Contacts of the helix formed by residues 370 - 383 (chain B) in PDB entry 3EZE
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 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301B MET* 3.2 35.3 + - - -
302B PHE* 3.6 5.9 + - + +
331B SER* 3.5 13.6 + - - -
365B ALA* 3.2 26.3 - - - +
366B GLU* 3.6 8.6 - - - +
367B GLY* 2.8 40.7 + - - +
368B GLU 5.0 0.4 - - - -
369B ASP* 1.3 76.2 - - - +
371B GLN* 1.3 78.8 + - + +
373B ALA* 3.8 1.3 - - - +
374B VAL* 3.5 27.9 + - - +
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Residues in contact with GLN 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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302B PHE* 5.5 12.1 - - + -
368B GLU 5.6 3.6 - - - +
369B ASP* 2.7 5.9 + - - -
370B GLU* 1.3 88.6 - - + +
372B LYS* 1.3 68.3 + - + +
374B VAL* 4.5 1.7 - - - +
375B GLU* 3.2 35.0 + - - +
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Residues in contact with LYS 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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329B PHE* 3.8 20.0 - - + -
369B ASP* 2.8 34.9 + - + +
371B GLN* 1.3 73.1 - - + +
373B ALA* 1.3 67.9 + - - +
375B GLU* 3.0 7.6 + - - +
376B HIS* 2.6 45.9 + - + +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B PHE* 4.1 19.1 - - + -
331B SER* 4.6 1.8 - - - +
333B ILE* 3.9 23.8 - - + -
365B ALA* 4.6 2.7 - - + -
369B ASP 3.1 8.7 + - - +
370B GLU* 3.8 10.8 - - - +
372B LYS* 1.3 78.0 - - - +
374B VAL* 1.3 60.9 + - - +
377B LEU* 2.6 53.6 + - + +
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.9 37.2 - - + +
304B GLN* 3.4 35.4 - - + +
363B ILE* 3.7 29.6 - - + +
365B ALA* 4.1 15.9 - - + +
370B GLU 3.5 16.1 + - - +
371B GLN 4.6 1.3 - - - +
373B ALA* 1.3 78.2 - - - +
375B GLU* 1.3 57.9 + - + +
377B LEU* 4.3 1.7 - - - +
378B VAL* 2.7 39.2 + - + +
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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
----------------------------------------------------------
302B PHE* 5.6 8.5 - - + -
371B GLN* 3.2 24.1 + - - +
372B LYS* 3.0 8.5 + - - +
373B ALA 2.8 4.9 + - - -
374B VAL* 1.3 81.0 - - + +
376B HIS* 1.3 66.9 + - + +
378B VAL* 4.0 3.2 - - - +
379B LYS* 3.4 31.5 + - - +
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Residues in contact with HIS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU* 4.2 28.3 - - + +
329B PHE* 4.6 8.2 - + + -
372B LYS* 2.6 55.1 + - + +
373B ALA* 2.7 4.4 + - - +
375B GLU* 1.3 76.3 - - + +
377B LEU* 1.3 60.4 + - - +
378B VAL 3.1 1.1 - - - -
379B LYS* 3.1 9.3 + - + +
380B LEU* 2.8 31.7 + - - +
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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
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322B PHE* 3.8 32.1 - - + +
325B GLU* 3.7 31.6 - - + -
326B ALA* 4.1 11.2 - - + +
329B PHE* 5.8 0.4 - - + -
333B ILE* 4.0 27.6 - - + -
363B ILE* 3.9 23.8 - - + -
373B ALA* 2.6 43.8 + - + +
374B VAL 4.5 0.2 - - - +
376B HIS* 1.3 72.8 - - - +
378B VAL* 1.3 57.2 + - - +
380B LEU* 4.0 4.7 - - + +
381B MET* 2.7 34.1 + - - +
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Residues in contact with VAL 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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304B GLN* 3.5 44.0 - - + +
305B GLU 5.6 0.4 - - - +
306B VAL* 4.0 15.1 - - + +
363B ILE* 4.3 12.8 - - + -
374B VAL* 2.7 32.3 + - + +
375B GLU* 4.0 4.9 - - - +
377B LEU* 1.3 80.0 - - - +
379B LYS* 1.3 61.2 + - + +
381B MET* 3.8 4.4 - - - +
382B ALA* 2.9 29.2 + - + +
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Residues in contact with LYS 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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375B GLU* 3.4 18.5 + - - +
376B HIS* 3.1 11.7 + - + +
378B VAL* 1.3 79.6 - - + +
380B LEU* 1.3 54.9 + - - +
382B ALA* 2.7 9.9 + - - -
383B GLU* 2.6 52.2 + - + +
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Residues in contact with LEU 380 (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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321B GLN* 3.9 40.8 - - + +
322B PHE* 4.3 12.1 - - + -
325B GLU* 3.7 38.8 - - + +
376B HIS 2.8 20.0 + - - +
377B LEU* 4.0 6.7 - - + +
379B LYS* 1.3 74.2 - - - +
381B MET* 1.3 60.8 + - - +
383B GLU* 4.3 7.9 - - + +
384B LEU* 3.0 42.7 + - + +
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Residues in contact with MET 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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306B VAL* 3.2 37.1 - - + +
308B ILE* 4.1 21.6 - - + +
309B THR* 4.6 9.0 + - - -
314B LEU* 4.2 25.6 - - + +
322B PHE* 3.4 39.9 - - + -
335B VAL* 5.6 3.4 - - + -
355B LEU* 5.4 4.3 - - + -
361B VAL* 3.6 19.3 - - + -
363B ILE* 4.2 5.6 - - + -
377B LEU 2.7 23.8 + - - +
378B VAL 3.9 3.6 - - - +
380B LEU* 1.3 74.9 - - - +
382B ALA* 1.3 60.7 + - - +
383B GLU 3.4 0.7 + - - -
384B LEU* 3.8 19.1 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL* 4.1 14.4 - - + -
307B THR 5.5 2.0 - - - -
309B THR* 3.8 19.4 + - + +
378B VAL* 2.9 20.8 + - + +
379B LYS* 2.7 13.0 + - - +
381B MET* 1.3 73.5 - - - +
383B GLU* 1.3 61.1 + - + +
384B LEU 3.6 0.4 - - - -
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LYS* 2.6 35.5 + - + +
380B LEU* 3.8 7.9 - - + +
381B MET 3.2 0.2 - - - -
382B ALA* 1.3 79.3 - - + +
384B LEU* 1.3 64.0 + - - +
385B GLU* 3.5 13.4 + - - +
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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