Contacts of the helix formed by residues 352 - 366 (chain A) in PDB entry 3G4G
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 THR 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A VAL 5.3 0.2 - - - +
351A PHE* 1.3 77.3 - - - +
353A ASP* 1.3 59.9 + - - +
354A LEU* 3.6 9.3 + - - +
355A GLU* 2.8 39.9 + - - +
356A ILE* 2.9 27.1 + - - +
472A ARG* 4.1 10.1 - - - +
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Residues in contact with ASP 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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295A ARG 5.0 6.3 - - - +
297A LEU* 4.0 9.0 - - + +
300A THR* 4.0 21.6 + - + +
301A PHE* 3.7 21.0 - - + -
352A THR* 1.3 73.2 - - - +
354A LEU* 1.3 57.8 + - - +
356A ILE* 3.6 20.5 - - - +
357A LEU* 2.9 29.8 + - - +
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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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301A PHE* 3.7 19.1 - - + -
352A THR* 3.2 9.2 + - - +
353A ASP* 1.3 76.8 - - - +
355A GLU* 1.3 57.5 + - - +
357A LEU* 3.8 2.3 - - + +
358A ALA* 3.0 28.4 + - - +
418A LEU* 4.0 21.8 - - + -
422A GLN* 3.6 48.2 - - + +
425A SER* 3.6 20.6 - - - +
426A LEU* 4.0 10.5 - - + +
429A MET* 4.0 9.4 - - + -
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Residues in contact with GLU 355 (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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351A PHE* 3.3 22.4 - - + -
352A THR* 2.8 43.3 + - - +
354A LEU* 1.3 74.7 - - + +
356A ILE* 1.3 65.0 + - - +
358A ALA* 3.4 2.2 + - - +
359A ALA* 3.1 24.9 + - - +
429A MET* 3.7 30.0 - - + +
469A TYR* 5.6 5.0 - - - -
472A ARG* 2.8 40.7 + - - +
476A LEU* 4.1 12.6 - - + +
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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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295A ARG* 3.7 44.4 - - + +
297A LEU* 4.7 8.3 - - + -
342A LEU* 4.2 24.2 - - + +
351A PHE* 3.9 20.2 - - + +
352A THR 2.9 18.4 + - - +
353A ASP* 3.6 25.1 - - - +
355A GLU* 1.3 76.3 - - - +
357A LEU* 1.3 66.7 + - - +
358A ALA 3.3 0.2 + - - -
359A ALA* 3.3 1.7 + - - +
360A ILE* 3.2 31.0 + - + +
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Residues in contact with LEU 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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292A PHE* 3.8 32.8 - - + -
297A LEU* 4.2 17.3 - - + -
301A PHE* 4.1 22.7 - - + -
303A ILE* 5.0 4.9 - - + -
353A ASP 2.9 18.1 + - - +
354A LEU* 3.8 5.8 - - + +
356A ILE* 1.3 79.1 - - - +
358A ALA* 1.3 54.4 + - - +
360A ILE* 3.9 1.9 - - - +
361A PHE* 3.0 31.0 + - + +
414A ILE* 5.8 1.1 - - + -
415A PHE* 3.8 23.8 - - + -
418A LEU* 4.2 13.0 - - + -
426A LEU* 3.5 24.0 - - + -
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Residues in contact with ALA 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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354A LEU 3.0 20.2 + - - +
355A GLU* 3.7 5.4 - - - +
356A ILE 3.2 0.4 - - - -
357A LEU* 1.3 76.9 - - - +
359A ALA* 1.3 56.2 + - - +
361A PHE* 4.6 0.4 - - - -
362A ALA* 2.9 30.8 + - - +
426A LEU* 3.8 16.4 - - + -
429A MET* 3.9 33.0 - - + -
430A VAL* 3.6 13.0 - - + +
433A ILE* 4.5 3.6 - - + -
476A LEU* 5.8 0.4 - - + -
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Residues in contact with ALA 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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338A THR* 4.1 17.3 - - + -
342A LEU* 4.3 5.8 - - + -
355A GLU 3.1 16.7 + - - +
356A ILE 4.0 2.9 - - - +
358A ALA* 1.3 73.2 - - - +
360A ILE* 1.3 60.4 + - - +
362A ALA* 3.8 2.7 - - - +
363A SER* 2.8 32.2 + - - -
433A ILE* 4.2 14.0 - - + +
476A LEU* 4.1 21.3 - - + -
480A VAL* 3.9 11.2 - - + +
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Residues in contact with ILE 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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288A MET* 3.6 24.7 - - - -
