Contacts of the helix formed by residues 384 - 397 (chain J) in PDB entry 2FRV
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 384 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139G GLY 4.8 7.9 - - - +
141G LYS* 3.1 50.7 + - + +
382J LYS 3.3 6.8 + - - -
383J HIS* 1.3 69.1 - - - +
385J PRO* 1.3 62.3 - - + +
387J VAL* 4.2 14.0 - - + +
388J LYS* 2.7 76.8 + - - +
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Residues in contact with PRO 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297J TYR* 3.6 21.3 - - + +
383J HIS* 3.1 34.3 - - + +
384J GLU* 1.3 96.9 - - + +
386J THR* 1.3 53.6 + - - +
388J LYS* 3.8 15.8 + - - +
389J ALA* 3.1 28.8 + - - +
420J THR* 3.9 8.7 - - + +
423J GLN* 3.9 19.4 + - - +
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Residues in contact with THR 386 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298J THR* 5.7 0.9 - - - +
375J VAL* 3.8 23.2 - - + +
378J ALA* 3.5 12.2 - - + +
379J TYR* 3.7 32.1 - - + +
383J HIS* 2.7 33.3 + - - -
385J PRO* 1.3 75.4 - - - +
387J VAL* 1.3 61.1 + - - +
389J ALA* 3.1 3.9 + - - +
390J VAL* 2.8 30.0 + - + +
416J ILE* 4.7 4.7 - - + +
420J THR* 4.0 14.6 + - - +
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Residues in contact with VAL 387 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G LYS* 5.8 1.3 - - - +
379J TYR* 3.8 34.3 - - + +
382J LYS* 3.8 28.7 - - + -
383J HIS 2.7 23.6 + - - +
384J GLU* 3.7 16.4 - - + +
386J THR* 1.3 72.0 - - - +
388J LYS* 1.3 66.9 + - + +
389J ALA 3.2 0.3 + - - -
391J ASP* 3.1 39.5 + - - +
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Residues in contact with LYS 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G LYS 4.0 21.3 - - - +
105G ALA* 6.2 0.2 - - - +
167G MET* 5.4 16.0 - - - +
384J GLU* 2.7 58.6 + - - +
385J PRO* 3.8 16.9 - - - +
387J VAL* 1.3 75.7 - - + +
389J ALA* 1.3 56.4 + - - +
391J ASP* 3.7 6.8 + - - +
392J LEU* 3.4 22.0 + - - +
423J GLN* 5.6 3.4 - - - +
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Residues in contact with ALA 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385J PRO 3.1 17.5 + - - +
386J THR* 3.1 4.0 + - - +
388J LYS* 1.3 73.2 - - - +
390J VAL* 1.3 64.0 + - - +
391J ASP 3.2 0.9 - - - -
392J LEU* 3.4 15.9 - - + +
393J VAL* 3.3 22.5 - - - +
416J ILE* 3.8 25.4 - - + -
419J LEU* 4.7 15.5 - - + -
420J THR* 4.5 7.2 - - + -
423J GLN* 6.0 0.4 - - - +
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Residues in contact with VAL 390 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375J VAL* 3.9 28.0 - - + -
379J TYR* 3.4 43.3 - - + -
386J THR* 2.8 22.1 + - + +
389J ALA* 1.3 70.9 - - - +
391J ASP* 1.3 67.0 + - - +
393J VAL* 3.3 4.7 + - - +
394J LEU* 3.0 48.1 + - + +
404J LEU* 4.4 14.4 - - + -
416J ILE* 3.9 14.8 - - + -
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Residues in contact with ASP 391 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379J TYR* 4.0 17.7 + - - -
387J VAL* 3.1 32.1 + - - +
388J LYS* 3.8 6.0 - - - +
389J ALA 3.2 0.4 - - - -
390J VAL* 1.3 81.1 - - - +
392J LEU* 1.3 63.9 + - - +
394J LEU* 4.1 8.7 - - - +
395J LYS* 2.9 28.8 + - + +
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Residues in contact with LEU 392 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258J ILE* 4.8 11.7 - - + -
262J LEU* 4.7 10.8 - - + -
388J LYS 3.4 11.1 + - - +
389J ALA* 3.4 16.2 - - + +
391J ASP* 1.3 78.3 - - - +
393J VAL* 1.3 59.8 + - + +
395J LYS* 3.6 20.6 - - + +
396J THR* 2.5 49.8 + - - +
419J LEU* 5.6 9.0 - - + -
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Residues in contact with VAL 393 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258J ILE* 5.5 5.4 - - + -
261J LEU* 6.4 1.6 - - + -
262J LEU* 3.7 31.2 - - + -
389J ALA 3.3 14.1 - - - +
390J VAL* 3.4 9.4 - - - +
392J LEU* 1.3 85.0 - - + +
394J LEU* 1.3 57.8 + - + +
395J LYS 3.0 3.6 - - - -
396J THR* 2.8 4.9 + - - -
397J LEU* 2.7 44.5 + - + +
404J LEU* 5.5 3.4 - - + -
412J ALA* 4.1 22.4 - - + +
416J ILE* 4.1 20.2 - - + -
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Residues in contact with LEU 394 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E LYS* 4.7 1.3 - - - -
379J TYR* 4.7 1.6 - - - +
390J VAL* 3.0 37.9 + - + +
391J ASP* 4.1 9.9 - - - +
393J VAL* 1.3 77.7 - - + +
395J LYS* 1.3 54.9 + - - +
397J LEU* 5.9 0.4 - - + -
398J GLY* 2.7 28.0 + - - -
399J VAL* 2.8 36.4 + - + +
400J GLY* 3.5 20.2 - - - +
401J PRO* 3.9 27.1 - - + -
403J ALA* 5.2 0.7 - - + -
404J LEU* 4.1 26.5 - - + -
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Residues in contact with LYS 395 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E LYS* 4.7 19.7 - - - +
391J ASP 2.9 19.0 + - - +
392J LEU* 3.7 21.8 - - + +
394J LEU* 1.3 80.5 - - - +
396J THR* 1.3 81.9 + - - +
398J GLY* 3.5 9.5 + - - -
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Residues in contact with THR 396 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262J LEU* 3.5 38.1 - - + +
392J LEU* 2.5 32.5 + - - +
393J VAL 2.8 4.8 + - - -
395J LYS* 1.3 98.6 + - - +
397J LEU* 1.3 60.2 + - + +
398J GLY 3.3 0.8 + - - -
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Residues in contact with LEU 397 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262J LEU* 3.4 37.2 - - + +
265J ALA* 3.9 15.7 - - + +
266J GLY* 3.9 18.4 - - - +
269J LYS* 2.8 41.1 + - + +
393J VAL* 2.7 36.6 + - + +
394J LEU* 5.9 0.7 - - + -
396J THR* 1.3 76.2 - - + +
398J GLY* 1.3 60.6 + - - +
399J VAL* 3.4 24.1 - - + +
408J LEU* 4.9 11.4 - - + -
412J ALA* 5.2 7.0 - - + -
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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