Contacts of the helix formed by residues 385 - 396 (chain C) in PDB entry 1KHU
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 ASN 385 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338C TYR* 3.4 30.3 + - - -
341C GLY* 2.7 31.5 + - - +
343C VAL* 5.5 0.2 - - - +
383C PHE* 3.5 25.5 - - + -
384C ASN* 1.3 70.5 - - - +
386C GLN* 1.3 61.9 + - - +
388C PHE* 2.8 3.6 + - - +
389C ALA* 2.5 38.8 + - - +
443C PRO* 4.7 3.8 - - - +
446C TRP* 3.2 37.2 - - + -
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Residues in contact with GLN 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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341C GLY* 5.4 1.1 - - - +
384C ASN* 3.2 13.3 + - - +
385C ASN* 1.3 84.9 + - - +
387C GLU* 1.3 74.9 + - - +
389C ALA* 3.4 7.6 + - - +
390C GLN* 3.1 31.0 + - - +
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Residues in contact with GLU 387 (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 ASN* 4.4 10.2 + - - +
363C HIS* 3.3 43.5 + - - +
384C ASN* 2.6 50.2 - - - +
386C GLN* 1.3 81.8 - - - +
388C PHE* 1.3 60.4 + - - +
390C GLN* 3.2 14.0 - - - +
391C LEU* 2.9 35.1 + - + +
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Residues in contact with PHE 388 (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 ASN* 4.1 6.5 + - - +
383C PHE* 3.8 15.7 - + + -
384C ASN 3.3 3.9 + - - +
385C ASN* 2.8 16.7 + - - +
387C GLU* 1.3 74.9 - - - +
389C ALA* 1.3 62.4 + - - +
390C GLN 3.0 1.3 - - - -
391C LEU* 3.0 7.7 + - + +
392C LEU* 2.8 42.0 + - + +
406C LEU* 3.8 22.4 - - + -
409C MET* 3.7 42.0 - - + -
410C CYS* 3.8 19.1 - - - -
443C PRO* 3.5 28.7 - - + -
446C TRP* 3.9 18.8 - + - -
447C LEU* 4.4 11.0 - - + -
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Residues in contact with ALA 389 (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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385C ASN 2.5 19.1 + - - +
386C GLN* 3.6 9.6 - - - +
388C PHE* 1.3 77.5 - - - +
390C GLN* 1.3 58.2 + - - +
392C LEU* 3.2 12.4 + - - +
393C ALA* 2.9 29.2 + - - +
446C TRP* 5.1 9.6 - - + -
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Residues in contact with GLN 390 (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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386C GLN* 3.1 27.4 + - - +
387C GLU* 3.2 15.8 - - - +
389C ALA* 1.3 80.1 - - - +
391C LEU* 1.3 65.5 + - + +
393C ALA* 3.2 8.7 + - + +
394C GLN* 3.0 51.0 + - + +
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Residues in contact with LEU 391 (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 TYR* 3.8 50.0 - - + +
387C GLU* 2.9 25.0 + - + +
388C PHE* 3.4 12.8 - - + +
390C GLN* 1.3 80.7 - - + +
392C LEU* 1.3 53.9 + - - +
394C GLN* 3.4 21.8 + - + +
395C SER* 2.7 31.5 + - - -
406C LEU* 4.1 23.5 - - + +
409C MET* 4.8 13.2 - - + -
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Residues in contact with LEU 392 (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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388C PHE* 2.8 22.0 + - + +
389C ALA* 3.4 13.0 - - - +
391C LEU* 1.3 78.0 - - - +
393C ALA* 1.3 58.8 + - - +
395C SER* 2.9 16.3 + - - -
396C VAL* 3.0 13.0 + - - +
403C VAL* 4.2 8.1 - - + -
406C LEU* 3.7 13.9 - - + +
446C TRP* 3.8 38.4 - - + +
447C LEU* 3.5 32.5 - - + +
450C VAL* 4.0 23.4 - - + +
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Residues in contact with ALA 393 (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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389C ALA 2.9 13.2 + - - +
390C GLN* 3.2 11.2 + - - +
392C LEU* 1.3 78.3 - - - +
394C GLN* 1.3 56.3 + - + +
396C VAL* 2.7 40.8 + - + +
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Residues in contact with GLN 394 (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 TYR* 4.9 7.2 + - - -
390C GLN* 3.0 52.1 + - + +
391C LEU* 3.4 20.5 + - + +
393C ALA* 1.3 75.7 - - + +
395C SER* 1.3 58.2 + - - +
396C VAL* 3.4 0.7 - - - -
397C ASN* 4.6 7.4 - - - +
398C HIS* 4.5 10.0 + - - +
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Residues in contact with SER 395 (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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391C LEU 2.7 18.6 + - - -
392C LEU* 2.9 9.6 + - - +
394C GLN* 1.3 74.4 - - - +
396C VAL* 1.3 54.1 + - - +
397C ASN* 2.5 19.4 + - - -
398C HIS* 3.3 18.8 + - - +
399C GLY 4.3 8.3 - - - +
402C THR* 4.3 17.0 - - - -
403C VAL* 4.5 12.2 - - - +
406C LEU* 3.3 19.7 - - - +
454C MET* 4.4 2.4 - - - +
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Residues in contact with VAL 396 (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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392C LEU 3.0 10.4 + - - +
393C ALA* 2.7 29.6 + - + +
394C GLN 4.7 0.4 - - - -
395C SER* 1.3 75.9 - - - +
397C ASN* 1.3 85.0 + - - +
450C VAL* 4.8 15.3 - - + -
454C MET* 3.3 28.1 - - + +
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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