Contacts of the helix formed by residues 370 - 377 (chain B) in PDB entry 3QFR
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 TYR 370 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B LEU* 3.5 19.9 - - - +
252B VAL* 5.0 1.4 - - + +
343B ALA* 5.4 1.8 - - + -
344B ASP 4.1 13.9 - - - -
345B LEU* 3.4 10.7 + - + +
347B VAL* 3.3 28.2 + - + -
349B MET* 3.6 31.3 - - + +
368B THR 3.9 0.2 + - - -
369B SER* 1.3 73.5 - - - +
371B ARG* 1.3 62.5 + - - +
373B ALA* 3.4 5.6 + - + +
374B LEU* 3.1 31.5 + - + +
444B ILE* 3.4 51.6 - - + +
445B ASP* 3.3 32.6 + - - +
448B CYS* 4.2 11.0 - - + -
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Residues in contact with ARG 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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334B VAL* 4.4 10.1 - - + +
335B ASN* 2.5 35.2 + - - +
345B LEU* 2.8 43.2 + - + +
346B ASP* 2.8 30.8 + - - +
369B SER* 3.0 5.6 - - - +
370B TYR* 1.3 75.1 - - - +
372B THR* 1.3 61.6 + - - +
374B LEU* 4.3 0.9 - - - +
375B THR* 2.6 39.4 + - - +
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Residues in contact with THR 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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261B VAL* 5.7 0.2 - - - +
262B TYR 3.7 5.4 + - - -
263B MET* 3.5 18.9 - - - +
264B GLY 3.3 29.8 - - - +
368B THR* 3.1 25.0 + - - +
369B SER* 2.7 22.1 + - - -
371B ARG* 1.3 77.0 - - - +
373B ALA* 1.3 65.1 + - - +
375B THR* 3.1 1.0 + - - -
376B TYR* 3.0 35.2 + - + -
377B TYR* 3.8 8.8 + - + -
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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
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349B MET* 5.2 1.3 - - + -
364B PHE* 3.8 33.7 - - + -
368B THR* 4.4 1.3 + - + -
369B SER 3.1 9.0 + - - +
370B TYR* 3.6 11.9 - - - +
372B THR* 1.3 78.8 - - - +
374B LEU* 1.3 57.3 + - - +
377B TYR* 3.0 22.8 + - - +
378B LEU* 2.9 36.9 + - + +
448B CYS* 4.8 4.9 - - - -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ASN* 2.7 30.0 + - - -
334B VAL* 3.6 30.7 - - + +
337B LEU* 4.7 15.5 - - + -
338B GLY 5.3 0.2 - - - +
341B LEU* 5.4 1.8 - - + -
345B LEU* 3.6 25.6 - - + -
370B TYR 3.1 17.7 + - - +
373B ALA* 1.3 79.6 - - - +
375B THR* 1.3 51.0 + - - +
378B LEU* 4.0 19.5 - - + +
380B ILE* 3.6 27.1 - - + +
444B ILE* 4.0 13.9 - - + -
447B LEU* 5.4 4.3 - - + -
448B CYS* 4.5 9.0 - - - -
451B LEU* 4.3 8.5 - - + -
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Residues in contact with THR 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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328B ALA* 3.3 13.9 - - + -
329B ASN* 2.7 43.9 + - - +
331B SER* 5.7 3.5 - - - -
334B VAL* 3.7 18.9 - - + +
371B ARG* 2.6 27.1 + - - +
372B THR 3.1 4.3 + - - -
374B LEU* 1.3 78.1 - - - +
376B TYR* 1.3 91.2 + - + +
454B LEU* 4.2 0.9 - - - +
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Residues in contact with TYR 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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263B MET 3.6 16.7 + - - -
264B GLY* 3.6 35.2 - - - +
266B MET* 4.8 10.3 - - + +
272B TYR* 6.0 3.8 - + - -
326B TYR 5.7 1.6 - - - -
327B PRO 4.2 9.6 - - - +
328B ALA* 3.6 28.4 - - + +
372B THR* 3.0 24.9 + - + +
375B THR* 1.3 92.2 - - + +
377B TYR* 1.3 66.6 + - + +
378B LEU 3.9 0.9 - - - -
454B LEU* 3.5 21.7 - - - +
496B TRP* 5.8 0.9 - + - -
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Residues in contact with TYR 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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262B TYR* 3.4 14.9 - - - +
264B GLY* 3.2 26.8 + - - -
265B GLU 2.7 30.9 + - - -
266B MET* 4.0 7.2 - - - -
364B PHE* 3.9 21.8 - + + -
365B PRO* 3.5 25.1 - - + +
368B THR* 4.0 9.2 - - - -
372B THR* 3.8 20.0 - - + -
373B ALA* 3.0 28.8 + - - +
376B TYR* 1.3 82.8 - - - +
378B LEU* 1.3 60.6 + - + +
453B ARG* 2.9 44.2 + - - +
454B LEU* 2.9 20.1 + - - -
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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