Contacts of the helix formed by residues 371 - 384 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B THR* 4.0 3.6 - - - -
369B GLU* 4.9 7.2 - - - -
370B PHE* 1.3 76.4 - - - +
372B PRO* 1.3 76.1 - - - +
373B ALA* 3.6 9.6 + - - +
374B MET* 3.0 44.1 + - - +
375B VAL* 3.1 12.0 + - - +
405B VAL* 5.1 0.5 - - - +
407B ASN* 5.2 2.4 + - - -
479B TYR* 4.1 9.0 - - - -
482B ASN* 4.6 11.4 - - - -
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Residues in contact with PRO 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 3.9 3.3 - - + -
285B GLU* 4.1 0.4 - - - +
286B VAL* 3.6 17.6 - - + +
371B SER* 1.3 90.4 - - - +
373B ALA* 1.3 61.5 + - - +
375B VAL* 3.2 4.1 + - + +
376B LYS* 3.0 23.4 + - - +
409B PHE* 3.5 17.3 - - + -
410B ALA 4.9 2.7 - - - +
412B THR* 3.4 25.1 - - + +
479B TYR* 3.4 46.2 - - + +
482B ASN* 4.6 4.3 - - - +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B SER* 3.2 7.4 + - - +
372B PRO* 1.3 79.8 - - - +
374B MET* 1.3 57.5 + - - +
376B LYS* 3.4 4.0 + - - +
377B SER* 3.0 26.3 + - - -
405B VAL* 3.6 18.0 - - + +
406B ASP 3.4 26.9 + - - +
407B ASN* 4.0 12.1 - - - +
409B PHE* 3.7 18.7 - - + -
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Residues in contact with MET 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B LYS* 5.3 1.8 - - + -
369B GLU* 3.1 41.5 - - + +
370B PHE* 3.6 23.6 - - + -
371B SER* 3.0 22.5 + - - +
373B ALA* 1.3 73.7 - - - +
375B VAL* 1.3 65.5 + - - +
377B SER* 3.1 10.5 + - - -
378B VAL* 3.0 27.0 + - - +
392B VAL* 4.0 16.6 - - + +
393B GLY* 3.7 29.6 - - - +
405B VAL* 4.1 16.8 - - + -
407B ASN* 6.2 0.2 - - - +
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 4.4 2.9 - - + -
282B THR* 4.0 15.5 - - + -
283B ILE* 3.7 21.8 - - + -
286B VAL* 3.8 22.7 - - + -
370B PHE* 3.7 29.6 - - + -
371B SER 3.1 14.1 + - - +
372B PRO 3.2 6.0 + - - +
374B MET* 1.3 75.8 - - - +
376B LYS* 1.3 64.6 + - - +
378B VAL* 3.1 7.1 + - - +
379B TYR* 3.0 46.4 + - + -
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B VAL* 4.6 3.1 - - - +
290B LEU* 3.9 17.3 - - + -
295B GLU* 4.3 16.2 + - - +
372B PRO 3.0 13.9 + - - +
373B ALA 3.4 10.1 - - - +
375B VAL* 1.3 77.7 - - - +
377B SER* 1.3 56.8 + - - +
379B TYR* 3.2 7.1 + - + +
380B ASP* 2.8 68.5 + - - +
406B ASP* 6.6 0.2 - - + -
409B PHE* 3.8 43.5 - - + -
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Residues in contact with SER 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA 3.0 13.5 + - - -
374B MET* 3.1 13.4 + - - -
376B LYS* 1.3 75.4 - - - +
378B VAL* 1.3 55.3 + - - +
380B ASP* 3.3 8.5 + - - +
381B ASN* 2.9 31.0 + - - +
392B VAL* 4.5 3.8 - - - -
403B LEU* 3.5 17.1 - - - +
404B PRO* 2.7 30.1 + - - +
405B VAL* 4.2 8.5 - - - -
406B ASP 5.5 0.7 - - - -
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 3.6 28.7 - - + -
325B THR* 3.9 25.6 - - + +
327B LEU* 4.4 11.2 - - + -
370B PHE* 4.7 4.9 - - + -
374B MET 3.0 18.7 + - - +
375B VAL* 3.1 10.7 + - - +
377B SER* 1.3 74.8 - - - +
379B TYR* 1.3 63.0 + - - +
381B ASN* 3.5 4.9 + - - +
382B MET* 3.5 21.0 + - + +
390B PHE* 4.1 23.8 - - + -
392B VAL* 4.2 12.8 - - + -
403B LEU* 4.3 7.9 - - + -
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Residues in contact with TYR 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ARG* 2.8 39.9 + - + +
273B ILE* 3.4 33.3 - - + +
283B ILE* 3.7 3.4 - - + +
286B VAL* 5.1 1.1 - - + -
287B ILE* 3.5 16.5 - - + +
290B LEU* 4.6 11.2 - - + -
295B GLU* 5.3 1.3 - - - +
297B ILE* 3.6 48.0 - - + -
298B GLY 2.7 25.8 + - - -
375B VAL* 3.0 37.6 + - + -
376B LYS* 3.7 7.6 - - + +
378B VAL* 1.3 76.2 - - - +
380B ASP* 1.3 65.0 + - - +
382B MET* 3.1 26.7 + - + +
383B SER 3.5 2.8 + - - -
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Residues in contact with ASP 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 4.9 4.3 + - - -
295B GLU* 5.2 3.1 - - - +
376B LYS* 2.8 58.0 + - - +
377B SER* 3.7 7.4 - - - +
379B TYR* 1.3 76.4 - - - +
381B ASN* 1.3 64.7 + - - +
383B SER* 3.1 8.6 + - - -
384B GLY* 3.0 21.8 + - - -
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Residues in contact with ASN 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B THR* 5.2 1.0 - - - +
359B LEU* 4.2 7.9 - - - +
377B SER 2.9 17.4 + - - +
378B VAL 3.5 8.0 + - - +
380B ASP* 1.3 74.1 - - - +
382B MET* 1.3 61.5 + - - +
384B GLY 3.3 3.6 + - - +
385B ALA* 4.2 6.5 - - - +
386B LYS* 2.7 35.2 + - - +
387B LYS* 2.9 51.4 + - - +
390B PHE* 3.6 18.0 - - - -
403B LEU* 3.8 21.1 - - + +
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Residues in contact with MET 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ARG* 3.7 18.8 - - + -
272B VAL 3.5 18.8 - - - +
273B ILE* 3.8 11.7 - - + -
323B VAL* 3.6 45.7 - - + +
325B THR* 3.2 40.2 - - + -
359B LEU* 4.3 2.7 - - + -
378B VAL 3.6 7.6 - - - +
379B TYR* 3.1 39.4 + - + +
381B ASN* 1.3 78.5 - - + +
383B SER* 1.3 52.8 - - - +
384B GLY 3.4 0.2 - - - -
386B LYS* 2.6 34.0 + - - +
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 3.0 33.8 + - - +
379B TYR 3.5 2.2 + - - -
380B ASP* 3.1 8.1 + - - -
382B MET* 1.3 79.6 - - - +
384B GLY* 1.3 59.9 - - - +
386B LYS* 4.0 6.8 + - - +
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ASP 3.0 13.4 + - - -
381B ASN 3.3 2.6 + - - -
383B SER* 1.3 79.0 - - - +
385B ALA* 1.3 64.0 + - - -
386B LYS* 3.3 11.8 + - - +
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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