Contacts of the helix formed by residues 349 - 369 (chain A) in PDB entry 2XAR
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 PRO 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A ALA 3.6 5.3 - - - +
348A LEU* 1.3 95.9 - - + +
350A LEU* 1.3 66.0 + - - +
351A ASP* 4.2 10.5 - - + +
352A GLU* 3.1 26.0 + - + +
353A SER* 3.1 11.1 + - - -
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A HIS* 4.0 19.3 - - + +
324A ASP* 4.0 27.1 - - + +
325A ILE* 4.8 7.9 - - + +
327A ASN* 5.8 3.1 - - - +
348A LEU 3.7 1.2 + - - -
349A PRO* 1.3 71.6 - - - +
351A ASP* 1.3 63.2 + - - +
353A SER* 3.2 8.2 + - - -
354A LEU* 3.0 52.1 + - + +
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 6.0 0.3 + - - -
349A PRO* 4.6 8.3 - - + -
350A LEU* 1.3 81.0 - - - +
352A GLU* 1.3 62.6 + - - +
354A LEU* 3.3 16.8 + - - +
355A LYS* 3.2 19.5 + - - +
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Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.4 31.3 - - + +
349A PRO* 3.1 25.0 + - + +
351A ASP* 1.3 78.4 - - - +
353A SER* 1.3 61.6 + - - +
355A LYS* 3.4 21.0 + - - +
356A ILE* 3.2 32.6 + - + +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A CYS* 4.1 25.6 - - - +
324A ASP* 4.2 17.4 + - - +
325A ILE* 3.5 15.7 - - - -
345A LEU 4.4 0.3 + - - -
348A LEU* 4.0 16.1 + - - +
349A PRO 3.1 11.1 + - - -
350A LEU* 3.2 12.6 + - - +
352A GLU* 1.3 74.9 - - - +
354A LEU* 1.3 64.6 + - - +
356A ILE* 3.3 4.5 + - - +
357A VAL* 3.1 26.7 + - - +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A HIS* 3.8 39.3 - - + +
68A LEU* 3.5 21.9 - - + +
70A ARG* 5.2 10.1 - - - +
325A ILE* 3.4 29.1 - - + +
350A LEU* 3.0 35.1 + - + +
351A ASP* 3.3 19.9 + - - +
353A SER* 1.3 72.5 - - - +
355A LYS* 1.3 61.0 + - - +
357A VAL 3.4 0.7 + - - -
358A LYS* 2.9 34.0 + - - +
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Residues in contact with LYS 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LYS* 5.9 3.1 - - - +
351A ASP 3.2 10.1 + - - +
352A GLU* 3.4 25.6 - - - +
354A LEU* 1.3 78.9 - - - +
356A ILE* 1.3 65.0 + - + +
358A LYS* 3.6 11.1 - - - +
359A GLU* 2.9 58.3 + - + +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LEU 5.1 1.4 - - - +
312A LYS* 5.7 7.4 - - + -
313A LEU* 3.7 35.0 - - + -
318A ALA* 4.1 16.8 - - + -
321A CYS* 3.7 28.9 - - + -
345A LEU* 4.5 0.2 - - + -
348A LEU* 3.9 22.2 - - + -
352A GLU* 3.2 26.5 + - + +
353A SER 3.3 6.3 + - - +
355A LYS* 1.3 81.4 - - + +
357A VAL* 1.3 59.7 + - - +
359A GLU* 3.9 8.8 - - - +
360A TYR* 3.0 25.6 + - - +
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.2 10.5 - - + -
318A ALA* 4.3 5.6 - - - +
321A CYS* 3.7 22.7 - - + -
322A TYR* 3.7 15.3 - - + +
325A ILE* 3.8 11.0 - - + -
353A SER 3.1 16.7 + - - +
354A LEU 4.0 2.2 - - - +
356A ILE* 1.3 72.9 - - + +
358A LYS* 1.3 66.8 + - - +
360A TYR* 3.2 7.2 + - - +
361A LEU* 3.0 24.2 + - + +
413A LEU* 3.8 28.9 - - + -
416A MET* 4.3 18.4 - - + -
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Residues in contact with LYS 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.9 33.0 + - + +
69A TRP* 3.7 33.9 - - + -
71A GLU* 4.1 21.2 - - - +
72A ASN* 4.0 15.2 + - - +
92A VAL* 6.3 0.4 - - - -
354A LEU 2.9 19.0 + - - +
355A LYS* 3.6 12.1 - - - +
357A VAL* 1.3 77.1 - - - +
359A GLU* 1.3 61.1 + - - +
361A LEU* 3.0 7.4 + - - +
362A ILE* 2.9 40.4 + - + +
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LEU* 3.6 41.8 - - + +
312A LYS* 3.2 29.9 - - - +
355A LYS* 2.9 56.1 + - + +
356A ILE* 3.9 5.5 - - - +
358A LYS* 1.3 76.9 - - + +
360A TYR* 1.3 60.0 + - - +
362A ILE* 3.7 14.5 - - + +
363A ALA* 2.8 30.5 + - - +
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Residues in contact with TYR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 5.8 1.6 + - - -
310A LEU 4.3 4.4 + - - -
311A ASP* 3.3 39.2 + - + +
315A ILE* 3.4 41.9 + - + +
318A ALA* 3.8 17.7 - - + -
356A ILE 3.0 15.1 + - - +
357A VAL* 3.2 12.5 + - - +
359A GLU* 1.3 77.8 - - - +
361A LEU* 1.3 62.1 + - + +
