Contacts of the helix formed by residues 340 - 354 (chain B) in PDB entry 3KXK
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 ASN 340 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B ILE* 5.2 1.8 - - - +
331B ILE* 5.9 0.4 - - + -
332B PRO* 2.7 43.3 + - - +
333B ILE* 4.1 5.1 - - + +
338B ARG 3.3 1.6 + - - -
339B THR* 1.3 82.7 - - + +
341B LEU* 1.3 59.1 + - - +
342B GLU* 3.1 4.0 - - - +
343B LEU* 3.0 29.2 + - + +
344B LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 341 (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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195B LEU* 5.4 3.1 - - + -
198B SER* 3.5 36.6 - - - +
199B LEU* 4.5 11.2 - - + +
333B ILE* 4.7 9.9 - - + -
334B SER 4.6 0.2 - - - +
335B ALA* 4.3 14.8 - - - +
338B ARG* 3.1 44.6 + - + +
339B THR 3.1 8.2 + - - +
340B ASN* 1.3 78.8 - - - +
342B GLU* 1.3 60.9 + - + +
344B LEU* 3.3 24.7 + - + +
345B ARG* 2.9 32.9 + - + +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ARG 4.7 0.9 + - - +
340B ASN* 3.1 1.3 - - - -
341B LEU* 1.3 77.6 - - + +
343B LEU* 1.3 63.8 + - - +
345B ARG* 3.4 24.1 + - - +
346B ASP* 3.1 33.3 + - - +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 4.3 24.2 - - + -
332B PRO* 5.7 1.1 - - + -
340B ASN* 3.0 37.4 + - - +
342B GLU* 1.3 77.6 - - - +
344B LEU* 1.3 63.5 + - - +
346B ASP* 3.1 17.1 + - + +
347B LYS* 2.9 43.0 + - + +
350B GLN* 5.8 0.2 - - - +
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Residues in contact with LEU 344 (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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195B LEU* 4.4 9.4 - - + -
199B LEU* 4.1 24.0 - - + -
262B ILE* 5.0 2.2 - - + -
296B LEU* 3.8 20.9 - - + -
298B THR* 3.9 10.5 - - + -
331B ILE* 3.6 26.4 - - + +
333B ILE* 4.2 17.7 - - + -
340B ASN 2.9 12.5 + - - +
341B LEU* 3.4 29.6 - - + +
343B LEU* 1.3 77.7 - - - +
345B ARG* 1.3 53.1 + - - +
347B LYS* 3.0 2.9 + - - +
348B ILE* 2.8 51.4 + - + +
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Residues in contact with ARG 345 (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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199B LEU* 4.3 33.5 + - + +
221B ILE* 4.6 9.3 - - + +
222B PRO* 3.5 27.8 + - - +
223B ILE* 3.7 42.9 - - + +
224B ASN* 4.7 2.2 - - - +
341B LEU* 2.9 16.9 + - - +
342B GLU* 3.5 31.6 + - - +
343B LEU 3.3 0.2 - - - -
344B LEU* 1.3 75.1 - - - +
346B ASP* 1.3 60.4 + - - +
348B ILE* 3.3 5.4 + - - +
349B TYR* 3.0 27.9 + - - +
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Residues in contact with ASP 346 (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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223B ILE* 5.6 0.9 - - - +
224B ASN* 5.7 2.3 + - - +
342B GLU* 3.1 20.1 + - - +
343B LEU* 3.1 18.9 + - + +
345B ARG* 1.3 79.0 - - - +
347B LYS* 1.3 57.1 + - - +
349B TYR* 3.1 8.6 + - - +
350B GLN* 2.9 45.3 + - - +
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Residues in contact with LYS 347 (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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296B LEU* 4.1 18.2 - - + -
328B PHE* 3.5 16.7 - - + -
329B ASP* 3.2 29.0 + - - +
331B ILE* 4.3 14.4 - - + -
