Contacts of the helix formed by residues 371 - 380 (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 PRO 371 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108J HIS* 4.1 0.9 - - - +
370J GLY* 1.3 82.6 - - - +
372J LEU* 1.3 58.1 + - - +
375J VAL* 2.8 36.0 + - - +
410J ARG* 4.9 2.2 - - + +
413J ALA* 3.6 8.1 - - - +
414J ARG* 3.6 62.1 - - + +
417J GLN* 3.5 34.0 - - + +
462J PRO 3.6 13.9 - - - +
463J ARG* 4.6 2.5 - - - -
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Residues in contact with LEU 372 (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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277J THR* 4.5 4.3 - - - +
280J PHE* 3.7 25.1 - - + -
368J GLU* 3.7 17.3 - - - +
369J VAL 6.2 0.2 - - - +
370J GLY 3.3 0.8 - - - -
371J PRO* 1.3 77.7 - - - +
373J ALA* 1.3 58.3 + - - +
375J VAL* 3.8 2.4 - - + -
376J LEU* 2.8 54.2 + - + +
404J LEU* 3.5 35.2 - - + +
405J PHE* 4.6 2.7 - - - -
406J SER 4.6 1.8 - - - +
409J GLY 3.7 16.2 - - - +
410J ARG* 4.2 25.3 + - + +
413J ALA* 3.6 13.3 - - + +
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Residues in contact with ALA 373 (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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280J PHE* 3.7 23.4 - - + +
281J LEU 3.6 15.3 - - - +
282J THR* 4.7 1.6 - - - -
368J GLU* 3.4 27.3 + - + +
369J VAL* 3.8 1.5 - - - -
370J GLY 3.0 15.7 + - - +
372J LEU* 1.3 79.7 - - - +
374J SER* 1.3 61.0 + - - +
376J LEU* 3.4 1.7 + - - +
377J VAL* 3.1 30.6 + - - +
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Residues in contact with SER 374 (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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282J THR* 3.6 19.5 + - - +
298J THR* 6.0 4.9 - - - -
299J PRO* 5.0 2.3 - - - +
370J GLY 2.8 22.3 + - - -
371J PRO 3.6 4.0 - - - -
373J ALA* 1.3 77.8 - - - +
375J VAL* 1.3 58.9 + - - +
377J VAL* 3.4 3.3 + - - +
378J ALA* 3.0 29.2 + - - +
417J GLN* 3.7 15.6 + - - -
460J ASN* 3.1 25.1 + - - -
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Residues in contact with VAL 375 (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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371J PRO 2.8 25.3 + - - +
372J LEU* 3.9 4.0 - - + +
374J SER* 1.3 70.7 - - - +
376J LEU* 1.3 66.5 + - + +
378J ALA* 4.5 4.9 - - - -
379J TYR* 3.0 28.5 + - + +
386J THR* 3.8 5.4 - - + +
390J VAL* 3.9 26.5 - - + -
404J LEU* 5.7 4.9 - - + -
413J ALA* 3.7 28.0 - - + +
416J ILE* 4.0 26.5 - - + -
417J GLN* 4.1 12.3 - - + +
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Residues in contact with LEU 376 (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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280J PHE* 4.0 18.8 - - + -
303J ILE* 3.7 12.8 - - + +
308J LEU* 3.6 29.6 - - + +
372J LEU* 2.8 39.8 + - + +
373J ALA* 3.9 4.0 - - - +
374J SER 3.3 0.2 - - - -
375J VAL* 1.3 78.3 - - + +
377J VAL* 1.3 56.6 + - - +
379J TYR* 4.0 3.9 - - + +
380J ALA* 2.9 31.9 + - - +
404J LEU* 4.2 26.0 - - + -
405J PHE* 3.3 35.9 - - + -
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Residues in contact with VAL 377 (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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280J PHE* 4.9 5.8 - - + +
282J THR* 3.5 24.7 - - + +
299J PRO* 3.9 5.6 - - + +
300J GLN 3.7 30.5 - - - +
301J GLY* 3.8 19.5 - - - +
303J ILE* 4.2 20.2 - - + -
311J VAL* 4.1 3.4 - - + -
373J ALA 3.1 16.8 + - - +
374J SER 3.8 0.7 - - - +
376J LEU* 1.3 73.0 - - - +
378J ALA* 1.3 66.6 + - - +
380J ALA* 3.3 3.1 + - - +
381J LYS* 2.9 34.0 + - + +
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Residues in contact with ALA 378 (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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298J THR* 5.5 3.6 - - + -
299J PRO* 3.4 25.5 - - + +
374J SER 3.0 17.5 + - - +
375J VAL* 4.5 1.3 - - - -
377J VAL* 1.3 77.2 - - - +
379J TYR* 1.3 54.1 + - - +
381J LYS* 3.2 2.8 + - - +
382J LYS 2.9 9.9 + - - -
383J HIS* 2.7 40.2 + - + +
386J THR* 3.5 26.2 - - + +
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Residues in contact with TYR 379 (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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308J LEU* 4.2 25.6 - - + -
375J VAL 3.0 20.9 + - - +
376J LEU* 4.0 3.4 - - + +
378J ALA* 1.3 74.2 - - - +
380J ALA* 1.3 63.1 - - - +
382J LYS* 2.9 21.7 + - - +
386J THR* 3.7 11.6 - - + +
387J VAL* 3.8 38.0 - - + +
390J VAL* 3.4 35.0 - - + +
391J ASP* 4.0 15.6 + - - -
394J LEU* 4.7 1.2 - - - +
401J PRO* 4.1 24.2 - - + +
404J LEU* 5.1 5.4 - - + -
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Residues in contact with ALA 380 (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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303J ILE* 4.3 1.6 - - + -
308J LEU* 3.1 36.5 - - + +
311J VAL* 3.3 23.3 - - + +
376J LEU 2.9 20.5 + - - +
377J VAL 3.7 0.2 - - - +
379J TYR* 1.3 80.4 - - - +
381J LYS* 1.3 57.1 + - - +
382J LYS* 3.0 15.9 + - - +
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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