Contacts of the helix formed by residues 371 - 384 (chain A) in PDB entry 1KEK
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 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A THR* 4.0 2.9 - - - -
369A GLU* 4.9 6.5 - - - -
370A PHE* 1.3 76.8 - - - +
372A PRO* 1.3 76.3 - - - +
373A ALA* 3.5 8.4 + - - +
374A MET* 2.9 45.5 + - - +
375A VAL* 3.0 10.4 + - - +
407A ASN* 4.9 4.1 + - - -
479A TYR* 4.3 7.6 - - - -
482A ASN* 4.6 13.7 - - - -
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Residues in contact with PRO 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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282A THR* 3.8 3.6 - - + -
285A GLU* 3.9 0.7 - - - +
286A VAL* 3.4 25.7 - - + +
371A SER* 1.3 88.9 - - - +
373A ALA* 1.3 56.0 + - - +
375A VAL* 3.1 3.6 + - + +
376A LYS 2.9 24.8 + - - -
409A PHE* 3.6 21.2 - - + -
410A ALA 5.0 1.6 - - - +
412A THR* 3.3 24.2 - - + +
479A TYR* 3.5 42.4 - - + +
482A ASN* 4.8 3.6 - - - +
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Residues in contact with ALA 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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371A SER* 3.2 6.0 + - - +
372A PRO* 1.3 77.1 - - - +
374A MET* 1.3 58.0 - - - +
376A LYS* 3.4 4.4 + - - +
377A SER* 3.0 26.7 + - - -
405A VAL* 3.7 17.2 - - + +
406A ASP 3.4 27.1 + - - +
407A ASN* 3.8 14.6 - - - +
409A PHE* 3.8 20.3 - - + -
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Residues in contact with MET 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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368A LYS* 5.3 1.6 - - + -
369A GLU* 3.0 42.0 - - + +
370A PHE* 3.7 15.3 - - + -
371A SER* 2.9 29.6 + - - +
373A ALA* 1.3 75.5 - - - +
375A VAL* 1.3 65.8 + - - +
377A SER* 3.2 9.8 - - - -
378A VAL* 3.0 26.3 + - - +
392A VAL* 4.0 13.3 - - + +
393A GLY* 3.6 28.5 - - - +
405A VAL* 4.0 23.3 - - + -
407A ASN* 6.0 1.1 - - - +
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Residues in contact with VAL 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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273A ILE* 4.4 3.1 - - + -
282A THR* 4.1 15.9 - - + -
283A ILE* 3.8 21.8 - - + -
286A VAL* 3.8 20.9 - - + -
370A PHE* 3.5 31.9 - - + -
371A SER 3.0 14.9 + - - +
372A PRO* 3.5 6.7 - - + +
374A MET* 1.3 77.7 - - - +
376A LYS* 1.3 61.5 + - - +
378A VAL* 3.1 8.3 + - - +
379A TYR* 3.0 45.4 + - + -
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Residues in contact with LYS 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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286A VAL* 4.6 2.9 - - - +
290A LEU* 3.9 20.2 - - + -
295A GLU* 4.3 16.2 - - - +
372A PRO 2.9 13.9 + - - +
373A ALA* 3.5 10.3 - - - +
375A VAL* 1.3 74.9 - - - +
377A SER* 1.3 58.7 + - - +
379A TYR* 3.1 7.1 + - + +
380A ASP* 2.8 62.0 + - - +
406A ASP* 6.5 1.3 - - + -
409A PHE* 3.9 38.8 - - + -
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Residues in contact with SER 377 (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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373A ALA 3.0 13.9 + - - -
374A MET* 3.2 14.8 - - - -
376A LYS* 1.3 77.8 - - - +
378A VAL* 1.3 56.6 + - - +
380A ASP* 3.7 8.4 - - - +
381A ASN* 2.8 31.4 + - - +
392A VAL* 4.5 6.1 - - - -