291A ILE* 3.6 27.1 - - + -
292A PHE* 3.9 16.8 - - + -
295A ARG* 3.7 24.2 - - - +
297A LEU* 4.5 5.4 - - + -
335A VAL* 3.8 15.4 - - + +
338A THR* 4.7 4.9 - - + -
339A HIS* 4.8 2.7 - - - +
342A LEU* 3.9 14.8 - - + -
356A ILE* 3.2 23.4 + - + +
357A LEU* 4.0 3.8 - - - +
359A ALA* 1.3 76.4 - - - +
361A PHE* 1.3 64.0 + - - +
363A SER* 3.4 7.2 + - - -
364A ALA* 3.1 21.7 + - - +
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Residues in contact with PHE 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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288A MET* 4.8 9.4 - - + -
292A PHE* 5.9 1.5 - + + -
311A TYR* 3.3 42.4 - + - -
357A LEU* 3.0 23.7 + - + +
358A ALA* 4.0 3.1 - - - +
360A ILE* 1.3 75.6 - - - +
362A ALA* 1.3 64.2 + - - +
364A ALA* 3.1 6.6 + - + +
365A ILE* 3.0 46.6 + - + +
403A GLY 4.0 8.7 - - - -
404A PHE* 4.1 16.6 - + - -
407A LEU* 4.5 4.7 - - + -
414A ILE* 4.1 15.7 - - + -
415A PHE* 3.9 34.5 - + + -
426A LEU* 4.6 0.2 - - + -
430A VAL* 3.8 19.7 - - + -
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Residues in contact with ALA 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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358A ALA 2.9 19.9 + - - +
359A ALA 3.8 4.7 - - - +
361A PHE* 1.3 75.3 - - - +
363A SER* 1.3 57.0 + - - +
365A ILE* 3.4 1.4 + - - +
366A HIS* 3.0 34.5 + - - +
430A VAL* 4.1 12.3 - - + -
433A ILE* 3.6 37.5 - - + -
434A VAL* 3.6 17.1 - - + +
480A VAL* 5.3 0.4 - - - -
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Residues in contact with SER 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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319A TYR* 4.5 0.5 + - - -
331A ALA* 4.1 5.4 - - - +
334A VAL* 4.1 5.7 - - - +
335A VAL* 3.6 26.5 - - - -
338A THR* 2.8 23.3 + - - -
359A ALA 2.8 18.0 + - - -
360A ILE* 3.5 7.6 - - - -
361A PHE 3.2 0.2 - - - -
362A ALA* 1.3 79.1 - - - +
364A ALA* 1.3 59.5 + - - +
366A HIS* 2.6 33.0 + - - -
480A VAL* 3.8 11.9 - - - +
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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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284A LEU* 3.9 11.4 - - + +
288A MET* 3.7 22.7 - - + -
315A LEU* 3.7 17.9 - - + +
319A TYR* 2.7 30.5 + - - -
331A ALA* 3.9 1.5 - - - +
335A VAL* 3.3 17.0 - - + +
360A ILE 3.1 10.2 + - - +
361A PHE* 3.1 9.6 + - + +
363A SER* 1.3 81.1 - - - +
365A ILE* 1.3 54.3 + - + +
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Residues in contact with ILE 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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311A TYR* 3.6 23.8 - - - +
315A LEU* 3.7 22.4 - - + -
319A TYR* 3.5 2.7 - - - -
361A PHE* 3.0 45.5 + - + +
362A ALA* 3.7 7.2 - - - +
364A ALA* 1.3 75.7 - - + +
366A HIS* 1.3 59.7 + - - +
367A ASP 2.8 13.0 + - - -
368A VAL* 2.9 19.2 + - - +
399A HIS* 3.7 11.1 - - - +
400A LEU* 4.1 29.6 - - + +
403A GLY* 4.1 21.5 - - - -
404A PHE* 4.5 1.6 - - + -
430A VAL* 4.1 4.0 - - + -
434A VAL* 4.3 2.9 - - + -
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Residues in contact with HIS 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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319A TYR* 4.5 0.6 + - - -
330A HIS* 3.9 5.6 - + - -
331A ALA* 4.5 7.2 - - - -
334A VAL* 3.8 26.7 - - + -
362A ALA 3.0 17.8 + - - +
363A SER* 2.6 27.6 + - - -
365A ILE* 1.3 75.4 - - - +
367A ASP* 1.3 71.5 + - + +
399A HIS* 2.8 22.8 - - - +
434A VAL* 4.1 23.9 - - + +
437A THR* 4.3 21.4 + - + -
480A VAL* 5.6 1.6 - - + -
484A ASP* 3.3 14.3 + - - -
801A ZN 2.3 35.9 - - - -
802A MG 4.2 1.5 - - - -
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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
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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