Contacts of the helix formed by residues 292 - 311 (chain D) in PDB entry 6UZA
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 292 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D SER* 4.0 2.0 - - - -
291D GLU* 1.3 79.5 - - + +
293D PRO* 1.3 62.3 - - - +
294D VAL* 3.4 5.9 + - - +
295D MET* 3.7 17.3 - - + +
296D THR* 3.1 24.9 + - - -
365D ARG* 3.1 25.2 + - - -
855D TYR* 2.9 29.5 + - + -
859D MET* 3.9 12.3 - - - +
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Residues in contact with PRO 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D LEU* 3.3 26.3 - - + +
287D SER 5.1 0.2 - - - +
290D SER* 3.6 10.3 - - - +
291D GLU 3.5 10.5 - - - +
292D ASP* 1.3 82.9 - - - +
294D VAL* 1.3 61.9 + - - +
296D THR* 3.9 3.5 - - - -
297D ALA* 2.9 30.7 + - - +
328D PHE* 3.7 22.0 - - + -
332D LEU* 4.5 3.8 - - + -
859D MET* 3.8 19.7 - - + -
863D ILE* 3.8 28.0 - - + -
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Residues in contact with VAL 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ASP* 3.3 2.6 - - - +
293D PRO* 1.3 75.0 - - - +
295D MET* 1.3 60.0 + - - +
297D ALA* 3.4 4.1 + - - +
298D LEU* 3.0 35.0 + - + +
328D PHE* 5.0 0.4 - - - -
329D VAL* 3.7 27.7 - - + +
332D LEU* 3.8 26.7 - - + -
345D ILE* 4.2 23.1 - - + +
365D ARG* 3.8 37.2 - - - +
377D PHE* 5.2 1.1 - - + -
859D MET* 4.2 10.3 - - + -
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Residues in contact with MET 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ASP* 3.7 26.7 + - + +
294D VAL* 1.3 78.2 - - - +
296D THR* 1.3 58.8 + - - +
298D LEU* 3.4 7.6 + - + +
299D GLU* 3.0 73.4 + - + +
365D ARG* 4.5 19.9 - - - +
368D LEU* 3.7 22.7 - - + -
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Residues in contact with THR 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ARG* 5.1 12.8 - - - +
286D LEU* 4.0 18.6 - - + -
289D SER* 6.1 0.4 - - - +
290D SER* 4.0 22.0 + - - +
292D ASP 3.1 17.2 + - - -
293D PRO* 3.9 4.3 - - - -
294D VAL 3.3 0.6 - - - -
295D MET* 1.3 78.7 - - - +
297D ALA* 1.3 56.2 + - - +
299D GLU* 3.5 4.6 + - - +
300D LEU* 2.9 33.6 + - + +
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D LEU* 4.1 14.1 - - + +
293D PRO 2.9 19.7 + - - +
294D VAL 3.9 0.2 - - - +
296D THR* 1.3 76.7 - - - +
298D LEU* 1.3 59.2 + - - +
300D LEU* 3.8 5.2 - - - +
301D SER* 2.9 29.8 + - - -
325D CYS* 3.9 11.8 - - - +
328D PHE* 3.7 14.6 - - + -
329D VAL* 3.7 25.1 - - + -
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Residues in contact with LEU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D VAL* 3.0 31.0 + - + +
295D MET* 3.8 8.5 - - + +
296D THR 3.3 0.4 - - - -
297D ALA* 1.3 76.8 - - - +
299D GLU* 1.3 61.3 + - + +
301D SER* 2.7 20.3 + - - +
302D ASN 3.0 6.6 + - - -
326D LYS* 6.2 0.7 - - + -
329D VAL* 4.7 15.5 - - + -
365D ARG* 4.0 33.7 - - + +
368D LEU* 4.8 13.5 - - + -
369D ALA* 4.8 11.0 - - + +
372D TYR* 3.5 24.3 - - + -
374D VAL* 3.8 32.3 - - + -
377D PHE* 5.9 3.4 - - + -
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Residues in contact with GLU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D MET* 3.0 48.7 + - + +
296D THR* 4.0 4.3 - - - +
298D LEU* 1.3 74.6 - - - +
300D LEU* 1.3 57.2 + - - +
302D ASN* 3.4 8.1 + - - +
303D GLU* 2.9 29.7 + - - +
368D LEU* 4.0 2.3 - - - +
372D TYR* 3.0 29.7 + - - -
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Residues in contact with LEU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ARG* 3.5 35.2 - - - +
277D TYR* 4.3 17.7 - - + -
280D LEU* 3.4 31.6 - - + +
281D ALA* 3.8 6.3 - - - +
286D LEU* 4.2 12.3 - - + -
296D THR* 2.9 19.3 + - + +
297D ALA 3.9 2.9 - - - +
299D GLU* 1.3 74.1 - - - +
301D SER* 1.3 61.6 + - - +
303D GLU* 3.9 7.4 - - - +
304D LEU* 2.9 43.2 + - + +
325D CYS* 3.8 21.8 - - - -
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Residues in contact with SER 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ALA 2.9 15.4 + - - -
298D LEU* 2.7 28.1 + - - +
300D LEU* 1.3 76.1 - - - +
