Contacts of the helix formed by residues 374 - 386 (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 ASP 374 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372C LYS* 3.2 10.6 + - + +
373C ASP* 1.3 79.8 - - - +
375C GLU* 1.3 66.8 + - - +
376C ASP* 3.4 19.5 - - - +
377C THR* 2.8 41.2 + - - +
378C ARG* 3.0 21.8 + - - +
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Residues in contact with GLU 375 (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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374C ASP* 1.3 73.6 + - - +
376C ASP* 1.3 58.4 - - - +
378C ARG* 3.8 6.4 - - - +
379C GLU* 2.8 46.1 + - + +
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Residues in contact with ASP 376 (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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374C ASP* 3.2 18.3 + - - +
375C GLU* 1.3 78.9 - - - +
377C THR* 1.3 62.4 + - - +
379C GLU* 3.6 15.2 + - - +
380C ALA* 3.1 22.9 + - - +
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Residues in contact with THR 377 (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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369C ASP* 3.4 48.2 - - + +
372C LYS* 4.4 14.3 + - + +
374C ASP* 2.8 37.3 + - - +
376C ASP* 1.3 77.8 - - - +
378C ARG* 1.3 62.1 + - - +
380C ALA* 3.1 8.8 + - - +
381C LEU* 3.0 22.9 + - + +
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Residues in contact with ARG 378 (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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369C ASP 5.6 0.2 + - - -
370C LEU* 3.0 37.2 + - - +
371C GLN 5.5 0.2 - - - -
372C LYS 4.4 11.0 + - - +
374C ASP 3.0 13.9 + - - +
375C GLU* 3.4 8.5 + - - +
377C THR* 1.3 78.2 - - - +
379C GLU* 1.3 58.1 + - + +
381C LEU* 3.1 11.2 + - - +
382C VAL* 2.9 39.1 + - + +
390C VAL* 4.1 20.4 - - - +
394C ILE* 3.8 25.9 - - - +
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Residues in contact with GLU 379 (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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375C GLU* 2.8 31.4 + - + +
376C ASP* 4.0 18.2 - - - +
378C ARG* 1.3 77.9 - - + +
380C ALA* 1.3 57.7 + - - +
382C VAL* 3.3 10.4 + - - +
383C LYS* 3.0 35.3 + - + +
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Residues in contact with ALA 380 (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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376C ASP 3.1 14.6 + - - +
377C THR* 3.1 12.9 + - + +
379C GLU* 1.3 76.0 - - - +
381C LEU* 1.3 65.6 + - + +
383C LYS* 3.3 13.6 + - - +
384C LYS* 3.0 23.6 + - - +
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Residues in contact with LEU 381 (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* 4.2 3.8 - - + -
366C ASP* 4.0 24.0 - - - +
369C ASP* 3.8 16.2 - - + +
370C LEU* 3.5 45.3 - - + +
377C THR* 3.0 18.1 + - + +
378C ARG* 3.1 14.3 + - - +
380C ALA* 1.3 73.8 - - + +
382C VAL* 1.3 62.0 + - - +
384C LYS* 3.3 4.7 + - + +
385C PHE* 2.8 58.8 + - + +
390C VAL* 3.6 11.4 - - + +
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Residues in contact with VAL 382 (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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378C ARG* 2.9 32.2 + - + +
379C GLU* 3.6 10.3 - - - +
380C ALA 3.2 0.2 - - - -
381C LEU* 1.3 75.6 - - - +
383C LYS* 1.3 61.7 + - + +
386C GLY* 2.7 27.3 + - - +
387C ALA* 3.8 28.9 - - + +
390C VAL* 4.0 20.4 - - + -
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Residues in contact with LYS 383 (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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359C TYR* 4.5 7.8 - - - -
379C GLU* 3.0 19.0 + - + +
380C ALA* 3.5 14.6 - - - +
381C LEU 3.3 0.2 - - - -
382C VAL* 1.3 80.1 - - + +
384C LYS* 1.3 61.5 + - - +
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Residues in contact with LYS 384 (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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359C TYR* 3.1 15.6 - - - -
360C PRO* 3.4 27.9 - - + +
361C ILE 5.4 0.7 - - - -
363C SER* 4.7 2.0 + - - -
366C ASP* 3.0 34.4 + - - +
380C ALA 3.0 16.4 + - - +
381C LEU* 3.8 6.3 - - + +
383C LYS* 1.3 77.9 - - - +
385C PHE* 1.3 80.1 + - + +
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Residues in contact with PHE 385 (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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359C TYR* 3.3 15.7 - - + -
360C PRO* 3.4 35.0 - - + -
361C ILE 3.5 15.3 - - - -
362C TRP* 3.6 49.4 - + + -
366C ASP* 3.3 37.9 - - + -
381C LEU* 2.8 26.2 + - + +
384C LYS* 1.3 91.5 - - + +
386C GLY* 1.3 64.7 + - - +
389C ASN* 2.8 41.4 + - + +
390C VAL* 4.1 1.8 - - + -
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Residues in contact with GLY 386 (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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359C TYR* 3.5 23.5 - - - -
382C VAL* 2.7 26.2 + - - -
385C PHE* 1.3 77.3 - - - +
387C ALA* 1.3 65.1 + - - -
388C GLN* 3.3 3.7 + - - -
389C ASN 3.3 1.0 + - - -
390C VAL* 3.2 19.3 + - - +
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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