Contacts of the helix formed by residues 357 - 369 (chain B) in PDB entry 1KTW
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 LYS 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B GLY* 4.7 6.8 + - - +
355B THR* 2.8 32.7 + - + +
356B GLN* 1.3 81.4 - - - +
358B ASP* 1.3 68.3 + - - +
359B ALA* 3.1 6.1 - - + +
360B CYS* 3.0 30.0 + - - +
361B LEU* 3.1 13.7 + - - +
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Residues in contact with ASP 358 (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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356B GLN* 4.0 3.3 + - - -
357B LYS* 1.3 72.1 - - - +
359B ALA* 1.3 61.5 + - - +
361B LEU* 3.8 7.1 - - - +
362B ASP* 2.9 37.8 + - - +
441B THR 4.9 1.5 - - - +
442B SER* 2.7 29.5 + - - -
443B LYS* 2.9 49.7 + - + +
444B TYR* 4.0 7.3 - - + -
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Residues in contact with ALA 359 (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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336B CYS* 5.2 0.7 - - - -
357B LYS* 3.0 4.4 + - + +
358B ASP* 1.3 79.0 - - - +
360B CYS* 1.3 66.7 + - - +
362B ASP* 3.5 8.0 + - - +
363B LYS* 3.4 19.2 + - - +
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Residues in contact with CYS 360 (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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332B LEU* 4.5 3.8 - - - +
334B ARG 5.3 0.2 - - - -
335B GLY 4.2 5.6 - - - -
336B CYS* 2.0 60.6 - - + -
354B VAL* 4.1 8.7 - - + +
355B THR* 3.9 14.6 - - - +
357B LYS* 3.0 23.8 + - - +
359B ALA* 1.3 83.1 - - - +
361B LEU* 1.3 62.1 + - - +
363B LYS* 3.4 7.1 + - - +
364B ALA* 3.2 20.4 + - - +
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Residues in contact with LEU 361 (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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308B PHE* 6.0 0.4 - - - -
309B VAL* 4.5 9.6 - - + +
354B VAL* 3.7 27.6 - - + +
355B THR 3.9 6.3 - - - +
356B GLN* 3.7 35.4 - - - +
357B LYS 3.1 17.8 + - - +
358B ASP 4.0 0.9 - - - +
359B ALA 3.3 0.2 - - - -
360B CYS* 1.3 74.6 - - - +
362B ASP* 1.3 64.8 + - - +
363B LYS 3.1 0.2 - - - -
364B ALA* 3.2 7.2 + - + +
365B LYS* 3.2 21.0 + - - +
370B ILE 4.7 1.2 - - - +
371B GLU* 5.6 2.1 - - - +
372B PRO* 3.8 24.9 - - + -
444B TYR* 3.6 37.4 + - + -
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Residues in contact with ASP 362 (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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358B ASP* 2.9 32.2 + - - +
359B ALA* 3.9 7.4 - - - +
361B LEU* 1.3 76.3 - - - +
363B LYS* 1.3 60.6 + - - +
365B LYS* 3.3 6.5 + - - +
366B LEU* 3.2 31.3 + - + +
443B LYS* 4.8 14.2 + - - +
444B TYR* 2.6 30.6 + - - -
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Residues in contact with LYS 363 (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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331B LYS 3.5 15.5 - - - -
332B LEU* 3.5 37.6 - - + +
359B ALA 3.4 10.1 + - - +
360B CYS* 3.4 9.4 + - - +
361B LEU 3.1 0.2 - - - -
362B ASP* 1.3 78.2 - - - +
364B ALA* 1.3 63.4 + - - +
366B LEU* 3.5 8.6 + - + +
367B GLU* 3.1 47.4 + - + +
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Residues in contact with ALA 364 (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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309B VAL* 4.7 10.5 - - + -
311B LEU* 5.7 0.2 - - + -
332B LEU* 3.5 24.0 - - + +
354B VAL* 4.4 15.0 - - + -
360B CYS 3.2 13.1 + - - +
361B LEU* 3.2 12.2 + - - +
363B LYS* 1.3 74.3 - - - +
365B LYS* 1.3 59.7 + - - +
368B TYR* 2.8 39.0 + - + +
369B GLY 3.6 0.2 + - - -
370B ILE* 3.9 9.8 - - + +
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Residues in contact with LYS 365 (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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361B LEU 3.2 11.0 + - - +
362B ASP* 3.6 10.3 - - - +
364B ALA* 1.3 76.2 - - - +
366B LEU* 1.3 68.8 + - + +
369B GLY* 2.7 31.5 + - - -
370B ILE 3.3 21.5 + - - +
371B GLU* 2.9 39.7 + - + +
444B TYR* 4.7 9.7 + - - +
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Residues in contact with LEU 366 (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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362B ASP* 3.2 20.8 + - + +
363B LYS* 3.9 12.3 - - + +
365B LYS* 1.3 88.3 - - + +
367B GLU* 1.3 70.6 + - + +
369B GLY 4.8 0.5 + - - -
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Residues in contact with GLU 367 (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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331B LYS* 2.9 51.2 + - + +
332B LEU* 4.6 0.7 - - + -
363B LYS* 3.1 47.0 + - + +
366B LEU* 1.3 86.6 - - - +
368B TYR* 1.3 78.6 + - + +
369B GLY 3.7 0.2 - - - -
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Residues in contact with TYR 368 (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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255B LYS* 5.2 1.7 + - - -
311B LEU* 3.7 47.3 - - + +
324B TRP* 5.3 9.5 - + - -
327B ALA 5.2 0.7 + - - -
328B VAL* 4.9 9.5 + - - +
331B LYS* 3.5 34.5 + - + +
332B LEU* 4.2 11.7 - - + -
364B ALA* 2.8 27.6 + - - +
367B GLU* 1.3 90.8 - - + +
369B GLY* 1.3 63.3 + - - +
370B ILE* 4.2 19.9 - - + +
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Residues in contact with GLY 369 (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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255B LYS* 3.2 27.5 + - - -
365B LYS* 2.7 29.9 + - - -
366B LEU 4.6 0.4 + - - -
367B GLU 3.7 0.8 - - - -
368B TYR* 1.3 73.1 - - - +
370B ILE* 1.3 55.8 + - - +
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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