Contacts of the helix formed by residues 340 - 359 (chain K) in PDB entry 6R1U
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 LEU 340 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K SER* 4.2 2.9 - - - +
88K GLY* 4.0 20.9 - - - +
89K GLU* 2.7 37.2 + - + +
139K TRP* 3.3 44.4 - - + +
192K ARG* 4.2 21.8 - - + +
193K VAL* 4.7 2.5 - - + -
196K VAL* 4.0 10.8 - - + +
201K TRP* 3.7 21.1 - - + +
339K GLY* 1.3 69.1 - - - -
341K VAL* 1.3 59.7 + - - +
342K ARG 3.0 0.4 - - - -
343K ILE* 2.8 45.8 + - + +
344K ARG 3.6 1.9 + - - -
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Residues in contact with VAL 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K GLU* 4.8 1.2 + - - +
136K LEU* 6.0 1.3 - - + -
201K TRP* 3.8 16.5 - - + -
202K TYR* 5.0 0.2 - - + -
205K LEU* 3.5 29.2 - - + -
209K PRO* 3.2 37.9 - - + -
306K MET* 5.0 2.0 - - - -
337K VAL* 4.2 14.4 - - + -
338K ARG 3.4 21.1 - - - +
339K GLY* 3.0 1.6 - - - -
340K LEU* 1.3 80.4 - - - +
342K ARG* 1.3 58.9 + - - +
344K ARG* 2.9 9.8 + - + +
345K CYS* 2.8 26.0 + - - -
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Residues in contact with ARG 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K TYR* 5.0 0.4 - - - -
139K TRP* 2.9 30.6 + - + +
140K VAL* 3.8 9.5 - - - +
141K GLN 4.6 0.6 - - - +
150K TRP* 3.5 20.9 - - + -
159K LEU* 3.5 18.0 - - - +
164K ALA* 3.9 17.6 - - - +
332K ILE* 3.2 37.2 + - - +
333K PRO* 4.5 0.6 - - - +
335K ILE* 2.6 25.7 + - + +
336K ILE* 4.7 0.6 - - - +
337K VAL* 3.4 42.8 - - + +
339K GLY 3.1 11.3 + - - +
340K LEU 3.0 0.8 - - - -
341K VAL* 1.3 81.3 - - - +
343K ILE* 1.3 57.3 + - + +
345K CYS* 3.4 3.6 + - - +
346K VAL* 2.9 32.1 + - + +
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Residues in contact with ILE 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139K TRP* 4.4 8.1 - - + -
150K TRP* 3.6 52.0 - - + +
193K VAL* 4.0 26.0 - - + -
196K VAL* 4.0 15.5 - - + -
340K LEU* 2.8 41.3 + - + +
342K ARG* 1.3 77.1 - - - +
344K ARG* 1.3 57.6 + - - +
346K VAL* 3.3 2.4 + - - +
347K GLN* 3.0 55.2 + - - +
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Residues in contact with ARG 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K VAL* 3.7 30.8 + - + +
197K SER* 5.6 1.4 - - - +
198K ASN 4.4 4.4 + - - -
199K HIS* 4.2 22.4 + - - +
201K TRP* 4.5 6.5 - - + -
202K TYR* 3.8 34.9 - - + +
299K GLU* 6.1 2.6 - - - +
300K TYR* 4.1 3.2 + - - -
306K MET* 3.9 27.8 - - + +
340K LEU 3.6 1.0 + - - -
341K VAL* 2.9 15.2 + - + +
343K ILE* 1.3 79.6 - - - +
345K CYS* 1.3 63.2 + - - +
347K GLN* 3.2 12.6 + - - +
348K GLU* 3.1 48.7 + - - +
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Residues in contact with CYS 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209K PRO* 3.8 34.1 - - - -
211K LEU* 4.7 8.3 - - - -
306K MET* 3.9 19.1 - - - -
310K LEU* 3.7 17.8 - - + +
335K ILE* 4.0 18.8 - - + -
337K VAL* 4.4 10.5 - - - -
341K VAL 2.8 15.6 + - - -
342K ARG 3.6 8.7 - - - +
344K ARG* 1.3 76.5 - - - +
346K VAL* 1.3 61.9 + - - +
348K GLU 3.1 1.7 + - - -
349K VAL* 3.1 21.3 + - - +
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Residues in contact with VAL 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K GLN* 4.6 5.2 - - - +
