Contacts of the helix formed by residues 359 - 371 (chain A) in PDB entry 2KWN
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 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A CYS* 3.1 13.2 - - - -
336A ASP* 3.9 12.2 + - - +
357A SER* 5.4 0.9 + - - -
358A TRP* 1.3 81.7 + - - +
360A CYS* 1.3 81.7 + - - +
363A CYS* 2.9 19.8 - - - +
364A TRP* 3.5 28.0 + - - +
367A LEU* 4.6 6.6 - - - +
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Residues in contact with CYS 360 (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 CYS* 3.5 15.2 - - + +
337A CYS* 3.8 3.1 - - - -
339A ARG* 4.4 0.7 - - + -
341A TYR* 3.2 23.8 - - + +
358A TRP* 3.7 25.1 - - + +
359A SER* 1.3 93.6 - - - +
361A HIS* 1.3 58.9 + - - +
362A LEU* 3.1 27.6 - - - -
363A CYS 3.3 3.8 - - - -
364A TRP* 3.1 18.9 - - - +
701A ZN 2.3 34.8 - - - -
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Residues in contact with HIS 361 (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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320A ILE* 3.5 17.8 - - + +
321A LEU* 4.0 9.6 - - + +
341A TYR* 2.7 46.6 + + + -
347A ASN* 5.3 19.4 + - + +
348A PRO* 5.9 3.1 - - + -
360A CYS* 1.3 74.7 - - - +
362A LEU* 1.3 91.8 + - + +
364A TRP* 4.1 4.5 - - - -
365A GLU* 2.8 43.1 + - + +
368A LYS* 4.6 2.2 + - - +
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Residues in contact with LEU 362 (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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320A ILE* 4.7 2.0 - - + -
337A CYS* 4.3 4.5 - - + -
339A ARG* 3.1 51.4 - - + +
341A TYR* 3.8 3.6 - - - +
360A CYS* 3.1 6.2 - - - -
361A HIS* 1.3 107.4 - - + +
363A CYS* 1.3 63.7 + - - +
365A GLU* 3.1 26.9 - - - +
366A LEU* 3.2 11.3 - - - +
701A ZN 4.5 1.3 - - - -
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Residues in contact with CYS 363 (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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301A ASN* 4.3 8.9 + - - +
336A ASP* 3.0 44.6 - - - +
337A CYS* 3.8 5.6 - - - -
359A SER* 2.9 17.5 - - - +
360A CYS* 3.3 1.4 - - - -
362A LEU* 1.3 80.6 - - - +
364A TRP* 1.3 53.8 + - - +
366A LEU* 3.2 9.1 - - - +
367A LEU* 2.6 38.6 + - + +
370A LYS* 4.6 1.4 - - - -
701A ZN 2.3 32.8 - - - -
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Residues in contact with TRP 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A PRO* 5.8 10.3 - - + -
359A SER* 3.5 31.4 - - - +
360A CYS 3.1 16.2 + - - +
361A HIS* 3.2 6.6 + - - +
363A CYS* 1.3 76.3 - - - +
365A GLU* 1.3 59.9 + - - +
366A LEU 2.8 1.3 - - - -
367A LEU* 2.6 52.8 + - + +
368A LYS* 2.7 40.4 + - + +
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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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361A HIS* 2.8 30.1 + - - +
362A LEU* 3.1 22.3 - - - +
364A TRP* 1.3 77.7 - - - +
366A LEU* 1.3 57.7 + - + +
368A LYS* 3.1 22.8 + - - +
369A GLU* 3.2 27.0 + - - +
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Residues in contact with LEU 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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301A ASN* 4.5 10.1 - - - +
362A LEU 3.2 12.8 - - - +
363A CYS* 3.2 13.2 + - - +
365A GLU* 1.3 82.4 - - + +
367A LEU* 1.3 53.3 + - - +
369A GLU* 3.6 10.5 - - + +
370A LYS* 2.7 68.7 + - + +
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Residues in contact with LEU 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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336A ASP* 4.9 2.9 - - - +
359A SER* 4.6 10.3 - - - +
363A CYS* 2.6 26.9 + - + +
364A TRP* 2.6 50.8 + - + +
366A LEU* 1.3 67.7 - - - +
368A LYS* 1.3 58.4 + - + +
369A GLU 2.9 1.3 - - - -
370A LYS* 2.8 42.2 + - - +
371A ALA* 2.8 16.4 + - - +
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Residues in contact with LYS 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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361A HIS* 4.6 2.6 + - - +
364A TRP* 2.7 48.8 + - + +
365A GLU* 3.1 38.4 - - - +
367A LEU* 1.3 74.0 - - + +
369A GLU* 1.3 60.9 + - - +
371A ALA* 4.0 15.9 + - - +
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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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365A GLU 3.2 19.2 + - - +
366A LEU* 3.6 15.1 - - + +
367A LEU 2.9 0.4 - - - -
368A LYS* 1.3 76.5 - - - +
370A LYS* 1.3 65.0 + - - +
371A ALA 3.2 7.6 - - - +
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Residues in contact with LYS 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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301A ASN* 3.3 26.4 - - - +
366A LEU* 2.7 47.3 + - + +
367A LEU* 2.8 29.3 + - - +
369A GLU* 1.3 70.1 - - - +
371A ALA* 1.3 68.3 + - - +
372A SER* 4.5 2.6 - - - -
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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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367A LEU 2.8 17.5 + - - +
368A LYS* 4.1 11.9 - - - +
369A GLU 3.2 11.0 - - - +
370A LYS* 1.3 81.0 - - - +
372A SER* 1.3 63.9 + - - +
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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