Contacts of the helix formed by residues 361 - 367 (chain N) in PDB entry 6CET
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 SER 361 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360N MET* 1.3 78.0 - - - +
362N TYR* 1.3 61.9 + - - +
363N HIS* 3.4 2.5 - - - -
364N GLU* 3.3 16.2 + - - +
365N LEU* 3.0 25.5 + - - +
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Residues in contact with TYR 362 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318M TYR* 5.8 14.6 - + - -
282N PHE* 6.1 2.7 - + - -
286N CYS* 6.1 2.1 - - + +
357N LYS* 3.5 24.7 + - + +
360N MET* 3.6 37.6 - - + -
361N SER* 1.3 76.9 - - - +
363N HIS* 1.3 87.9 + - + +
365N LEU* 3.2 9.7 + - - +
366N ASP* 2.9 40.9 + - - +
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Residues in contact with HIS 363 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282N PHE* 4.5 9.2 - - + -
357N LYS* 3.0 61.9 - - + +
358N THR* 3.5 3.6 + - - -
360N MET* 3.3 26.0 - - + -
361N SER 3.8 0.4 - - - -
362N TYR* 1.3 102.5 - - + +
364N GLU* 1.3 87.4 + - + +
366N ASP* 3.8 11.4 - - - -
367N GLU* 2.9 52.7 + - - +
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Residues in contact with GLU 364 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264N CYS* 5.2 8.7 - - - -
358N THR* 3.3 37.5 + - - +
360N MET 3.7 13.6 - - - +
361N SER* 3.3 16.9 + - - +
362N TYR 3.2 0.6 - - - -
363N HIS* 1.3 93.3 - - + +
365N LEU* 1.3 53.4 + - - +
367N GLU* 5.1 2.2 - - - -
368N ARG* 2.6 44.5 + - + +
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Residues in contact with LEU 365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379M ASN* 6.0 2.2 - - - +
361N SER* 3.0 12.7 + - - +
362N TYR* 3.3 9.9 - - - +
363N HIS 3.2 0.2 - - - -
364N GLU* 1.3 74.5 - - - +
366N ASP* 1.3 77.8 + - - +
367N GLU 3.0 2.1 + - - -
368N ARG* 4.5 2.2 - - - -
369N LEU* 3.1 27.6 + - + +
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Residues in contact with ASP 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316M LEU* 6.3 1.1 - - - -
318M TYR* 4.7 16.4 - - - -
379M ASN* 5.4 4.2 - - - +
407M HIS* 5.8 3.3 - - - -
282N PHE* 4.5 13.1 - - + -
362N TYR* 2.9 37.2 + - - +
363N HIS* 3.0 6.9 + - - +
365N LEU* 1.3 88.3 - - - +
367N GLU* 1.3 71.0 + - - +
369N LEU 4.0 9.0 - - - +
370N GLU 5.6 0.2 - - - +
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Residues in contact with GLU 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261N GLN* 5.7 1.6 - - - +
266N SER* 3.2 30.3 + - - +
279N ARG* 5.4 13.4 - - + -
282N PHE* 3.2 42.5 - - + -
283N GLN* 4.1 5.9 - - - +
363N HIS* 2.9 36.7 + - + +
364N GLU* 3.8 2.5 - - - -
366N ASP* 1.3 83.5 - - - +
368N ARG* 1.3 56.6 + - - +
369N LEU 3.5 1.6 - - - +
370N GLU* 3.3 25.1 - - + +
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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