150K TRP* 3.9 28.0 - - + -
332K ILE* 3.7 46.8 - - + +
335K ILE* 4.3 17.0 - - + -
342K ARG* 2.9 31.0 + - + +
343K ILE 3.7 4.7 - - - +
345K CYS* 1.3 75.1 - - - +
347K GLN* 1.3 64.3 + - + +
349K VAL* 3.2 18.4 - - - +
350K GLU* 4.3 2.6 + - - +
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Residues in contact with GLN 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K TRP* 5.2 4.8 - - + +
193K VAL* 5.2 3.2 + - - +
196K VAL* 4.4 4.1 - - - +
197K SER* 3.7 34.0 + - - +
343K ILE* 3.0 41.2 + - + +
344K ARG* 3.6 17.1 + - - +
345K CYS 3.2 0.4 - - - -
346K VAL* 1.3 79.4 - - + +
348K GLU* 1.3 65.0 + - - +
349K VAL 3.5 0.2 - - - -
350K GLU* 4.2 11.0 + - - +
351K ARG* 4.5 8.5 - - - +
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Residues in contact with GLU 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297K PHE* 5.3 0.5 - - - -
300K TYR* 2.7 31.4 + - - +
306K MET* 4.2 4.5 - - + -
310K LEU* 3.8 13.9 - - + -
344K ARG* 3.1 44.9 + - - +
345K CYS* 3.1 4.9 + - - +
347K GLN* 1.3 79.3 - - - +
349K VAL* 1.3 65.3 + - - +
350K GLU 3.1 2.5 - - - -
351K ARG* 2.9 52.8 + - - +
352K ILE* 3.2 20.4 + - + +
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Residues in contact with VAL 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310K LEU* 4.2 13.2 - - + +
313K LEU* 5.8 1.3 - - + -
314K ILE* 4.0 18.3 - - + +
328K PRO* 4.6 11.2 - - + -
331K CYS* 3.9 24.7 - - + -
332K ILE* 4.4 14.6 - - + -
335K ILE* 4.0 17.7 - - + -
345K CYS 3.1 12.4 + - - +
346K VAL* 3.2 20.9 - - - +
348K GLU* 1.3 78.4 - - - +
350K GLU* 1.3 62.7 + - + +
352K ILE* 3.5 4.1 + - - +
353K LEU* 2.9 32.4 + - + +
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Residues in contact with GLU 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328K PRO* 4.1 19.0 - - + +
346K VAL 5.0 2.0 - - - +
347K GLN 4.2 8.4 + - - +
348K GLU 3.1 0.8 + - - -
349K VAL* 1.3 83.2 - - + +
351K ARG* 1.3 66.6 + - + +
353K LEU* 3.4 5.8 + - - +
354K TYR* 3.2 67.2 + - + +
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Residues in contact with ARG 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296K GLU* 4.4 6.1 + - - -
297K PHE* 3.4 37.0 - - + -
299K GLU* 2.9 28.7 + - - -
347K GLN 4.5 8.1 - - - +
348K GLU* 2.9 46.2 + - - +
350K GLU* 1.3 79.1 - - + +
352K ILE* 1.3 61.7 + - + +
354K TYR* 3.4 6.8 + - - +
355K PHE* 3.2 22.2 + - - +
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Residues in contact with ILE 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297K PHE* 4.2 14.6 - - + -
300K TYR* 5.3 1.3 - - - +
307K TYR* 3.6 49.1 - - + +
310K LEU* 3.7 38.1 - - + -
311K ARG* 4.3 9.9 - - - -
314K ILE* 3.9 16.4 - - + -
348K GLU* 3.2 19.6 + - + +
349K VAL 3.9 3.6 - - - +
351K ARG* 1.3 73.2 - - + +
353K LEU* 1.3 59.6 + - - +
355K PHE* 3.4 1.3 + - + +
356K MET* 2.8 44.6 + - + +
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Residues in contact with LEU 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314K ILE* 3.7 25.3 - - + +
326K LEU* 3.8 20.2 - - + +
327K THR 3.4 9.2 - - - +
328K PRO* 3.3 46.7 - - + -
331K CYS* 4.1 4.3 - - - -
349K VAL 2.9 18.8 + - - +
350K GLU* 3.6 5.4 - - - +
352K ILE* 1.3 76.5 - - - +
354K TYR* 1.3 64.2 + - + +
356K MET* 3.3 5.4 + - - +
