Contacts of the helix formed by residues 365 - 373 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 6.1 1.0 - - - +
331B ALA* 3.6 9.2 - - - -
333B PRO* 4.4 7.9 - - + +
335B GLU* 3.3 20.8 - - + +
364B ALA* 1.3 77.8 - - - +
366B HIS* 1.3 68.9 + - - +
367B LEU* 3.4 3.1 - - + +
368B THR* 2.7 23.8 + - + +
369B ALA* 2.9 23.0 + - - +
433B LYS* 4.1 18.1 + - - -
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Residues in contact with HIS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 2.6 42.3 + + - -
184B SER* 2.9 36.3 + - - -
213B GLY* 4.0 5.6 - - - -
331B ALA* 4.2 0.6 - - - +
334B ASP* 2.7 40.4 + - - +
335B GLU* 2.9 16.0 + - - +
336B ILE* 3.7 31.8 - - + +
337B VAL* 3.6 23.9 - - + +
365B GLU* 1.3 71.1 - - - +
367B LEU* 1.3 68.0 + - + +
370B GLU* 3.1 11.5 + - - +
431B PHE* 4.6 8.2 - + - -
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLU* 5.0 1.8 - - - +
336B ILE* 4.0 18.6 - - + -
365B GLU* 4.6 2.4 - - + +
366B HIS* 1.3 79.9 - - + +
368B THR* 1.3 66.0 + - + +
370B GLU* 3.3 35.9 - - - +
371B ILE* 3.7 3.5 + - - +
429B SER* 3.0 32.1 - - - +
431B PHE* 3.9 27.6 - - + -
433B LYS* 3.7 27.1 - - + +
434B PRO 3.6 24.7 - - - +
435B PHE* 3.6 17.4 - - + -
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ALA* 3.5 7.1 - - - -
365B GLU* 2.7 47.0 + - + +
367B LEU* 1.3 77.6 - - + +
369B ALA* 1.4 59.2 + - - +
371B ILE* 3.2 6.6 + - - +
372B PHE* 3.0 46.9 + - + -
434B PRO 4.2 9.4 - - - +
436B GLY* 4.2 23.6 - - - +
437B PRO* 5.8 0.9 - - + -
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 3.9 8.3 - - - +
329B TRP* 2.9 24.4 + - + -
330B HIS 4.4 0.9 - - - -
331B ALA* 3.6 30.1 - - + +
361B TYR* 4.2 10.1 - - + -
364B ALA* 4.1 6.1 - - + -
365B GLU 2.9 18.1 + - - +
368B THR* 1.4 74.3 + - - +
370B GLU* 1.3 65.3 + - - +
371B ILE 3.2 0.2 - - - -
372B PHE* 3.8 12.3 - - - -
373B GLY 3.1 11.4 + - - -
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B TYR* 3.4 20.4 + - - -
122B ASP* 2.6 37.4 - - - +
183B TYR* 3.4 44.4 + - + -
329B TRP* 4.4 6.2 + - - -
366B HIS* 3.1 9.3 + - - +
367B LEU* 3.3 35.4 - - - +
368B THR 3.1 0.2 - - - -
369B ALA* 1.3 78.3 - - - +
371B ILE* 1.3 60.8 + - + +
374B LEU* 3.7 19.2 + - - +
431B PHE* 5.4 2.8 - - - -
435B PHE* 3.6 15.2 - - + -
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASP* 4.9 6.1 - - + -
367B LEU 4.0 3.6 - - - +
368B THR 3.2 4.9 + - - +
370B GLU* 1.3 79.1 - - + +
372B PHE* 1.3 66.9 + - - +
373B GLY 3.2 2.2 - - - -
374B LEU* 3.1 16.7 + - + +
375B VAL* 4.4 2.3 + - - +
421B LEU* 3.9 27.4 - - + +
424B LEU* 4.1 22.0 - - + -
435B PHE* 3.6 45.8 - - + -
436B GLY 4.0 9.4 - - - +
437B PRO 3.5 23.1 - - - +
438B ILE* 3.9 19.6 - - + +
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Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B TYR* 3.2 33.8 + + + -
363B ILE 3.7 9.9 - - - -
364B ALA* 3.6 31.4 - - + -
368B THR* 3.0 35.3 + - + +
369B ALA* 3.4 4.7 + - - +
371B ILE* 1.3 75.4 - - - +
373B GLY* 1.3 59.9 + - - +
376B PRO* 3.4 14.7 - - - +
400B ALA 3.9 3.3 - - - +
402B ALA* 5.3 2.1 + - - +
437B PRO* 3.3 32.1 - - + -
438B ILE* 3.5 18.0 - - - +
439B THR 3.6 3.8 - - - -
440B PRO* 3.6 42.0 - - + -
441B PRO* 4.0 9.9 - - + -
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Residues in contact with GLY 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B PHE* 4.0 3.5 - - - -
329B TRP* 3.6 27.6 - - - -
361B TYR* 3.3 13.2 + - - -
369B ALA 3.1 10.1 + - - -
372B PHE* 1.3 78.2 - - - +
374B LEU* 1.3 54.7 + - - +
376B PRO* 3.4 5.5 - - - +
377B SER* 2.8 37.2 + - - -
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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
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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