Contacts of the helix formed by residues 313 - 334 (chain B) in PDB entry 1LK9
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 ASP 313 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TYR* 3.9 1.1 - - - -
300B VAL 5.1 0.2 - - - +
303B MET* 3.9 10.7 - - - +
304B VAL* 3.8 8.8 + - - +
307B GLN 3.3 21.2 + - - +
308B LYS* 3.6 5.4 - - - -
309B GLY 3.6 6.2 + - - -
310B THR* 3.1 10.0 + - - +
312B ARG* 1.3 75.4 - - - +
314B LEU* 1.3 68.9 + - - +
315B ASN* 3.1 15.6 + - - -
316B THR* 2.8 25.2 + - - +
317B PHE* 2.9 22.3 + - - +
352B TYR* 2.7 28.7 + - - -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.8 28.0 - - + -
72B TYR* 3.2 45.3 + - + +
73B TRP* 4.4 5.6 - - + +
232B HIS* 3.9 8.7 - - + +
252B PHE* 3.5 39.0 - - + +
253B THR* 4.0 10.1 - - + -
300B VAL* 3.7 35.1 + - + +
303B MET* 4.7 1.8 - - - +
313B ASP* 1.3 74.0 + - - +
315B ASN* 1.3 58.9 + - - +
318B GLY* 2.9 26.3 + - - -
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Residues in contact with ASN 315 (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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116B VAL* 4.0 10.0 - - - +
230B TRP* 4.3 0.7 - - - -
231B PRO* 3.3 31.1 - - + +
232B HIS* 3.5 8.7 + - - -
252B PHE* 3.2 30.7 - - - -
300B VAL* 4.7 2.2 - - - +
304B VAL* 3.4 16.6 - - - +
313B ASP* 3.1 9.3 + - - +
314B LEU* 1.3 76.7 - - - +
316B THR* 1.3 58.1 + - - +
319B PHE* 3.1 26.2 + - - +
352B TYR* 3.2 38.4 + - + +
353B PHE* 3.9 4.5 - - - -
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY* 3.0 33.5 + - - +
310B THR 3.2 24.5 - - - +
311B MET 4.6 0.2 - - - +
313B ASP* 2.8 22.9 + - - -
315B ASN* 1.3 74.5 - - - +
317B PHE* 1.3 61.2 + - - +
319B PHE* 5.6 0.9 - - + -
320B LYS* 2.8 51.3 + - + +
353B PHE* 3.5 20.1 - - + -
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Residues in contact with PHE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.6 20.0 - + - -
69B LEU* 3.8 17.0 - - + -
71B GLU* 3.7 27.4 - - + -
72B TYR* 3.7 43.7 - + + -
75B GLN* 4.3 9.6 - - - -
310B THR 4.3 1.2 + - - -
311B MET* 3.7 41.7 - - + +
313B ASP 2.9 15.3 + - - +
314B LEU 3.6 3.6 - - - +
316B THR* 1.3 77.1 - - - +
318B GLY* 1.3 60.9 - - - +
320B LYS* 3.9 0.5 - - - +
321B LYS* 2.9 61.5 + - + +
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Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.7 22.7 - - - -
69B LEU* 4.5 0.9 - - - -
232B HIS* 3.9 17.0 - - - -
314B LEU 2.9 17.8 + - - -
317B PHE* 1.3 77.2 - - - +
319B PHE* 1.3 66.2 + - - +
322B LEU* 2.9 29.5 + - - +
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PRO 3.5 9.6 - - - +
232B HIS* 3.6 10.5 - - - +
315B ASN 3.1 19.3 + - - +
316B THR* 3.9 2.7 - - + +
318B GLY* 1.3 74.4 - - - +
320B LYS* 1.3 75.6 + - + +
322B LEU* 3.9 0.5 - - - +
323B ARG* 2.8 54.6 + - + +
353B PHE* 3.9 21.1 - + + -
355B ARG* 3.9 23.1 - - - -
357B ARG* 3.4 39.7 - - + -
358B PRO* 3.8 29.8 - - + -
360B SER* 3.4 9.6 - - - -
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Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY 5.4 2.9 + - - +
