Contacts of the helix formed by residues 351 - 364 (chain A) in PDB entry 3H8E
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 GLU 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL* 3.5 29.9 - - + +
267A LYS* 4.5 9.9 + - - -
269A ILE* 4.1 22.1 - - + +
322A ASN* 3.2 26.0 + - + +
348A THR 3.6 11.7 - - - +
349A ASP* 2.5 45.2 + - - +
350A ALA* 1.3 72.0 - - - +
352A GLY* 1.3 70.7 + - - +
353A ARG 3.2 2.0 - - - -
354A LEU* 3.0 21.9 + - + +
355A VAL* 3.2 12.7 + - - +
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Residues in contact with GLY 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS* 3.6 34.7 - - - +
269A ILE* 4.5 0.4 - - - -
350A ALA 3.7 0.4 - - - -
351A GLU* 1.3 86.9 - - - +
353A ARG* 1.3 57.9 + - - +
355A VAL* 3.3 8.6 + - - +
356A LEU* 3.0 38.1 + - - +
377A LEU* 4.8 4.1 - - - +
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Residues in contact with ARG 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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350A ALA* 3.5 32.1 + - - +
352A GLY* 1.3 76.3 - - - +
354A LEU* 1.3 61.4 + - + +
356A LEU* 3.8 3.1 - - - -
357A CYS* 2.9 31.0 + - - +
377A LEU* 3.8 29.4 + - + +
378A THR* 4.0 9.1 - - - +
427A LEU* 5.3 0.8 - - - +
436A ASN* 3.0 32.2 + - + -
437A ILE* 4.4 7.6 - - - +
438A GLY 5.1 0.8 - - - +
443A GLY 5.1 1.4 + - - -
446A THR* 4.7 5.3 + - - -
447A ALA* 3.7 36.3 - - - +
450A PHE* 3.5 36.1 - - + +
451A LEU* 3.7 17.1 - - + +
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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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233A ALA* 3.4 29.2 - - + +
234A PHE 3.6 4.6 + - - -
236A ALA* 5.4 0.2 - - + -
237A VAL* 3.5 22.9 - - + -
343A VAL* 3.9 27.8 - - + -
345A ILE* 3.9 30.7 - - + -
347A ASN 5.4 0.2 - - - +
348A THR* 5.7 1.3 - - - +
350A ALA 3.5 21.1 - - - +
351A GLU* 3.0 9.8 + - + +
352A GLY 3.0 0.4 - - - -
353A ARG* 1.3 75.7 - - - +
355A VAL* 1.3 65.1 + - - +
357A CYS* 3.4 17.8 + - - -
358A ASP 3.7 2.4 + - - -
436A ASN* 4.0 13.9 - - + +
450A PHE* 4.0 12.6 - - + -
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PHE* 3.2 38.3 - - + +
237A VAL* 3.8 34.1 - - + -
267A LYS* 4.8 3.6 - - + -
269A ILE* 4.0 16.4 - - + -
318A ALA* 3.7 23.8 - - + +
320A ALA* 4.3 4.7 - - + -
351A GLU 3.2 4.5 + - - +
352A GLY* 3.4 14.4 - - - +
354A LEU* 1.3 77.2 - - - +
356A LEU* 1.3 66.8 + - + +
358A ASP* 3.7 0.9 + - - +
359A THR* 2.9 27.3 + - - -
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 3.6 28.3 - - + -
266A GLY 4.2 1.1 - - - +
267A LYS* 3.9 25.6 - - + +
318A ALA* 4.7 3.8 - - + -
352A GLY 3.0 25.2 + - - +
355A VAL* 1.3 79.3 - - + +
357A CYS* 1.4 60.7 + - - +
359A THR* 3.1 3.8 + - - -
360A LEU* 2.8 34.8 + - + +
373A ASP* 4.3 13.9 - - + +
374A ILE 5.0 0.4 - - - +
375A ALA* 3.7 27.6 - - + -
377A LEU* 4.4 2.7 - - + -
451A LEU* 3.7 32.3 - - + -
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Residues in contact with CYS 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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233A ALA* 3.8 17.7 - - - -
337A THR* 4.0 6.7 - - - -
353A ARG 2.9 17.8 + - - +
354A LEU* 3.4 16.4 - - - -
355A VAL 3.4 0.6 - - - -
356A LEU* 1.4 76.4 - - - +
358A ASP* 1.3 66.1 + - - +
360A LEU* 3.3 8.5 + - - +
361A THR* 3.1 23.6 + - - -
450A PHE* 3.8 10.8 - - + -
451A LEU* 4.5 2.0 - - + -
454A PHE* 3.6 52.7 - - + -