343B LEU* 2.9 34.8 + - + +
344B LEU* 3.6 8.1 - - - +
346B ASP* 1.3 73.6 - - - +
348B ILE* 1.3 61.4 + - - +
350B GLN* 3.4 30.7 + - - +
351B LEU* 3.0 29.5 + - - +
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Residues in contact with ILE 348 (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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182B ILE* 4.8 11.9 - - + +
199B LEU* 5.4 7.2 - - + -
221B ILE* 5.8 0.2 - - + -
223B ILE* 3.7 11.2 - - + -
228B ILE* 3.7 29.8 - - + -
230B LEU* 5.0 6.3 - - + -
262B ILE* 3.5 31.9 - - + -
296B LEU* 3.7 21.1 - - + -
344B LEU* 2.8 35.1 + - + +
345B ARG* 3.6 7.2 - - - +
346B ASP 3.3 0.2 - - - -
347B LYS* 1.3 72.5 - - - +
349B TYR* 1.3 57.7 + - - +
351B LEU* 3.4 9.8 + - + +
352B ALA* 2.9 26.3 + - - +
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Residues in contact with TYR 349 (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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223B ILE* 3.7 23.1 - - + +
224B ASN* 3.4 36.1 - - + +
225B ASN* 5.5 1.6 + - - +
226B ARG* 3.5 34.0 - - + +
228B ILE* 4.6 3.1 - - + -
345B ARG 3.0 13.8 + - - +
346B ASP* 3.1 11.9 + - - +
348B ILE* 1.3 72.9 - - - +
350B GLN* 1.3 62.3 + - + +
351B LEU 3.1 1.3 - - - -
352B ALA* 3.0 6.2 + - + +
353B THR* 2.7 56.4 + - + +
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 3.9 14.3 - - + -
343B LEU* 5.8 0.6 - - - +
346B ASP* 2.9 32.1 + - - +
347B LYS* 3.4 42.5 + - - +
349B TYR* 1.3 83.0 - - + +
351B LEU* 1.3 57.6 + - - +
353B THR* 3.7 5.8 + - - -
354B GLN* 3.1 27.4 + - - +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 4.6 12.6 - - + -
260B ALA* 3.7 27.4 - - + -
261B LEU 5.5 0.7 - - - +
262B ILE* 6.1 0.7 - - + -
294B PRO* 3.8 26.7 - - + +
296B LEU* 4.8 16.8 - - + +
328B PHE* 3.6 38.8 - - + -
347B LYS 3.0 17.5 + - - +
348B ILE* 3.6 11.2 - - + +
349B TYR 3.1 0.2 - - - -
350B GLN* 1.3 76.0 - - - +
352B ALA* 1.3 66.3 + - - +
354B GLN* 3.2 27.4 + - + +
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Residues in contact with ALA 352 (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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180B PRO* 4.1 30.4 - - + +
182B ILE* 6.0 3.8 - - + +
226B ARG* 4.4 18.3 + - - +
228B ILE* 3.6 24.9 - - + -
348B ILE 2.9 18.3 + - - +
349B TYR* 3.5 5.4 - - - +
351B LEU* 1.3 75.5 - - - +
353B THR* 1.3 66.2 + - - +
354B GLN 3.3 5.0 + - - +
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Residues in contact with THR 353 (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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226B ARG* 4.0 15.0 - - - +
349B TYR* 2.7 48.6 + - + +
350B GLN* 3.8 7.4 - - - -
352B ALA* 1.3 73.4 - - - +
354B GLN* 1.3 64.9 + - - +
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Residues in contact with GLN 354 (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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294B PRO* 4.6 12.5 - - - +
328B PHE* 3.5 27.2 - - - -
350B GLN 3.1 17.8 + - - +
351B LEU* 3.5 26.7 - - + +
352B ALA 3.2 5.1 - - - +
353B THR* 1.3 83.4 - - - +
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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