Contacts of the helix formed by residues 365 - 373 (chain A) in PDB entry 3GUU
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 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A ALA* 3.3 15.3 - - - +
333A PRO* 4.3 8.7 - - + +
335A GLU* 3.3 28.0 - - + +
364A ALA* 1.3 79.3 - - - +
366A HIS* 1.3 68.0 + - - +
367A LEU 3.4 3.4 - - - +
368A THR* 3.0 18.6 + - + +
369A ALA* 3.0 17.7 + - - +
433A LYS* 4.2 9.8 + - - -
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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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183A TYR* 2.6 47.2 + + - -
184A SER* 2.8 33.5 + - - -
213A GLY 4.0 5.6 - - - -
331A ALA* 4.7 0.2 - - - -
334A ASP* 2.9 38.7 + - - +
335A GLU* 2.9 17.2 + - - +
336A ILE* 3.8 28.8 - - + +
337A VAL* 3.5 23.2 - - + +
365A GLU* 1.3 71.2 - - - +
367A LEU* 1.3 72.7 + - + +
370A GLU 3.3 6.4 + - - -
431A PHE* 4.4 8.3 - + - -
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU* 4.9 0.6 + - - +
336A ILE* 4.1 17.7 - - + -
365A GLU* 3.4 2.0 - - - +
366A HIS* 1.3 77.7 - - + +
368A THR* 1.3 66.7 + - + +
370A GLU* 3.2 37.6 - - - +
371A ILE* 3.8 3.6 + - - +
429A SER* 3.4 26.9 - - - +
431A PHE* 3.8 30.5 - - + -
433A LYS* 3.7 30.5 - - + +
434A PRO 3.6 22.0 - - - +
435A PHE* 3.8 16.0 - - + -
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Residues in contact with THR 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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364A ALA* 3.7 7.1 - - - -
365A GLU* 3.0 37.2 + - + +
367A LEU* 1.3 80.1 - - + +
369A ALA* 1.3 54.9 + - - +
371A ILE* 3.2 5.9 + - - +
372A PHE* 3.0 48.8 + - + -
434A PRO 4.4 7.9 - - - +
436A GLY* 3.9 27.4 - - - +
437A PRO* 5.4 1.1 - - + -
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Residues in contact with ALA 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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183A TYR* 3.8 8.5 - - - +
329A TRP* 2.7 28.7 + - + -
331A ALA* 3.7 28.9 - - + +
361A TYR* 4.2 9.6 - - + -
364A ALA* 4.2 5.8 - - + +
365A GLU 3.0 20.4 + - - +
368A THR* 1.3 73.3 + - - +
370A GLU* 1.3 64.5 + - - +
372A PHE* 3.8 12.2 - - - -
373A GLY 3.2 7.6 + - - -
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Residues in contact with GLU 370 (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 TYR* 3.4 18.8 + - - -
122A ASP* 2.3 40.2 - - - +
183A TYR* 3.5 43.8 + - + -
329A TRP* 4.3 6.2 + - - -
366A HIS 3.3 7.9 + - - +
367A LEU* 3.2 36.8 - - - +
368A THR 3.2 0.4 - - - -
369A ALA* 1.3 77.9 - - - +
371A ILE* 1.3 62.3 + - + +
374A LEU* 3.7 18.4 + - - +
431A PHE* 4.8 4.3 - - - -
435A PHE* 3.7 14.9 - - + -
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Residues in contact with ILE 371 (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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122A ASP* 4.9 2.0 - - + -
367A LEU 3.8 3.6 + - - +
368A THR 3.2 5.4 + - - +
369A ALA 3.2 0.2 - - - -
370A GLU* 1.3 81.4 - - + +
372A PHE* 1.3 65.2 + - - +
374A LEU* 2.9 23.0 + - + +
375A VAL 4.3 1.7 + - - -
421A LEU* 3.8 37.4 - - + +
424A LEU* 4.0 14.6 - - + -
435A PHE* 3.8 43.7 - - + -
436A GLY 4.0 7.9 - - - +
437A PRO 3.5 28.3 - - - +
438A ILE* 3.9 11.7 - - + +
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Residues in contact with PHE 372 (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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361A TYR* 3.2 33.7 + + + -
363A ILE 3.8 17.5 - - - -
364A ALA* 3.9 13.5 - - + -
368A THR* 3.0 38.4 + - + +
369A ALA* 3.5 7.4 + - - -
371A ILE* 1.3 75.3 - - - +
373A GLY* 1.3 57.3 + - - +
375A VAL 4.6 0.2 + - - -
376A PRO* 3.4 18.4 - - - +
400A ALA 3.9 2.1 - - - +
401A ILE* 5.4 0.3 - - - -
402A ALA 5.2 1.4 + - - -
437A PRO* 3.2 34.8 - - + -
438A ILE 3.4 18.5 - - - +
439A THR 3.6 3.8 - - - -
440A PRO* 3.6 46.2 - - + -
441A PRO* 4.3 7.4 - - + -
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Residues in contact with GLY 373 (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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327A PHE* 3.9 4.2 - - - -
329A TRP* 3.6 28.6 - - - -
361A TYR* 3.4 12.7 + - - -
369A ALA 3.2 6.5 + - - -
371A ILE 3.2 0.8 - - - -
372A PHE* 1.3 78.1 - - - +
374A LEU* 1.3 58.8 + - - +
375A VAL 3.6 0.4 - - - -
376A PRO* 3.7 6.5 - - - +
377A SER* 2.9 30.0 + - - -
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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