Contacts of the helix formed by residues 323 - 343 (chain B) in PDB entry 1K0Y
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 THR 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.6 3.4 + - - +
320B LYS 3.5 17.9 - - - +
321B GLU* 3.0 9.6 + - - +
322B PHE* 1.4 73.6 - - - +
324B PRO* 1.4 70.4 - - + +
325B PRO* 3.3 14.7 - - - +
326B VAL* 3.1 23.3 + - + +
327B GLN 2.8 25.3 + - - -
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Residues in contact with PRO 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 4.7 9.0 - - + +
30A GLU* 4.2 20.9 - - + +
31A ARG* 3.7 48.4 - - + +
34A LEU* 3.8 21.9 - - + +
35A SER* 4.7 1.4 + - - -
323B THR* 1.4 87.2 - - + +
325B PRO* 1.4 63.3 - - + +
327B GLN* 3.4 3.2 + - + +
328B ALA* 3.0 26.9 + - - +
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Residues in contact with PRO 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 5.6 1.6 - - - +
34A LEU* 4.2 15.0 - - + -
207B GLU* 5.3 2.6 - - - +
210B ALA* 6.1 0.2 - - - -
323B THR* 3.3 15.3 - - - +
324B PRO* 1.4 96.4 - - + +
326B VAL* 1.4 65.1 + - + +
328B ALA* 3.3 7.3 + - + +
329B ALA* 3.1 21.1 + - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA* 4.2 26.7 - - + +
214B LEU* 4.2 12.8 - - + -
321B GLU 4.2 11.0 - - - +
322B PHE* 3.9 22.0 - - + -
323B THR* 3.1 26.2 + - + +
325B PRO* 1.4 78.1 - - + +
327B GLN* 1.4 61.9 + - - +
329B ALA* 3.2 8.1 + - - +
330B TYR* 3.0 35.7 + - + -
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.0 39.3 + - - +
35A SER* 3.6 17.1 + - - +
103A HIS* 4.0 1.2 + - - -
104A CYS* 4.0 19.2 - - - -
107A VAL* 3.5 22.7 - - - +
311B VAL* 4.1 2.2 - - + +
322B PHE* 3.5 28.2 - - + -
323B THR 2.8 16.1 + - - +
324B PRO 3.7 6.7 - - - +
325B PRO 3.3 0.2 - - - -
326B VAL* 1.4 73.5 - - - +
328B ALA* 1.4 50.0 + - - +
330B TYR* 3.1 3.1 + - - +
331B GLN* 2.8 61.9 + - - +
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.7 32.8 - - + +
35A SER* 3.5 12.4 - - - +
207B GLU* 4.9 6.7 - - - +
324B PRO 3.0 15.8 + - - +
325B PRO* 3.3 10.3 + - + +
327B GLN* 1.4 75.4 - - - +
329B ALA* 1.4 61.1 + - - +
331B GLN* 3.3 3.9 + - - +
332B LYS* 3.2 30.0 + - - +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 4.7 2.6 - - + +
207B GLU* 3.9 38.1 + - + +
210B ALA* 4.9 3.6 - - + -
211B VAL* 3.8 21.3 - - + -
325B PRO 3.1 12.8 + - - +
326B VAL* 3.2 11.0 + - - +
328B ALA* 1.4 74.8 - - - +
330B TYR* 1.4 62.7 + - + +
332B LYS* 3.2 16.4 + - - +
333B VAL* 3.2 15.4 + - - +
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Residues in contact with TYR 330 (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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211B VAL* 2.7 54.9 + - + +
214B LEU* 3.9 19.8 - - + +
215B TRP* 3.5 34.6 + + - +
271B PHE* 5.2 7.0 - + - -
275B LEU* 5.4 0.7 - - + -
310B LEU* 5.9 0.4 - - + -
311B VAL* 4.5 9.0 - - + -
314B LEU* 3.7 27.1 - - + -
322B PHE* 4.1 15.5 - + + -
326B VAL* 3.0 32.9 + - + +
327B GLN 3.7 5.6 - - - +
329B ALA* 1.4 72.3 - - - +
331B GLN* 1.4 60.3 + - - +
333B VAL* 3.2 12.2 + - + +
334B VAL* 2.9 40.5 + - + +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.5 29.4 - - - +
36A PHE* 3.9 21.0 - - + -
103A HIS* 2.8 26.1 + - - -
308B ASN* 3.7 19.2 + - - -
311B VAL* 3.5 13.6 - - + +
327B GLN* 2.8 37.3 + - + +
328B ALA* 3.6 6.3 - - - +
329B ALA 3.3 0.4 - - - -
330B TYR* 1.4 71.8 - - - +
332B LYS* 1.4 62.4 + - + +
334B VAL* 3.4 11.9 - - - +
335B ALA* 3.0 26.2 + - - +
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Residues in contact with LYS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER 6.1 0.7 - - - +
201B VAL* 4.0 23.4 - - + +
202B HIS* 4.0 21.3 + - - +
203B LEU* 4.5 7.6 - - + -
204B THR* 5.7 1.4 - - - +
207B GLU* 3.0 39.7 + - - +
328B ALA* 3.2 16.5 + - - +
329B ALA 3.2 7.1 + - - +
331B GLN* 1.4 74.9 - - + +
333B VAL* 1.4 57.1 + - - +
335B ALA* 3.4 6.1 + - - +
336B GLY* 2.8 26.0 + - - -
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 5.4 3.1 - - - -
203B LEU* 4.0 24.5 - - + -
211B VAL* 4.1 16.2 - - + -
271B PHE* 3.9 24.0 - - + -
275B LEU* 4.0 16.8 - - + -
