Contacts of the helix formed by residues 366 - 376 (chain A) in PDB entry 5K9S
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 ARG 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A ASP* 3.5 43.1 + - + +
326A GLU* 3.6 19.6 + - - +
329A GLN* 3.1 36.8 + - - +
365A GLY* 1.3 76.2 - - - +
367A GLN* 1.3 61.3 + - - +
368A ASP* 3.0 33.0 + - - +
369A GLN* 2.9 31.3 + - - +
370A ILE* 2.9 12.3 + - - +
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A GLY 3.8 0.2 + - - -
366A ARG* 1.3 73.4 - - - +
368A ASP* 1.3 57.8 + - - +
370A ILE* 3.3 8.6 + - - +
371A GLN* 3.0 22.0 + - - +
407A GLY 3.1 27.6 + - - +
408A GLY 4.1 6.7 + - - -
409A THR* 3.3 35.0 - - + +
412A GLN* 3.1 14.4 + - - +
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Residues in contact with ASP 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLN* 3.7 9.2 - - - +
366A ARG* 3.0 39.7 + - - +
367A GLN* 1.3 78.5 - - - +
369A GLN* 1.3 72.0 + - - +
371A GLN* 3.3 9.7 + - - +
372A GLN* 3.2 31.0 + - - +
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Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ASP* 3.0 33.4 + - - +
328A THR* 4.1 9.8 - - - +
329A GLN* 2.9 41.0 + - - +
332A ILE* 4.0 17.8 - - + +
362A ILE* 4.7 10.2 - - + +
365A GLY* 3.6 8.0 - - - -
366A ARG* 2.9 37.2 + - + +
368A ASP* 1.3 82.7 - - - +
370A ILE* 1.3 65.1 + - - +
371A GLN 3.1 0.9 - - - -
372A GLN* 3.2 17.6 + - - +
373A VAL* 3.2 17.8 + - - +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ILE 4.8 0.8 + - - +
363A THR* 3.6 37.5 - - - +
365A GLY 4.3 6.1 - - - +
366A ARG 2.9 15.4 + - - +
367A GLN* 3.6 9.0 - - - +
369A GLN* 1.3 75.7 - - - +
371A GLN* 1.3 61.5 + - - +
373A VAL* 3.1 12.4 + - - +
374A VAL* 3.0 19.2 + - - +
404A TYR* 3.7 35.0 - - + +
407A GLY* 3.7 32.3 - - - +
408A GLY* 3.8 5.6 - - - +
412A GLN* 3.6 22.4 - - + +
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Residues in contact with GLN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A GLN 3.0 13.3 + - - +
368A ASP* 3.4 14.6 - - - +
369A GLN 3.1 0.4 - - - -
370A ILE* 1.3 78.3 - - - +
372A GLN* 1.3 57.2 + - + +
374A VAL* 3.1 19.4 + - - +
375A ASN* 2.8 65.6 + - - +
412A GLN* 3.0 28.1 + - - +
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLN* 3.1 31.2 + - - +
332A ILE* 3.4 21.6 + - + +
333A ASP* 5.6 0.6 + - - -
337A LEU* 3.8 13.8 - - + +
368A ASP* 3.2 20.1 - - - +
369A GLN* 3.2 7.6 + - - +
371A GLN* 1.3 74.5 - - + +
373A VAL* 1.3 60.0 - - - +
375A ASN* 4.1 11.7 - - - +
376A HIS* 2.9 48.2 + - - +
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LEU* 4.4 9.9 - - + -
359A MET* 3.8 26.9 - - + -
362A ILE* 3.7 25.8 - - + -
363A THR* 4.5 14.6 - - + -
369A GLN 3.2 14.6 + - - +
370A ILE* 3.1 13.9 + - + +
372A GLN* 1.3 77.7 - - - +
374A VAL* 1.3 61.4 + - - +
376A HIS* 3.6 0.7 + - - -
377A GLY 3.6 2.3 + - - -
378A LEU* 3.2 36.5 + - + +
379A VAL* 4.3 13.1 + - + +
382A LEU* 4.8 4.5 - - + -
404A TYR* 5.2 4.0 - - + -
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ILE 3.0 14.8 + - - +
371A GLN* 3.1 27.1 + - - +
373A VAL* 1.3 77.7 - - - +
375A ASN* 1.3 58.8 + - - +
377A GLY* 2.9 21.1 + - - -
379A VAL* 4.2 11.7 - - + -
404A TYR* 3.4 28.0 - - + +
412A GLN* 4.5 9.6 - - + -
415A TYR* 3.8 34.5 + - + -
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Residues in contact with ASN 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A GLN* 2.8 55.7 + - - +
372A GLN* 4.1 11.0 - - - +
373A VAL 3.4 0.2 - - - -
374A VAL* 1.3 75.8 - - - +
376A HIS* 1.3 63.7 + - + +
377A GLY* 3.1 3.5 + - - -
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Residues in contact with HIS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ILE* 5.4 4.2 + - + -
335A GLY* 5.6 5.3 + - - -
337A LEU* 3.5 38.9 + - + +
338A ALA* 3.8 22.0 + - + +
341A PRO* 5.0 5.5 - - - +
372A GLN* 2.9 44.5 + - + +
373A VAL 4.2 3.4 - - - +
374A VAL 3.3 0.2 - - - -
375A ASN* 1.3 79.5 - - + +
377A GLY* 1.3 62.0 + - - +
378A LEU* 3.3 15.2 + - + +
381A PHE* 5.6 0.3 - - - -
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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