302D ASN* 1.3 55.4 + - - +
304D LEU 3.5 0.2 + - - -
305D ALA* 3.0 26.0 + - - +
322D SER* 3.0 29.7 + - - +
325D CYS* 3.8 20.3 - - - +
326D LYS* 4.2 18.3 - - - +
372D TYR* 4.8 3.9 - - - +
374D VAL* 4.8 3.3 - - - +
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Residues in contact with ASN 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU 3.0 9.6 + - - +
299D GLU* 3.7 11.4 + - - +
301D SER* 1.3 83.0 + - - +
303D GLU* 1.3 57.1 + - - +
305D ALA* 3.3 6.3 + - - +
306D VAL* 2.9 40.7 + - - +
372D TYR* 3.4 51.4 + - + -
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Residues in contact with GLU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ARG* 2.7 35.5 + - - +
248D PRO 5.4 0.3 - - - +
277D TYR* 2.6 34.9 + - + +
299D GLU 2.9 18.0 + - - +
300D LEU* 3.7 8.1 - - + +
302D ASN* 1.3 78.7 - - - +
304D LEU* 1.3 58.7 + - - +
306D VAL* 3.3 6.0 + - - +
307D LEU* 3.0 39.3 + - + +
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D TYR* 3.8 32.5 - - + -
281D ALA* 4.0 15.3 - - + -
300D LEU* 2.9 29.8 + - + +
303D GLU* 1.3 77.0 - - - +
305D ALA* 1.3 58.8 + - - +
307D LEU* 3.4 3.8 + - + +
308D ALA* 2.9 28.8 + - - +
318D TYR* 3.6 35.5 - - + +
321D LEU* 3.7 34.5 - - + +
322D SER* 3.9 15.3 - - - +
325D CYS* 4.0 6.7 - - - -
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Residues in contact with ALA 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D SER 3.0 19.0 + - - +
302D ASN* 3.8 7.6 - - - +
303D GLU 3.3 0.2 - - - -
304D LEU* 1.3 76.4 - - - +
306D VAL* 1.3 60.2 + - + +
308D ALA* 3.7 11.5 + - - +
309D ASN* 3.0 22.7 - - - +
318D TYR 5.5 0.2 - - - -
319D LYS* 4.9 10.5 + - + +
322D SER* 4.1 12.0 + - - +
326D LYS* 5.6 5.2 - - - +
372D TYR 6.0 2.0 - - - +
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Residues in contact with VAL 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D ASN* 2.9 34.9 + - - +
303D GLU* 3.6 7.6 - - - +
304D LEU 3.2 0.4 - - - -
305D ALA* 1.3 77.1 - - - +
307D LEU* 1.3 64.8 + - + +
308D ALA 3.2 0.2 - - - -
309D ASN* 3.1 9.8 + - - +
310D ILE* 3.0 47.3 + - + +
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D TYR* 5.4 11.0 - - + +
273D ARG* 3.7 17.5 - - - +
277D TYR* 3.7 34.1 - - + +
303D GLU* 3.0 37.3 + - + +
304D LEU* 3.4 7.4 + - + +
306D VAL* 1.3 82.6 - - + +
308D ALA* 1.3 61.2 + - - +
310D ILE* 3.9 13.5 - - + +
311D GLU* 3.1 35.4 + - + +
318D TYR* 3.7 25.0 - - + +
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Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D LEU 2.9 17.6 + - - +
305D ALA* 3.8 9.6 - - - +
306D VAL 3.2 0.6 - - - -
307D LEU* 1.3 77.7 - - - +
309D ASN* 1.3 57.4 + - - +
311D GLU 3.5 11.3 - - - +
312D LYS* 4.8 1.4 - - - -
315D LYS* 3.4 31.2 - - + +
318D TYR* 3.7 21.3 - - + +
319D LYS* 4.0 27.8 - - + +
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Residues in contact with ASN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D ALA 3.0 18.0 - - - +
306D VAL* 3.1 7.5 + - - +
308D ALA* 1.3 83.1 + - - +
310D ILE* 1.3 66.5 + - + +
311D GLU 3.4 2.6 - - - -
312D LYS* 4.6 4.5 + - - +
315D LYS* 5.2 5.2 - - - +
319D LYS* 4.4 16.7 + - - +
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Residues in contact with ILE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D TYR* 3.6 27.1 - - + -
252D PHE* 3.6 35.9 - - + -
306D VAL* 3.0 39.2 + - + +
307D LEU* 4.3 10.8 - - + -
309D ASN* 1.3 81.1 - - + +
311D GLU* 1.3 60.1 + - + +
312D LYS* 3.6 3.5 + - - +
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Residues in contact with GLU 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D TYR* 3.3 44.9 + - + +
270D SER* 4.1 16.1 + - - +
273D ARG* 3.7 17.5 + - - -
307D LEU* 3.1 20.0 + - + +
308D ALA* 3.5 15.9 - - - +
310D ILE* 1.3 75.9 - - + +
312D LYS* 1.3 60.3 + - - +
313D GLU* 2.9 30.0 - - + +
314D PHE* 3.8 17.4 - - + -
315D LYS* 4.4 2.4 + - - +
318D TYR* 3.9 18.2 + - + -
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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