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Residues in contact with ASP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A MET* 3.0 38.6 - - + +
233A ALA* 3.0 19.2 + - - -
234A PHE* 2.9 36.1 + - + -
337A THR* 3.3 11.6 - - - -
338A MET* 2.8 26.3 + - - +
339A SER 4.6 0.3 + - - -
354A LEU 3.7 0.6 + - - +
355A VAL 3.7 1.4 + - - +
356A LEU 3.3 0.6 - - - -
357A CYS* 1.3 77.7 - - - +
359A THR* 1.3 57.9 + - - +
361A THR* 3.3 8.2 + - - -
362A TYR* 3.0 25.5 + - - +
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A MET* 4.8 2.4 - - - +
234A PHE* 4.5 4.3 - - - -
247A LEU* 3.8 21.3 - - + +
265A VAL* 3.7 19.3 - - + -
316A LEU* 3.6 33.0 - - + +
318A ALA* 3.4 15.2 - - + +
355A VAL 2.9 18.0 + - - -
356A LEU 3.1 4.8 + - - -
358A ASP* 1.3 75.3 - - - +
360A LEU* 1.3 59.2 + - - +
362A TYR* 3.2 7.7 + - + +
363A ALA* 2.9 27.0 + - - +
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 4.3 11.9 - - + -
356A LEU* 2.8 19.3 + - + +
357A CYS 3.5 8.1 - - - +
359A THR* 1.3 73.1 - - - +
361A THR* 1.3 66.2 + - - +
363A ALA* 3.2 11.0 + - - +
364A GLU* 4.0 0.5 - - - +
371A VAL* 3.8 21.5 - - + -
373A ASP* 4.1 10.8 - - + +
451A LEU* 3.9 40.2 - - + +
454A PHE* 3.9 13.9 - - + +
455A ALA* 4.8 1.8 - - + -
458A TYR* 2.7 37.1 + - - +
460A TRP* 3.9 24.5 - - + +
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Residues in contact with THR 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A MET* 3.9 25.9 - - + +
339A SER* 3.7 38.7 + - - +
357A CYS 3.1 14.1 + - - -
358A ASP* 3.3 9.2 + - - -
360A LEU* 1.3 76.3 - - - +
362A TYR* 1.4 64.2 + - - +
364A GLU* 3.1 39.2 + - - +
365A ARG* 4.6 1.4 + - - -
454A PHE* 3.9 11.0 + - - +
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Residues in contact with TYR 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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219A GLU* 4.4 10.0 + - - -
221A LEU* 3.8 20.8 - - + +
225A LYS* 6.1 0.4 - - - -
229A LEU* 3.8 18.8 - - + -
231A MET* 3.6 32.3 - - + -
247A LEU* 4.1 7.9 - - + -
249A VAL* 4.0 22.1 - - + +
316A LEU* 4.1 11.4 - - + -
338A MET* 3.9 6.8 - - + -
358A ASP 3.0 6.8 + - - +
359A THR* 3.2 11.4 + - - +
361A THR* 1.4 76.3 - - - +
363A ALA* 1.3 62.5 + - - +
364A GLU 3.1 1.7 + - - -
365A ARG* 2.9 76.8 + - - +
366A PHE* 3.9 18.0 - + - -
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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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263A VAL* 4.2 14.0 - - + +
265A VAL* 4.8 0.9 - - + -
316A LEU* 3.7 16.6 - - + -
359A THR 2.9 13.6 + - - +
360A LEU* 3.5 12.6 - - - +
361A THR 3.1 0.6 - - - -
362A TYR* 1.3 76.2 - - - +
364A GLU* 1.3 64.8 + - - +
365A ARG 3.1 0.9 + - - -
366A PHE* 3.2 27.3 + - - +
368A PRO* 3.8 9.5 - - - +
371A VAL* 4.5 6.7 - - + -
458A TYR* 4.1 14.4 - - + +
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Residues in contact with GLU 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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339A SER* 6.1 0.3 - - - -
360A LEU 4.0 2.0 - - - +
361A THR* 3.1 29.9 + - - +
363A ALA* 1.3 78.6 - - - +
365A ARG* 1.3 63.2 - - - +
367A LYS* 3.1 34.7 + - - +
368A PRO* 4.1 0.7 - - - +
454A PHE 4.3 11.6 - - - +
457A ALA* 3.8 24.8 + - + +
458A TYR* 3.7 24.7 - - + -
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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