Contacts of the helix formed by residues 364 - 376 (chain A) in PDB entry 1KNU
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 MET 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A CYS* 5.2 2.9 - - - -
330A LEU* 3.9 8.3 - - + -
334A MET* 3.5 28.0 - - + -
339A VAL* 4.8 9.4 - - + -
353A LEU* 4.0 31.0 - - + -
360A PHE 5.0 0.6 + - - +
361A GLY 4.9 2.2 + - - +
363A PHE* 1.3 86.8 - - + +
365A GLU* 1.3 68.0 + - - +
366A PRO* 3.3 3.4 - - - -
367A LYS* 2.7 23.1 + - + +
368A PHE* 3.0 30.1 + - + -
1001A YPA 3.5 45.1 - - + +
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Residues in contact with GLU 365 (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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350A ARG* 2.5 57.3 + - - +
354A LYS* 3.9 43.4 + - + +
361A GLY 5.1 6.3 + - - +
362A ASP* 4.7 4.1 + - - +
364A MET* 1.3 74.7 - - - +
366A PRO* 1.3 70.1 - - + +
368A PHE* 3.1 6.5 + - - +
369A GLU* 2.9 35.9 + - - +
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Residues in contact with PRO 366 (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 ASP 3.8 12.3 - - - +
363A PHE 3.7 15.5 - - - +
364A MET 3.4 2.0 - - - -
365A GLU* 1.3 94.3 - - + +
367A LYS* 1.3 64.5 + - + +
369A GLU* 3.4 16.0 + - + +
370A PHE 3.0 21.7 + - - -
445A ILE* 3.4 28.5 - - + +
448A GLU* 3.9 28.3 - - + +
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Residues in contact with LYS 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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327A TYR* 3.5 41.5 - - + -
330A LEU* 4.2 10.5 - - + -
334A MET* 3.9 18.5 - - + +
363A PHE* 2.9 29.2 + - - +
364A MET* 2.7 20.8 + - + +
366A PRO* 1.3 75.8 - - + +
368A PHE* 1.3 57.1 + - - +
370A PHE* 3.3 8.2 + - - +
371A ALA* 2.7 36.2 + - - +
445A ILE* 3.5 22.7 + - + +
449A HIS* 2.8 38.3 + - - +
452A LEU* 6.1 0.2 - - - +
1001A YPA 5.2 1.1 - - - -
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Residues in contact with PHE 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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334A MET* 3.6 24.7 - - + -
335A ASN 4.0 12.3 - - - -
336A LYS* 4.9 0.4 - - - -
338A GLY* 3.2 41.1 - - - -
339A VAL* 3.9 3.1 - - + -
350A ARG* 3.6 50.0 - - + +
353A LEU* 3.8 22.7 - - + -
364A MET* 3.0 46.4 + - + -
365A GLU* 3.5 7.4 - - - +
367A LYS* 1.3 77.8 - - - +
369A GLU* 1.3 57.3 + - - +
371A ALA* 3.5 4.3 - - + +
372A VAL* 2.8 38.0 + - + +
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Residues in contact with GLU 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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350A ARG* 3.7 17.7 - - - +
365A GLU* 2.9 23.6 + - - +
366A PRO* 3.6 21.4 - - + +
367A LYS 3.2 0.2 - - - -
368A PHE* 1.3 76.9 - - - +
370A PHE* 1.3 61.8 + - - +
372A VAL* 3.6 5.6 + - - +
373A LYS* 3.4 31.5 + - - +
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Residues in contact with PHE 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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327A TYR* 3.8 26.2 - - + -
328A THR* 4.1 6.7 - - - -
331A ALA* 4.4 2.9 - - + -
366A PRO 3.0 17.6 + - - +
367A LYS* 3.6 6.1 - - - +
369A GLU* 1.3 74.5 - - - +
371A ALA* 1.3 59.5 + - - +
373A LYS* 3.0 8.1 + - + +
374A PHE* 2.7 69.1 + + + +
438A LYS* 3.7 19.3 - - + -
441A ASP* 3.4 40.8 - - + -
442A LEU* 3.7 31.9 - - + -
445A ILE* 4.3 15.0 - - + -
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Residues in contact with ALA 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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331A ALA* 3.9 25.8 - - + -
334A MET* 3.5 32.5 - - + -
367A LYS 2.7 21.7 + - - +
368A PHE* 3.5 5.2 - - + +
370A PHE* 1.3 74.2 - - + +
372A VAL* 1.3 55.0 + - + +
374A PHE* 4.4 0.2 - - - -
375A ASN* 2.7 42.4 + - - +
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Residues in contact with VAL 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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335A ASN 4.9 2.7 - - - +
336A LYS* 4.0 33.9 - - + +
350A ARG* 4.1 13.5 - - - +
368A PHE* 2.8 25.9 + - + +
369A GLU* 3.9 6.7 - - - +
371A ALA* 1.3 73.6 - - + +
373A LYS* 1.3 62.5 + - + +
375A ASN* 4.2 5.7 - - - +
376A ALA* 3.5 16.1 + - - +
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Residues in contact with LYS 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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369A GLU* 3.4 17.1 + - - +
370A PHE* 3.0 8.9 + - + +
372A VAL* 1.3 78.8 - - + +
374A PHE* 1.3 62.2 + - - +
376A ALA* 3.0 26.2 - - + +
377A LEU* 4.0 7.6 + - - +
438A LYS* 4.6 14.7 + - + +
441A ASP* 4.7 16.6 - - - +
396B ASP* 5.6 10.5 - - + -
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Residues in contact with PHE 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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230A LYS* 5.9 3.1 - - - -
328A THR* 4.2 11.7 - - + -
331A ALA* 4.2 15.7 - - + -
370A PHE* 2.7 46.2 + + + +
371A ALA* 3.9 3.4 - - - +
373A LYS* 1.3 74.3 - - - +
375A ASN* 1.3 64.1 + - - +
377A LEU* 3.1 25.6 + - + +
378A GLU 4.2 0.7 + - - -
379A LEU* 3.6 32.1 + - + +
384A LEU* 4.1 13.9 - - + -
387A PHE* 4.0 19.5 - + - -
435A LEU* 3.4 24.5 - - + -
438A LYS* 3.4 30.4 - - + +
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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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230A LYS* 4.5 17.1 + - - +
234A ARG* 3.9 12.4 - - - +
331A ALA* 3.1 30.6 + - - +
334A MET 3.1 27.5 + - - -
335A ASN* 5.0 2.2 - - - +
371A ALA* 2.7 28.8 + - - +
372A VAL* 4.2 5.9 - - - +
374A PHE* 1.3 74.6 - - - +
376A ALA* 1.3 57.0 + - - +
378A GLU* 2.7 32.6 + - - +
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Residues in contact with ALA 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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372A VAL 3.5 9.8 + - - +
373A LYS* 3.0 23.1 + - + +
375A ASN* 1.3 79.2 - - - +
377A LEU* 1.3 64.1 + - + +
378A GLU* 3.3 12.8 + - - +
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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