Contacts of the helix formed by residues 362 - 368 (chain R) in PDB entry 6XOX
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 362 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317R ILE* 5.8 0.7 - - - -
320R ASN* 4.4 3.1 + - - -
321R PHE* 3.5 36.1 - - + +
324R PHE* 3.7 37.1 - - + +
357R ILE* 3.3 16.6 + - + -
360R LEU* 3.3 24.0 + - - +
361R GLY* 1.3 71.0 - - - +
363R HIS* 1.3 58.9 + - - +
364R GLU 3.1 0.2 - - - -
365R VAL* 3.0 34.6 + - + +
366R ILE* 4.4 1.2 + - - +
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Residues in contact with HIS 363 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357R ILE* 4.0 22.5 + - + +
358R PRO* 5.3 1.8 - - - +
361R GLY* 3.6 9.2 - - - -
362R THR* 1.3 77.7 - - - +
364R GLU* 1.3 83.4 + - + +
365R VAL 3.1 0.2 - - - -
366R ILE* 3.0 39.0 + - + +
367R PHE* 4.1 8.2 - + - -
390R PHE* 3.5 47.3 - + + +
391R THR* 4.0 8.1 + - - -
394R GLN* 3.2 37.0 + - + -
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Residues in contact with GLU 364 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R ARG* 4.8 0.2 + - - -
241R TYR* 2.7 47.4 + - - -
310R ARG* 5.6 2.4 + - - -
317R ILE* 3.3 22.9 - - + +
361R GLY* 3.8 9.9 - - - +
362R THR 3.1 1.2 - - - -
363R HIS* 1.3 98.6 + - + +
365R VAL* 1.3 53.8 + - - +
366R ILE 3.1 0.4 - - - -
367R PHE* 3.1 32.7 + - + -
368R ALA* 2.6 36.8 + - - +
391R THR* 3.8 13.9 + - - +
394R GLN* 4.6 2.4 - - - +
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Residues in contact with VAL 365 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317R ILE* 3.7 19.7 - - + +
318R GLY* 5.6 0.7 - - - -
321R PHE* 3.7 52.7 - - + -
362R THR* 3.0 20.6 + - + +
364R GLU* 1.3 78.4 - - - +
366R ILE* 1.3 63.0 + - + +
367R PHE 3.1 0.7 + - - -
368R ALA* 3.3 16.4 + - + +
369R PHE* 3.4 15.4 - - - -
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Residues in contact with ILE 366 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362R THR 5.3 0.9 - - - +
363R HIS* 3.0 26.1 + - + +
365R VAL* 1.3 80.1 - - + +
367R PHE* 1.3 71.2 + - + +
369R PHE* 3.2 24.8 - - + -
383R LYS* 6.5 0.9 - - + -
386R THR* 5.7 4.9 - - - +
390R PHE* 6.1 8.5 - - + -
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Residues in contact with PHE 367 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310R ARG* 5.2 15.0 + - - -
363R HIS* 4.1 11.0 - + - -
364R GLU* 3.1 47.1 + - + -
366R ILE* 1.3 96.7 - - + +
368R ALA* 1.3 61.9 + - - +
369R PHE* 3.2 18.9 - - - +
370R VAL* 5.2 2.3 - - - +
383R LYS* 4.5 24.6 + - + +
387R GLU* 3.3 57.2 - - + -
390R PHE* 5.9 1.6 - + - -
391R THR* 4.6 1.8 - - - -
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Residues in contact with ALA 368 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310R ARG* 5.6 4.9 + - - +
314R LEU* 3.6 36.1 - - + +
317R ILE* 4.1 15.0 - - + -
364R GLU 2.6 19.8 + - - +
365R VAL* 3.3 17.3 + - + +
367R PHE* 1.3 71.8 - - - +
369R PHE* 1.3 64.7 + - + +
370R VAL* 3.4 10.0 + - - +
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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