Contacts of the helix formed by residues 371 - 380 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F HIS* 4.1 1.1 - - - +
370F GLY* 1.3 82.2 - - - +
372F LEU* 1.3 56.9 + - - +
375F VAL* 2.8 35.7 + - - +
410F ARG* 4.9 2.7 - - + +
413F ALA* 3.6 7.4 - - - +
414F ARG* 3.6 61.2 - - + +
417F GLN* 3.5 34.0 - - + +
462F PRO 3.6 14.8 - - - +
463F ARG* 4.6 2.2 - - - +
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Residues in contact with LEU 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F THR* 4.5 4.3 - - - +
280F PHE* 3.7 25.1 - - + -
368F GLU* 3.7 20.0 - - - +
370F GLY 3.3 0.8 - - - -
371F PRO* 1.3 78.0 - - - +
373F ALA* 1.3 58.8 + - - +
375F VAL* 3.8 2.0 - - + -
376F LEU* 2.8 53.2 + - + +
404F LEU* 3.5 36.6 - - + +
405F PHE* 4.6 2.7 - - - -
406F SER 4.6 1.8 - - - +
409F GLY 3.7 15.9 - - - +
410F ARG* 4.2 25.7 + - + +
413F ALA* 3.6 13.2 - - + +
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Residues in contact with ALA 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F PHE* 3.7 24.4 - - + +
281F LEU 3.6 15.7 - - - +
282F THR* 4.7 1.3 - - - -
368F GLU* 3.4 27.1 + - + +
369F VAL* 3.8 1.7 - - - -
370F GLY 3.0 15.2 + - - +
372F LEU* 1.3 79.7 - - - +
374F SER* 1.3 62.8 + - - +
376F LEU* 3.9 1.8 - - - +
377F VAL* 3.1 30.0 + - - +
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Residues in contact with SER 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F THR* 3.6 20.1 + - - +
298F THR* 6.0 5.3 - - - -
299F PRO* 5.0 2.3 - - - +
370F GLY 2.8 22.0 + - - -
371F PRO 3.6 3.8 - - - -
373F ALA* 1.3 77.8 - - - +
375F VAL* 1.3 59.3 + - - +
377F VAL* 3.4 3.5 + - - +
378F ALA* 3.0 28.9 + - - +
417F GLN* 3.7 14.4 + - - -
460F ASN* 3.1 25.6 + - - -
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Residues in contact with VAL 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371F PRO 2.8 25.4 + - - +
372F LEU* 3.9 3.4 - - + +
374F SER* 1.3 70.1 - - - +
376F LEU* 1.3 67.0 + - + +
378F ALA* 4.5 5.2 - - - -
379F TYR* 3.0 27.7 + - - +
386F THR* 3.8 5.6 - - + +
390F VAL* 3.9 26.2 - - + -
404F LEU* 5.7 5.2 - - + -
413F ALA* 3.7 28.5 - - + +
416F ILE* 4.0 26.5 - - + -
417F GLN* 4.1 13.0 - - + +
420F THR* 6.1 0.2 - - - +
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Residues in contact with LEU 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F PHE* 4.0 19.1 - - + -
303F ILE* 3.7 13.1 - - + +
308F LEU* 3.6 29.1 - - + +
372F LEU* 2.8 40.7 + - + +
373F ALA* 3.9 3.8 - - - +
375F VAL* 1.3 77.3 - - + +
377F VAL* 1.3 57.5 + - - +
379F TYR* 4.0 4.5 - - + +
380F ALA* 2.9 31.9 + - - +
404F LEU* 4.2 26.5 - - + -
405F PHE* 3.3 35.4 - - + -
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Residues in contact with VAL 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F PHE 4.9 5.4 - - - +
282F THR* 3.5 25.1 - - + +
299F PRO* 3.9 5.6 - - + +
300F GLN 3.7 31.0 - - - +
301F GLY* 3.8 19.3 - - - +
302F VAL 4.5 0.2 - - - +
303F ILE* 4.2 20.0 - - + -
311F VAL* 4.1 4.0 - - + +
373F ALA 3.1 16.4 + - - +
374F SER 3.8 1.3 - - - +
375F VAL 3.3 0.2 - - - -
376F LEU* 1.3 74.3 - - - +
378F ALA* 1.3 64.9 + - - +
380F ALA* 3.3 3.4 + - - +
381F LYS* 2.9 33.1 + - + +
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Residues in contact with ALA 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F THR* 5.5 3.4 - - + -
299F PRO* 3.4 25.3 - - + +
374F SER 3.0 17.6 + - - +
375F VAL* 4.5 1.6 - - - -
377F VAL* 1.3 76.1 - - - +
379F TYR* 1.3 54.2 + - - +
381F LYS 3.2 2.8 + - - -
382F LYS 2.9 9.4 + - - -
383F HIS* 2.7 38.6 + - + +
386F THR* 3.5 26.5 - - + +
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Residues in contact with TYR 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308F LEU* 4.2 25.1 - - + -
375F VAL 3.0 19.6 + - - +
376F LEU* 4.0 4.7 - - + +
378F ALA* 1.3 74.6 - - - +
380F ALA* 1.3 61.9 - - - +
382F LYS* 2.9 22.9 + - - +
386F THR* 3.7 11.8 - - + +
387F VAL* 3.8 36.7 - - + +
390F VAL* 3.4 36.5 - - + +
391F ASP* 4.0 16.3 + - - -
394F LEU* 4.7 1.2 - - - +
401F PRO* 4.1 23.4 - - + +
404F LEU* 5.1 5.6 - - + -
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Residues in contact with ALA 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F ILE* 4.3 1.3 - - + -
308F LEU* 3.1 36.7 - - + +
311F VAL* 3.3 23.6 - - + +
376F LEU 2.9 20.2 + - - +
377F VAL 3.7 0.2 - - - +
379F TYR* 1.3 80.2 - - - +
381F LYS* 1.3 58.3 + - - +
382F LYS* 3.0 15.2 + - - +
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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