403A LEU* 3.9 13.4 - - - +
404A PRO* 2.5 30.6 + - - +
405A VAL* 4.0 7.8 - - - +
406A ASP 5.7 0.4 - - - -
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Residues in contact with VAL 378 (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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273A ILE* 3.5 28.5 - - + -
325A THR* 3.8 25.4 - - + +
327A LEU* 4.5 12.6 - - + -
370A PHE* 4.8 2.9 - - + -
374A MET 3.0 16.0 + - - +
375A VAL* 3.1 9.8 + - - +
377A SER* 1.3 80.2 - - - +
379A TYR* 1.3 64.5 + - - +
381A ASN* 3.6 4.0 + - - +
382A MET* 3.6 18.6 + - + +
390A PHE* 4.1 24.5 - - + -
392A VAL* 4.3 12.8 - - + -
403A LEU* 4.1 8.7 - - + -
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Residues in contact with TYR 379 (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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271A ARG* 2.9 48.6 + - + +
273A ILE* 3.4 31.4 - - + +
283A ILE* 3.6 3.1 - - - +
286A VAL* 5.0 1.1 - - + -
287A ILE* 3.3 21.2 - - + +
290A LEU* 4.7 9.0 - - + -
295A GLU* 5.0 3.6 - - - +
297A ILE* 3.7 39.3 - - + -
298A GLY 2.7 22.3 + - - -
375A VAL* 3.0 39.4 + - + -
376A LYS* 3.1 6.7 + - + +
378A VAL* 1.3 78.6 - - - +
380A ASP* 1.3 61.2 + - - +
382A MET* 3.2 26.6 + - + +
383A SER 3.5 2.3 + - - -
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Residues in contact with ASP 380 (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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271A ARG* 4.7 2.3 + - - +
295A GLU* 5.2 3.5 - - - +
376A LYS* 2.8 63.1 + - - +
377A SER* 3.7 7.3 + - - +
379A TYR* 1.3 68.4 - - - +
381A ASN* 1.3 59.5 + - - +
383A SER* 3.0 12.8 + - - -
384A GLY* 2.8 27.2 + - - -
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Residues in contact with ASN 381 (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 THR* 5.2 0.2 - - - +
359A LEU* 4.0 9.9 - - - +
377A SER 2.8 18.9 + - - +
378A VAL 3.6 7.7 + - - +
380A ASP* 1.3 77.0 - - - +
382A MET* 1.3 59.1 + - - +
384A GLY 3.3 4.8 + - - +
385A ALA* 4.1 8.1 - - - +
386A LYS* 2.8 30.2 + - - +
387A LYS* 2.9 51.0 + - - +
390A PHE* 3.9 17.4 - - - -
403A LEU* 4.0 20.3 - - + +
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Residues in contact with MET 382 (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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271A ARG* 3.7 18.3 - - + -
272A VAL 3.8 14.8 - - - +
273A ILE* 3.9 8.5 - - + -
323A VAL* 3.7 42.2 - - + +
325A THR* 3.0 41.5 - - + -
359A LEU* 4.2 2.9 - - + -
378A VAL 3.6 8.7 + - - +
379A TYR* 3.2 45.5 + - + +
381A ASN* 1.3 77.1 - - - +
383A SER* 1.3 59.2 + - - +
386A LYS* 3.0 29.3 + - - -
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 3.7 29.5 + - - +
379A TYR 3.5 1.4 + - - -
380A ASP* 3.0 15.7 + - - -
382A MET* 1.3 81.1 - - - +
384A GLY* 1.3 59.5 + - - +
386A LYS* 3.9 8.4 + - - +
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Residues in contact with GLY 384 (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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380A ASP 2.8 15.3 + - - -
381A ASN 3.3 1.0 + - - -
383A SER* 1.3 79.3 - - - +
385A ALA* 1.3 65.1 + - - -
386A LYS* 3.2 14.0 + - - +
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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