Contacts of the helix formed by residues 373 - 383 (chain B) in PDB entry 4I6J
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 CYS 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B VAL 3.5 1.1 + - - -
372B SER* 1.3 72.0 - - - +
374B SER* 1.3 59.0 + - - +
376B PHE* 3.1 7.7 + - - +
377B VAL* 2.9 34.8 + - - +
397B LEU* 4.2 10.1 - - - -
398B ILE 2.6 34.0 + - - +
399B PRO* 3.7 9.9 - - - -
400B ASP* 4.0 2.9 + - - +
403B TYR* 3.6 29.6 - - + +
404B SER 4.7 0.7 - - - -
405B LEU* 4.1 19.5 - - - -
408B ILE* 3.8 20.0 - - + -
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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
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372B SER* 3.1 2.6 - - - -
373B CYS* 1.3 79.0 - - - +
375B ALA* 1.3 57.3 + - - +
377B VAL* 3.3 3.5 + - - +
378B GLU* 2.9 28.7 + - - +
400B ASP* 2.3 35.6 + - - -
402B LYS* 3.8 17.5 - - - +
403B TYR* 3.9 13.3 - - - -
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Residues in contact with ALA 375 (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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348B ASP* 3.3 40.6 - - + +
351B LEU* 5.8 1.5 - - + +
352B ILE* 4.5 8.8 - - + +
371B VAL* 4.1 2.2 - - + -
372B SER* 2.9 22.2 + - - +
374B SER* 1.3 73.5 - - - +
376B PHE* 1.3 54.7 + - - +
378B GLU* 3.1 14.1 + - - +
379B PHE* 2.7 34.7 + - - +
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Residues in contact with PHE 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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351B LEU* 4.2 21.3 - - + -
364B ILE* 6.0 0.2 - - + -
366B LEU* 5.2 0.2 - - + -
371B VAL* 3.7 11.8 - - + +
372B SER 2.9 16.8 + - - +
373B CYS* 3.5 4.9 - - - +
375B ALA* 1.3 78.2 - - - +
377B VAL* 1.3 62.6 + - + +
379B PHE* 3.1 15.7 + + - +
380B VAL* 3.0 29.2 + - + +
390B LEU* 3.8 21.3 - - + -
392B ILE* 3.7 39.9 - - + -
396B VAL* 6.1 0.9 - - + -
397B LEU* 3.9 26.2 - - + -
408B ILE* 5.4 2.7 - - + -
412B VAL* 3.5 32.3 - - + -
420B TRP* 4.1 10.8 - + - -
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Residues in contact with VAL 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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373B CYS 2.9 16.3 + - - +
374B SER 3.6 7.6 - - - +
376B PHE* 1.3 72.7 - - - +
378B GLU* 1.3 67.3 + - - +
380B VAL* 3.1 6.9 + - - +
381B LYS* 2.9 48.0 + - - +
403B TYR* 3.8 29.8 - - + +
408B ILE* 3.8 23.6 - - + -
411B GLU* 4.2 15.9 - - + +
412B VAL* 4.9 7.4 - - + -
415B HIS* 4.5 6.4 - - + +
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Residues in contact with GLU 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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352B ILE* 3.4 34.4 - - + +
374B SER 2.9 13.1 + - - +
375B ALA* 3.4 13.4 - - - +
377B VAL* 1.3 77.8 - - - +
379B PHE* 1.3 62.8 + - - +
381B LYS* 3.5 12.4 + - + +
382B MET* 3.2 35.1 + - + +
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Residues in contact with PHE 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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351B LEU* 2.9 65.7 - - + -
352B ILE* 5.2 3.1 - - + +
354B ILE* 4.9 1.8 - - + -
355B ALA* 3.6 23.6 - - + -
361B LEU* 4.0 17.5 - - + -
364B ILE* 4.3 15.7 - - + -
375B ALA 2.7 14.3 + - - +
376B PHE* 3.1 17.3 - + - +
377B VAL 3.1 0.2 - - - -
378B GLU* 1.3 77.3 - - - +
380B VAL* 1.3 73.2 + - + +
382B MET* 3.2 18.7 + - - +
383B CYS* 3.5 32.6 + - - -
387B LEU* 4.0 13.2 - - + -
390B LEU* 4.9 2.0 - - + -
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Residues in contact with VAL 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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376B PHE* 3.0 38.9 + - + +
377B VAL* 3.1 4.9 + - - +
379B PHE* 1.3 84.1 - - + +
381B LYS* 1.3 64.2 + - - +
383B CYS* 4.9 0.9 - - - -
384B GLY* 2.8 42.6 - - - +
387B LEU* 4.8 2.9 - - + -
390B LEU* 4.3 7.2 - - + -
412B VAL* 4.2 19.3 - - + +
415B HIS* 3.5 25.6 - - + +
416B LEU* 4.1 17.3 - - + -
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Residues in contact with LYS 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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377B VAL* 2.9 34.0 + - + +
378B GLU* 3.7 11.9 - - + +
379B PHE 3.3 0.2 - - - -
380B VAL* 1.3 78.7 - - - +
382B MET* 1.3 63.7 + - + +
383B CYS 4.6 1.4 - - - +
384B GLY* 4.7 1.2 - - - -
403B TYR* 4.4 5.3 + - - -
411B GLU* 3.9 6.3 + - - -
415B HIS* 3.5 44.0 + - + +
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Residues in contact with MET 382 (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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352B ILE* 3.9 20.9 - - + +
355B ALA* 3.9 17.3 - - + +
356B GLU* 3.9 45.8 - - + +
378B GLU* 3.2 24.9 - - + +
379B PHE* 3.2 5.6 + - - +
380B VAL 3.2 0.4 - - - -
381B LYS* 1.3 79.4 - - + +
383B CYS* 1.3 68.2 + - - +
386B ARG* 3.3 10.5 + - - -
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Residues in contact with CYS 383 (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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355B ALA* 4.1 9.4 - - + +
361B LEU* 4.5 4.7 - - + +
379B PHE* 3.5 48.7 + - - -
381B LYS 4.6 0.6 - - - +
382B MET* 1.3 82.3 - - - +
384B GLY* 1.3 57.4 + - - +
385B GLY* 2.8 17.7 + - - -
386B ARG* 3.2 46.3 + - + +
387B LEU* 3.9 22.7 - - + -
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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