Contacts of the helix formed by residues 373 - 381 (chain B) in PDB entry 3E20
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 LEU 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B VAL* 3.9 28.0 - - + -
306B MET* 3.9 18.8 - - + -
323B LEU* 4.4 2.9 - - + -
325B MET* 2.8 38.4 + - + +
327B ARG* 4.1 12.1 - - + +
341B TYR* 4.1 20.6 - - + -
371B MET 3.9 2.0 + - - -
372B LEU* 1.3 68.1 - - - +
374B SER* 1.3 64.4 + - - +
376B TRP* 3.0 9.5 + - + +
377B LEU* 2.9 52.3 + - + +
408B ILE* 4.0 14.6 - - + -
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 2.9 34.6 - - - -
16B ARG* 5.6 0.7 + - - -
319B CYS* 4.5 14.1 - - - -
321B ALA 4.5 3.4 - - - -
323B LEU* 4.5 25.9 - - - +
325B MET 4.4 1.0 + - - -
372B LEU* 4.6 10.8 - - - +
373B LEU* 1.3 80.0 - - - +
375B GLU* 1.3 60.2 + - - +
377B LEU* 3.7 2.7 + - - +
378B ALA* 3.4 14.9 + - - +
390B PHE* 3.5 17.8 - - - -
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 5.4 4.0 - - + +
13B LYS* 5.9 7.9 - - + -
371B MET* 4.2 20.2 - - + +
372B LEU* 2.7 35.2 + - + +
374B SER* 1.3 76.4 + - - +
376B TRP* 1.3 64.0 + - - +
378B ALA* 3.2 17.0 + - + +
379B GLU* 3.5 18.6 + - + +
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Residues in contact with TRP 376 (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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306B MET* 4.3 12.8 - - - -
309B LEU* 4.6 5.2 - - + -
310B GLN* 5.5 4.7 - - - -
327B ARG* 3.1 64.1 - - - +
341B TYR* 5.3 1.6 - - - -
371B MET* 3.9 23.0 - - + -
372B LEU 2.8 10.4 + - - +
373B LEU* 3.7 9.0 - - + +
375B GLU* 1.3 78.2 - - - +
377B LEU* 1.3 88.8 + - + +
379B GLU* 3.2 1.9 + - - -
380B HIS* 3.1 75.6 + + + +
384B TYR* 3.8 28.9 - + - -
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B MET* 3.5 24.0 - - + -
309B LEU* 3.7 17.9 - - + -
317B LEU* 3.7 20.9 - - + -
319B CYS* 4.5 16.8 - - + -
373B LEU* 2.9 33.6 + - + +
374B SER 3.9 4.0 - - - +
376B TRP* 1.3 86.3 - - + +
378B ALA* 1.3 57.9 + - - +
379B GLU 2.9 10.8 + - - -
381B TYR* 2.9 35.1 + - + +
388B LEU* 3.9 12.3 - - + -
390B PHE* 5.2 0.7 - - + -
408B ILE* 3.9 19.3 - - + -
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Residues in contact with ALA 378 (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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9B ILE* 5.0 7.4 - - + +
12B TRP* 4.0 13.5 - - + +
13B LYS* 4.9 14.5 + - + -
374B SER 3.4 11.6 + - - +
375B GLU* 3.2 14.1 + - + +
377B LEU* 1.3 78.2 - - - +
379B GLU* 1.3 65.1 + - + +
381B TYR* 3.9 15.0 - - - -
388B LEU* 3.9 11.0 - - - +
390B PHE* 4.0 18.2 - - + -
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Residues in contact with GLU 379 (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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13B LYS* 4.6 17.7 + - + +
371B MET* 6.0 2.7 - - - -
375B GLU* 3.5 16.6 + - + +
376B TRP* 3.2 1.7 + - - +
377B LEU 2.9 0.8 - - - -
378B ALA* 1.3 87.0 - - + +
380B HIS* 1.3 81.4 + - + +
381B TYR* 3.8 1.8 - - - -
382B LYS* 5.3 3.1 - - - +
383B ASP* 4.4 2.6 - - - +
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Residues in contact with HIS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B MET* 5.6 4.3 - - + -
376B TRP* 3.1 69.8 + + + +
379B GLU* 1.3 92.6 - - + +
381B TYR* 1.3 71.0 + - - +
382B LYS* 2.9 4.0 - - - -
383B ASP* 2.7 34.4 + - - +
384B TYR* 3.3 15.4 - + + -
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Residues in contact with TYR 381 (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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6B GLU* 3.4 35.2 + - - +
9B ILE* 4.7 15.1 - - + +
309B LEU* 5.5 7.0 - - + -
317B LEU* 5.1 7.6 - - + -
377B LEU* 2.9 30.6 + - + +
378B ALA 3.9 17.7 - - - -
379B GLU 5.0 0.4 - - - -
380B HIS* 1.3 78.1 - - - +
382B LYS* 1.3 87.9 + - + +
384B TYR* 3.1 21.9 + - - +
386B ALA* 2.9 17.6 - - + +
387B ASN* 3.3 31.6 - - - -
388B LEU* 3.6 36.8 - - + -
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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