363A ALA* 3.3 6.2 + - - +
364A ALA* 2.8 29.9 + - + -
367A LYS* 4.6 9.7 + - - -
416A MET* 3.7 19.3 - - - -
419A TYR* 3.7 32.8 - + - +
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.7 29.2 - - + -
69A TRP* 4.6 12.6 - - + +
88A TYR* 3.8 2.4 + - - -
357A VAL* 3.0 15.2 + - + +
358A LYS 3.0 8.7 + - - +
360A TYR* 1.3 73.3 - - + +
362A ILE* 1.3 61.9 + - - +
364A ALA* 3.4 5.7 - - - +
365A THR* 3.2 24.3 + - - -
411A LYS* 3.9 39.5 + - + +
412A PRO 4.4 5.6 - - - +
413A LEU* 4.1 21.5 - - + +
416A MET* 4.1 23.3 - - + -
419A TYR* 4.2 14.6 - - + -
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Residues in contact with ILE 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A TRP* 4.0 10.3 - - + -
88A TYR* 3.6 12.6 - - - +
92A VAL* 3.8 21.8 - - + -
93A ILE* 4.2 17.2 - - + +
96A LEU* 5.3 11.2 - - + -
307A ILE* 3.8 21.8 - - + +
310A LEU* 5.7 6.5 - - + -
358A LYS* 2.9 39.0 + - + +
359A GLU* 3.7 16.4 - - + +
361A LEU* 1.3 75.4 - - - +
363A ALA* 1.3 67.0 + - - +
365A THR* 2.9 15.6 + - - -
366A ALA* 3.0 11.1 + - - +
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Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ILE 3.5 17.2 + - - +
308A GLN* 3.3 26.9 - - - +
310A LEU* 4.9 0.2 - - - +
311A ASP* 3.6 18.8 - - + +
359A GLU 2.8 17.0 + - - +
360A TYR 3.5 4.7 - - - +
362A ILE* 1.3 76.4 - - - +
364A ALA* 1.3 63.1 + - - +
366A ALA* 2.8 4.9 + - - +
367A LYS* 2.8 30.7 + - - +
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A TYR* 2.8 24.9 + - + +
361A LEU* 3.4 12.3 - - - +
363A ALA* 1.3 72.1 - - - +
365A THR* 1.3 66.0 + - - +
367A LYS* 3.1 22.8 + - - +
368A ASP* 3.3 13.3 + - - +
411A LYS* 3.8 19.1 - - + -
419A TYR* 4.1 19.1 - - + +
500A IHP 5.1 3.9 + - - +
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 2.6 31.5 + - + -
93A ILE* 4.0 7.6 - - + -
361A LEU 3.2 6.9 + - - -
362A ILE 2.9 10.1 + - - -
364A ALA* 1.3 80.0 - - - +
366A ALA* 1.3 58.5 + - - +
368A ASP* 3.0 15.6 + - - +
369A CYS* 3.1 12.4 + - - +
407A ASP 4.8 1.0 - - - +
408A LEU* 3.8 23.3 - - + -
409A SER 2.8 40.8 + - - +
411A LYS* 4.1 7.8 + - - +
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Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 5.9 0.6 - - + +
97A LEU* 6.0 1.1 - - + -
169A PRO* 5.5 0.5 - - - +
304A LEU* 3.7 17.3 - - + +
307A ILE* 3.7 36.3 - - + -
308A GLN* 3.1 23.8 + - + +
362A ILE 3.0 1.2 + - - -
363A ALA 2.8 12.8 + - - +
365A THR* 1.3 76.6 - - - +
367A LYS* 1.3 60.6 + - - +
369A CYS* 3.2 22.4 - - - +
408A LEU* 5.2 2.5 - - - -
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Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LYS* 3.1 36.8 + - - +
171A CYS* 3.8 31.1 + - + +
173A PHE* 4.9 1.5 - - - -
308A GLN* 3.5 30.7 - - + +
311A ASP* 3.1 38.6 + - - -
360A TYR* 4.6 12.1 + - - -
363A ALA* 2.8 20.7 + - - +
364A ALA* 3.1 13.7 + - - +
366A ALA* 1.3 78.1 - - - +
368A ASP* 1.3 57.1 + - + +
369A CYS 3.7 0.7 - - - -
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Residues in contact with ASP 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LYS* 3.0 36.3 + - - +
170A LYS* 3.2 14.2 + - - +
364A ALA 3.3 9.3 + - - +
365A THR 3.0 5.1 + - - +
367A LYS* 1.3 79.6 - - + +
369A CYS* 1.3 66.5 + - - +
370A SER* 4.3 1.6 + - - -
407A ASP* 4.2 11.0 - - - +
411A LYS* 3.8 8.5 + - - +
500A IHP 2.7 58.3 + - - +
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Residues in contact with CYS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LYS* 4.0 2.9 - - - +
169A PRO* 3.5 17.2 - - - +
304A LEU* 3.6 29.4 - - - -
365A THR 3.1 7.3 + - - +
366A ALA* 3.2 23.9 - - - +
367A LYS 4.9 0.9 - - - +
368A ASP* 1.3 83.6 + - - +
370A SER* 1.3 63.1 + - - +
405A PHE* 4.1 13.2 - - - -
406A ILE 3.2 12.3 - - - +
407A ASP* 3.4 11.9 - - - +
408A LEU* 3.5 22.9 - - + -
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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
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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