311B MET* 3.4 39.4 - - + +
316B THR* 2.8 34.6 + - + +
319B PHE* 1.3 89.6 - - + +
321B LYS* 1.3 62.4 + - + +
323B ARG* 3.9 4.5 - - - +
324B GLU* 3.1 30.0 + - + +
355B ARG* 6.2 0.4 - - - +
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Residues in contact with LYS 321 (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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68B PHE* 4.0 17.9 - - + -
71B GLU* 3.5 32.3 + - - +
311B MET* 3.7 23.3 - - + +
317B PHE* 2.9 44.4 + - + +
320B LYS* 1.3 77.8 - - - +
322B LEU* 1.3 65.1 + - - +
324B GLU* 3.5 21.0 + - - +
325B ARG* 3.4 30.6 + - - +
408B GLN* 6.1 3.4 - - - +
1F NAG 5.3 0.2 - - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.6 33.2 - - + -
232B HIS* 3.6 16.6 - - + +
233B TYR* 3.4 39.9 - - + -
318B GLY 2.9 18.4 + - - +
321B LYS* 1.3 74.7 - - - +
323B ARG* 1.3 62.0 + - - +
325B ARG* 3.1 9.0 + - - +
326B TRP* 2.9 28.8 + - - +
360B SER* 4.0 12.6 - - - +
361B PRO 4.5 6.5 - - - +
404B LEU* 3.5 28.2 - - + +
405B ILE* 3.8 10.8 - - + -
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Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PHE* 2.8 40.8 + - + +
320B LYS* 3.9 4.9 - - - +
321B LYS 3.3 0.2 - - - -
322B LEU* 1.3 77.6 - - - +
324B GLU* 1.3 63.3 + - - +
326B TRP* 3.2 21.1 + - - +
327B VAL* 2.9 49.1 + - + +
346B GLN* 5.4 4.8 + - - -
358B PRO* 3.3 34.8 - - + +
359B PRO* 2.9 31.3 + - - +
360B SER* 3.9 6.2 - - - -
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Residues in contact with GLU 324 (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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320B LYS* 3.1 17.9 + - + +
321B LYS* 3.8 27.4 + - - +
322B LEU 3.2 0.2 - - - -
323B ARG* 1.3 78.9 - - + +
325B ARG* 1.3 61.8 + - - +
327B VAL* 3.5 6.6 + - - +
328B ASN* 3.1 30.1 + - - +
408B GLN* 5.7 0.5 + - - -
1F NAG 3.9 25.8 + - + +
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.8 20.0 - - - +
321B LYS* 3.4 18.4 + - - +
322B LEU* 3.1 13.1 + - - +
324B GLU* 1.3 75.6 - - - +
326B TRP* 1.3 59.1 + - - +
328B ASN 3.2 0.9 + - - -
329B ILE* 2.9 28.8 + - - +
404B LEU* 2.8 47.9 + - + +
406B LYS 2.8 31.9 + - - +
407B THR 4.0 5.1 + - - -
408B GLN* 3.3 35.6 - - - +
411B PHE* 3.4 51.5 - - + +
1F NAG 4.2 7.4 - - + +
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Residues in contact with TRP 326 (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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322B LEU 2.9 12.7 + - - +
323B ARG* 3.5 33.4 - - - +
325B ARG* 1.3 75.7 - - - +
327B VAL* 1.3 56.7 + - - +
329B ILE* 4.0 6.7 - - + -
330B THR* 2.7 64.4 + - + +
341B TYR* 3.9 19.4 - + + -
342B GLN* 3.4 33.2 - - - -
344B LEU* 4.5 5.6 - - + -
346B GLN* 5.2 6.0 + - - +
359B PRO* 3.7 23.0 - - - +
360B SER* 4.5 0.2 - - - -
361B PRO* 3.5 34.3 - - + +
363B TYR 3.9 10.5 - - - -
364B ALA* 3.9 15.9 - - + -
404B LEU* 3.7 14.7 - - + +
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Residues in contact with VAL 327 (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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323B ARG* 2.9 58.2 + - + +
