Contacts of the helix formed by residues 363 - 371 (chain C) in PDB entry 3K6G
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 363 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338C LYS* 5.9 1.6 - - - -
361C ILE 3.8 1.5 + - - -
362C TRP* 1.3 75.4 - - - +
364C ARG* 1.3 65.0 + - - +
365C GLN* 3.6 7.6 + - - +
366C ASP* 2.6 38.6 + - - +
367C ASP* 3.1 24.0 + - - +
384C LYS* 4.7 2.2 + - - -
312F ASP* 3.3 24.7 - - - -
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Residues in contact with ARG 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C LYS* 5.7 1.0 - - - +
363C SER* 1.3 72.7 - - - +
365C GLN* 1.3 63.9 + - - +
367C ASP* 3.1 15.1 + - - +
368C ILE* 3.0 36.0 + - + +
397C ARG* 3.7 26.1 - - - +
300E ASP* 2.7 44.3 + - + +
302E GLU* 3.6 25.1 - - - +
303E ALA* 4.1 4.6 - - - +
309F ASP* 4.0 14.3 + - - -
310F GLN* 3.3 39.4 - - + +
312F ASP* 2.7 17.2 + - - +
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Residues in contact with GLN 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C SER* 3.3 7.9 + - - +
364C ARG* 1.3 79.4 - - - +
366C ASP* 1.3 58.7 + - - +
368C ILE* 3.3 22.3 + - - +
369C ASP* 2.9 66.7 + - - +
372C LYS* 4.2 6.1 - - - +
299E GLN* 5.6 7.1 - - - +
312F ASP* 5.2 1.0 + - - -
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Residues in contact with ASP 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C ILE 4.3 1.4 - - - +
362C TRP* 3.5 25.6 - - + -
363C SER* 2.6 35.4 + - - +
364C ARG 3.2 0.6 - - - -
365C GLN* 1.3 80.2 - - - +
367C ASP* 1.3 56.9 + - - +
369C ASP* 3.3 7.0 + - - +
370C LEU* 2.9 28.4 + - - +
381C LEU* 4.0 10.8 - - + +
384C LYS* 3.0 33.2 + - - +
385C PHE* 3.3 18.1 - - + -
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Residues in contact with ASP 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C LYS* 5.8 1.4 + - - +
362C TRP* 3.4 9.2 - - - +
363C SER 3.1 17.5 + - - +
364C ARG* 3.1 21.2 + - - +
366C ASP* 1.3 73.2 - - - +
368C ILE* 1.3 66.0 + - - +
370C LEU* 3.4 17.9 + - - +
371C GLN* 3.7 14.0 + - - +
393C ARG* 2.8 47.6 + - - +
397C ARG* 3.5 30.2 + - - +
309F ASP* 4.8 4.5 - - - +
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Residues in contact with ILE 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C ARG* 3.0 37.8 + - + +
365C GLN* 3.6 28.0 - - - +
367C ASP* 1.3 77.8 - - - +
369C ASP* 1.3 62.8 + - - +
371C GLN* 3.2 16.6 + - - +
372C LYS* 3.8 21.8 + - + +
299E GLN* 3.7 25.4 - - + +
300E ASP* 3.9 26.9 - - + +
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Residues in contact with ASP 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C GLN* 2.9 51.4 + - - +
366C ASP* 3.3 10.0 + - - +
368C ILE* 1.3 76.4 - - - +
370C LEU* 1.3 62.2 + - - +
372C LYS* 3.0 44.0 + - - +
377C THR* 3.4 25.9 - - + +
378C ARG* 5.6 0.5 + - - -
381C LEU* 3.8 11.5 - - + +
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Residues in contact with LEU 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C TRP* 4.4 7.2 - - + -
366C ASP 2.9 13.9 + - - +
367C ASP* 3.5 13.9 - - - +
368C ILE 3.2 0.6 - - - -
369C ASP* 1.3 77.3 - - - +
371C GLN* 1.3 75.4 + - - +
372C LYS 3.5 0.3 + - - -
378C ARG* 3.0 34.3 + - - +
381C LEU* 3.5 19.7 - - + +
390C VAL* 3.9 19.5 - - + -
393C ARG* 3.6 38.1 - - + +
394C ILE* 3.9 29.8 - - + +
397C ARG* 5.1 4.0 - - + -
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Residues in contact with GLN 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C ASP 3.8 11.5 + - - +
368C ILE* 3.2 9.3 + - - +
369C ASP 3.1 0.8 - - - -
370C LEU* 1.3 99.2 + - - +
372C LYS* 1.3 62.7 + - - +
373C ASP* 3.8 10.1 + - - +
378C ARG* 5.5 0.4 - - - -
394C ILE* 5.5 6.3 + - - +
397C ARG* 5.2 12.7 - - - +
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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