Contacts of the helix formed by residues 383 - 390 (chain F) in PDB entry 6M17
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 383 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379F CYS* 4.4 3.6 - - - -
382F VAL* 1.3 88.8 - - - +
384F PRO* 1.3 77.5 - - - +
385F THR* 3.4 1.6 + - - +
386F LYS* 2.3 43.8 + - - +
387F LEU* 4.0 1.4 - - - +
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Residues in contact with PRO 384 (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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365F TYR* 5.4 1.2 - - - +
369F TYR* 3.3 51.4 - - + +
377F PHE* 4.0 15.0 - - + +
379F CYS* 4.0 19.3 - - + +
382F VAL 3.6 0.2 - - - -
383F SER* 1.3 93.7 - - - +
385F THR* 1.3 62.8 + - + +
387F LEU* 3.1 32.7 + - + +
388F ASN 4.9 0.2 + - - -
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Residues in contact with THR 385 (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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369F TYR* 3.5 28.5 - - + +
383F SER* 5.2 0.7 - - - +
384F PRO* 1.3 77.1 - - + +
386F LYS* 1.3 96.7 + - - +
387F LEU 3.3 2.2 + - - -
388F ASN* 4.3 4.5 + - - +
389F ASP* 3.3 12.3 - - - +
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Residues in contact with LYS 386 (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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382F VAL* 4.6 10.6 - - + +
383F SER* 2.3 45.7 + - - +
384F PRO 3.2 1.4 - - - -
385F THR* 1.3 103.1 + - - +
387F LEU* 1.3 65.2 + - - +
389F ASP* 3.4 20.1 + - + +
390F LEU* 4.0 16.6 + - + +
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Residues in contact with LEU 387 (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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365F TYR* 3.5 47.9 - - + +
369F TYR* 6.2 0.7 - - + -
377F PHE* 5.0 7.2 - - + -
379F CYS* 4.1 13.2 - - - -
382F VAL* 3.8 36.1 - - + +
383F SER 4.0 0.7 - - - +
384F PRO* 3.1 34.6 + - + +
385F THR 3.3 0.2 - - - -
386F LYS* 1.3 74.4 - - - +
388F ASN* 1.3 58.0 + - - +
389F ASP 2.9 11.3 + - - -
390F LEU* 3.4 18.2 + - + +
392F PHE* 5.3 8.4 - - + -
432F CYS* 4.2 4.7 - - - -
515F PHE* 4.0 19.7 - - + -
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Residues in contact with ASN 388 (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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363F ALA 2.9 26.0 - - - +
364F ASP* 3.4 9.1 - - - +
365F TYR* 3.5 9.8 + - + +
366F SER* 3.3 39.3 - - - +
384F PRO 4.9 0.2 + - - -
385F THR 4.3 4.3 + - - +
387F LEU* 1.3 75.2 - - - +
389F ASP* 1.3 70.2 + - - +
390F LEU 3.8 0.7 - - - -
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Residues in contact with ASP 389 (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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385F THR 3.3 16.5 - - - +
386F LYS* 3.4 16.7 - - + +
387F LEU 3.0 0.8 - - - -
388F ASN* 1.3 93.8 + - - +
390F LEU* 1.3 64.6 + - - +
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Residues in contact with LEU 390 (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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365F TYR* 5.7 1.9 - - - -
382F VAL* 5.1 12.6 - - + -
386F LYS* 4.1 14.4 - - + +
387F LEU* 3.4 10.6 + - - +
388F ASN 5.3 0.2 - - - -
389F ASP* 1.3 82.1 + - - +
391F CYS* 1.3 90.3 + - - +
392F PHE* 3.8 37.4 - - + -
517F LEU* 6.1 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