324B GLU* 3.8 6.7 - - - +
326B TRP* 1.3 77.2 - - - +
328B ASN* 1.3 65.5 + - - +
330B THR* 3.3 5.7 + - - -
331B ALA* 3.0 31.2 + - + +
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Residues in contact with ASN 328 (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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324B GLU* 3.1 18.3 + - - +
325B ARG 3.7 3.4 - - - +
327B VAL* 1.3 86.3 - - - +
329B ILE* 1.3 63.5 + - - +
331B ALA* 3.4 5.9 + - - +
332B LEU* 3.2 16.6 + - - +
411B PHE* 4.0 12.4 - - + -
415B MET* 3.5 18.1 - - + +
1F NAG 1.5 63.5 + - - +
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Residues in contact with ILE 329 (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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325B ARG 2.9 20.9 + - - +
326B TRP* 3.6 28.3 - - + +
328B ASN* 1.3 76.8 - - - +
330B THR* 1.3 62.8 + - + +
332B LEU* 3.2 2.1 + - - +
333B LEU* 3.0 35.0 + - + +
364B ALA* 4.1 7.6 - - + -
402B LEU* 4.0 14.1 - - + -
404B LEU* 4.1 15.3 - - + -
411B PHE* 4.4 2.5 - - + -
414B LEU* 3.9 25.1 - - + -
415B MET* 3.9 15.7 - - - +
418B LEU* 3.7 29.8 - - + -
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B TRP* 2.7 64.3 + - + +
327B VAL* 3.3 7.8 + - - -
329B ILE* 1.3 75.9 - - + +
331B ALA* 1.3 65.8 + - - +
333B LEU 3.4 0.3 + - - -
334B ASP* 3.0 33.2 + - - +
341B TYR* 3.5 41.5 - - + -
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Residues in contact with ALA 331 (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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327B VAL* 3.0 23.6 + - + +
328B ASN* 3.7 6.5 - - - +
329B ILE 3.3 0.2 - - - -
330B THR* 1.3 79.5 + - - +
332B LEU* 1.3 60.3 + - - +
334B ASP* 3.6 14.1 + - - +
335B GLN* 3.5 22.4 + - - +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASN 3.2 13.8 + - - +
329B ILE 3.7 3.8 - - - +
330B THR 3.2 0.2 - - - -
331B ALA* 1.3 75.2 - - - +
333B LEU* 1.3 65.6 + - - +
334B ASP 3.1 1.6 - - - -
335B GLN* 3.0 39.9 + - - +
415B MET* 3.6 22.4 - - + +
418B LEU* 3.9 20.9 - - + -
419B LYS* 3.6 51.4 - - + +
422B VAL* 3.3 32.0 - - + +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ILE* 3.0 38.5 + - + +
330B THR* 4.1 0.4 - - - +
332B LEU* 1.3 74.0 - - - +
334B ASP* 1.3 61.7 + - - +
335B GLN 3.1 0.7 + - - -
336B SER* 3.1 20.1 + - - +
339B PHE* 3.8 37.0 + - + +
340B SER 5.1 0.7 - - - +
341B TYR* 3.8 32.8 - - + -
364B ALA* 5.3 1.1 - - + -
366B VAL* 4.2 26.7 - - + -
380B PHE* 6.0 0.2 - - + -
418B LEU* 3.8 23.8 - - + -
422B VAL* 4.0 15.4 - - + +
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Residues in contact with ASP 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B THR* 3.0 22.6 + - - +
331B ALA* 3.6 10.8 - - - +
332B LEU 3.1 0.4 - - - -
333B LEU* 1.3 76.2 - - - +
335B GLN* 1.3 60.8 + - + +
336B SER* 3.2 6.2 + - - +
341B TYR* 2.7 35.1 + - - -
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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