278B LEU* 4.5 17.5 - - + -
281B LEU* 4.6 2.3 - - - +
329B ALA 3.2 11.6 + - - +
330B TYR* 3.2 14.4 + - + +
332B LYS* 1.4 76.6 - - - +
334B VAL* 1.4 59.6 + - + +
336B GLY* 3.1 2.8 + - - -
337B VAL* 2.8 34.1 + - + +
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 4.1 25.8 - - + -
303B PHE 5.2 1.6 - - - +
307B GLY* 3.8 40.7 - - - +
308B ASN* 5.0 1.3 - - - +
310B LEU* 4.5 8.5 - - + -
311B VAL* 4.2 10.5 - - + -
330B TYR* 2.9 22.8 + - + +
331B GLN* 3.4 23.8 - - - +
333B VAL* 1.4 75.9 - - + +
335B ALA* 1.4 60.6 + - - +
337B VAL* 3.9 5.3 - - - +
338B ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLN 3.0 19.5 + - - +
332B LYS* 3.7 6.7 - - - +
334B VAL* 1.4 76.7 - - + +
336B GLY* 1.4 58.2 + - - +
338B ALA* 3.3 5.2 + - - +
339B ASN* 2.9 39.4 + - - +
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Residues in contact with GLY 336 (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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201B VAL* 3.5 28.5 - - - -
281B LEU* 3.7 9.8 - - - +
332B LYS 2.8 11.1 + - - -
333B VAL 3.1 3.8 + - - -
335B ALA* 1.4 73.7 - - - +
337B VAL* 1.4 58.6 + - - +
339B ASN* 3.4 7.3 + - - +
340B ALA* 3.0 28.4 + - - +
1400B SO4 4.6 2.0 + - - -
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 3.9 26.0 - - + +
274B GLY 6.2 0.7 - - - -
275B LEU* 5.6 2.9 - - + -
281B LEU* 4.2 22.7 - - + -
285B PHE* 4.4 18.6 - - + -
333B VAL* 2.8 24.8 + - + +
334B VAL 4.0 3.6 - - - +
336B GLY* 1.4 72.9 - - - +
338B ALA* 1.4 66.1 + - - +
340B ALA* 3.1 7.1 + - - +
341B LEU* 2.9 32.9 + - + +
348B HEM 4.1 26.0 - - + -
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Residues in contact with ALA 338 (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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300B PRO 5.4 0.7 - - - +
303B PHE* 3.9 38.8 - - + +
304B ARG* 4.3 20.6 - - - +
334B VAL 3.0 19.1 + - - +
335B ALA* 3.3 7.2 + - - +
337B VAL* 1.4 77.0 - - - +
339B ASN* 1.4 63.1 + - - +
341B LEU* 3.4 3.4 + - - +
342B ALA* 3.1 24.3 + - - +
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Residues in contact with ASN 339 (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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282B LYS* 5.3 3.1 - - + +
304B ARG* 5.0 11.3 - - - +
335B ALA* 2.9 24.7 + - - +
336B GLY* 3.8 6.8 - - - +
338B ALA* 1.4 77.3 - - - +
340B ALA* 1.4 58.2 + - - +
342B ALA* 3.2 7.2 + - - +
343B HIS* 3.0 30.4 + - - +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 3.6 37.9 - - + +
282B LYS* 4.0 10.7 - - + +
285B PHE* 4.1 12.7 - - + +
289B SER* 3.8 3.6 - - - -
336B GLY 3.0 17.9 + - - +
337B VAL 3.1 5.4 + - - +
339B ASN* 1.4 77.2 - - - +
341B LEU* 1.4 58.6 + - - +
343B HIS* 2.6 32.6 + - - -
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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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285B PHE* 4.1 17.0 - - + -
288B LEU* 3.9 32.1 - - + +
289B SER* 2.8 28.0 + - - +
292B HIS* 4.4 10.1 - - + +
303B PHE* 3.6 33.2 - - + -
337B VAL* 2.9 24.4 + - + +
338B ALA* 5.1 0.2 - - - -
340B ALA* 1.4 76.6 - - - +
342B ALA* 1.4 57.9 + - - +
343B HIS 3.5 0.2 - - - -
345B TYR* 3.3 13.9 - - - -
348B HEM 3.7 41.7 - - + -
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO* 3.7 28.7 - - + -
303B PHE* 4.7 0.4 - - + -
338B ALA 3.1 16.3 + - - +
339B ASN* 3.2 7.4 + - - +
341B LEU* 1.4 75.7 - - - +
343B HIS* 1.4 64.6 + - - +
344B LYS 3.4 1.8 - - - -
345B TYR* 3.2 27.9 + - - +
438C THR* 6.0 0.7 - - + -
802D CNO 5.0 5.8 - - - +
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Residues in contact with HIS 343 (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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282B LYS* 3.1 60.4 + - + +
286B ALA* 3.7 11.3 - - - +
289B SER* 4.2 0.2 + - - -
339B ASN 3.0 13.9 + - - +
340B ALA* 2.6 25.3 + - - -
342B ALA* 1.4 75.5 - - - +
344B LYS* 1.4 97.4 + - + +
345B TYR 3.6 4.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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