 3.8 12.6 - - - +
362F ASP* 3.0 19.9 + - - -
368F GLU* 1.3 77.6 - - - +
370F ARG* 1.3 52.6 + - - +
371F HIS 3.1 0.2 - - - -
372F THR* 2.3 32.7 + - - -
373F LEU* 2.8 19.4 + - - +
385F TYR* 4.8 0.7 - - - -
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Residues in contact with ARG 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLU 5.5 0.2 + - - -
294C VAL 2.8 27.7 + - - -
295C LEU* 3.6 20.1 - - + +
296C PRO* 3.6 18.6 - - - +
299C GLU* 3.8 19.7 + - - +
302C ILE* 4.8 0.5 - - - +
362F ASP* 3.8 3.1 + - - -
367F LEU* 3.3 54.6 + - - +
369F GLY* 1.3 76.5 - - - +
371F HIS* 1.3 52.3 + - + +
373F LEU* 3.0 14.1 + - + +
374F ARG* 2.8 52.2 + - - +
385F TYR* 2.5 30.5 + - + +
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Residues in contact with HIS 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F SER* 5.7 4.3 + - - -
338F CYS* 4.3 16.6 - - - -
367F LEU 5.0 3.5 + - - -
368F GLU* 3.0 33.9 + - + +
370F ARG* 1.3 77.3 - - + +
372F THR* 1.3 60.5 + - - +
374F ARG* 3.0 39.6 + - - +
375F SER* 3.2 11.4 + - - -
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Residues in contact with THR 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F VAL* 5.4 4.5 - - - +
337F GLY 3.5 19.2 + - - +
338F CYS* 3.7 20.4 - - + -
339F SER 3.9 7.0 - - - +
342F VAL* 5.9 4.9 - - + -
343F SER* 3.3 21.5 - - - +
360F VAL* 4.0 9.8 - - - +
369F GLY* 2.3 32.3 + - - -
371F HIS* 1.3 73.4 - - - +
373F LEU* 1.3 56.5 + - - +
375F SER* 2.7 21.0 + - - -
376F LEU* 2.9 27.7 + - - +
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Residues in contact with LEU 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 4.0 11.0 - - + -
302C ILE* 3.8 23.1 - - + -
306C VAL* 4.0 14.4 - - + -
360F VAL* 3.8 24.1 - - + +
369F GLY 2.8 12.6 + - - +
370F ARG* 3.0 18.1 + - + +
372F THR* 1.3 74.9 + - - +
374F ARG* 1.3 61.4 + - - +
376F LEU* 3.0 14.5 + - - +
377F VAL* 3.0 23.1 + - + +
383F ALA* 3.7 29.4 - - + -
385F TYR* 3.7 32.8 - - + -
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Residues in contact with ARG 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C GLU* 2.8 42.9 + - - +
302C ILE* 4.3 19.3 - - + +
370F ARG* 2.8 27.6 + - - +
371F HIS* 3.0 39.3 + - - +
373F LEU* 1.3 73.4 - - - +
375F SER* 1.3 57.2 + - - +
377F VAL* 3.0 6.8 + - - +
378F HIS* 2.8 53.9 + - + -
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Residues in contact with SER 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F SER* 3.6 19.6 + - - -
347F GLN* 3.3 34.6 + - - +
371F HIS 3.2 3.4 + - - -
372F THR* 2.7 28.9 + - - -
374F ARG* 1.3 77.2 - - - +
376F LEU* 1.3 61.3 + - - +
378F HIS* 4.4 8.3 - - - +
379F ALA* 3.4 13.5 - - - +
381F VAL* 5.3 0.2 - - - +
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Residues in contact with LEU 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F SER* 5.1 7.0 - - - +
346F LEU* 3.8 28.3 - - + -
347F GLN* 6.0 0.7 - - + -
358F VAL* 3.7 34.1 - - + -
360F VAL* 3.7 23.8 - - + -
372F THR* 2.9 19.9 + - - +
373F LEU* 3.0 10.9 + - - +
375F SER* 1.3 85.9 - - - +
377F VAL* 1.3 58.5 + - - +
379F ALA 4.2 1.3 - - - -
381F VAL* 2.9 52.7 + - + +
383F ALA* 3.9 16.2 - - + -
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Residues in contact with VAL 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ASP* 4.7 8.7 - - - +
302C ILE* 3.7 50.3 - - + +
305C LYS* 4.6 27.4 - - + +
306C VAL* 5.5 1.1 - - + -
373F LEU* 3.0 22.6 + - + +
374F ARG 3.0 4.1 + - - +
376F LEU* 1.3 80.1 - - + +
378F HIS* 1.3 65.5 + - + +
379F ALA 3.2 1.6 - - - -
380F GLY* 3.2 13.6 + - - +
381F VAL 4.7 4.0 - - - +
383F ALA* 5.2 2.7 - - + -
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Residues in contact with HIS 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ASP* 5.1 10.3 + - - -
302C ILE* 4.7 9.5 - - + +
347F GLN* 5.8 2.0 - - - +
374F ARG* 2.8 43.2 + - + +
375F SER* 4.7 5.0 + - - -
377F VAL* 1.3 84.6 - - + +
379F ALA* 1.3 59.0 + - - +
380F GLY 3.8 0.2 + - - -
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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
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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