357K THR* 2.9 34.5 + - - +
362K ILE* 3.5 25.9 - - + +
363K ASN* 5.1 0.2 - - - +
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Residues in contact with TYR 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328K PRO* 4.3 14.5 - - + +
350K GLU* 3.2 53.5 + - + +
351K ARG* 3.9 6.1 - - - +
353K LEU* 1.3 82.3 - - + +
355K PHE* 1.3 61.1 + - - +
357K THR* 4.3 1.8 - - - -
358K ARG* 2.9 30.3 + - - +
375K LEU 3.7 25.4 - - - -
376K LEU* 3.5 13.4 - - + +
377K PRO* 3.5 34.3 - - + +
380K TYR* 4.7 11.5 + - - +
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Residues in contact with PHE 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292K ASP 3.7 22.9 - - - -
293K GLU* 3.8 24.7 - - + -
295K TYR* 6.4 0.2 - + - -
296K GLU* 3.5 32.8 - - + -
297K PHE* 3.7 20.9 - + + -
307K TYR* 3.9 7.4 - - - -
351K ARG 3.2 17.0 + - - +
352K ILE 3.7 4.7 - - - +
353K LEU 3.3 0.2 - - - -
354K TYR* 1.3 74.9 - - - +
356K MET* 1.3 71.8 + - + +
358K ARG* 3.4 21.9 + - - +
359K LYS* 3.0 55.6 + - + +
222L LEU* 3.8 13.5 - - + -
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Residues in contact with MET 356 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293K GLU* 4.5 9.6 - - - +
307K TYR* 5.0 0.4 - - - -
311K ARG* 3.6 31.6 - - + -
314K ILE* 4.4 12.3 - - + -
315K LEU* 4.6 15.7 - - + -
352K ILE* 2.8 37.6 + - + +
353K LEU 3.5 4.5 - - - +
355K PHE* 1.3 85.7 - - + +
357K THR* 1.3 61.7 + - - +
359K LYS* 3.6 1.6 + - + -
360K GLY 3.2 3.8 + - - -
361K LEU* 3.0 58.8 + - + +
362K ILE* 3.7 19.2 + - + -
222L LEU* 4.6 8.3 - - + -
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Residues in contact with THR 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353K LEU* 2.9 21.5 + - - +
354K TYR* 3.7 6.4 - - - -
355K PHE 3.2 0.2 - - - -
356K MET* 1.3 74.8 - - - +
358K ARG* 1.3 68.1 + - - +
360K GLY* 3.0 13.7 + - - -
362K ILE* 3.7 12.3 - - - +
363K ASN* 3.2 32.1 + - + +
375K LEU* 3.8 27.5 + - + +
376K LEU* 4.0 10.5 - - + -
400K GLN* 4.2 1.0 - - - +
404K PHE* 3.5 27.7 - - + -
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Residues in contact with ARG 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296K GLU* 4.1 16.3 + - - -
354K TYR 2.9 18.4 + - - +
355K PHE* 3.6 28.9 + - - +
357K THR* 1.3 78.3 - - - +
359K LYS* 1.3 79.7 + - - +
360K GLY* 3.4 0.9 + - - -
376K LEU* 4.2 8.1 - - + -
380K TYR* 3.9 28.5 + - + +
400K GLN* 4.9 0.5 - - - +
404K PHE* 3.7 15.9 - - - -
813K VAL 4.7 1.2 - - - +
817K SER* 3.2 39.7 + - - +
820K ALA* 4.0 12.6 - - + -
821K ALA* 3.5 36.8 - - - +
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Residues in contact with LYS 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292K ASP* 2.6 33.1 + - - +
355K PHE* 3.0 54.1 + - + +
356K MET* 4.0 1.1 - - - +
358K ARG* 1.3 92.1 - - - +
360K GLY* 1.3 59.8 + - - +
361K LEU* 3.5 19.7 - - + -
813K VAL* 3.7 7.5 - - - +
817K SER* 3.6 20.2 + - - +
221L LEU* 3.3 39.0 + - - +
222L LEU* 4.3 3.8 - - + -
224L GLN* 4.3 10.5 - - + +
225L THR 4.8 5.5 + - - -
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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
------------------------------------------------------------
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