Contacts of the helix formed by residues 371 - 380 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108L HIS* 4.1 1.3 - - - +
370L GLY* 1.3 83.7 - - - +
372L LEU* 1.3 57.2 + - - +
374L SER* 4.2 0.2 - - - -
375L VAL* 2.8 35.7 + - - +
410L ARG* 4.9 2.7 - - + +
413L ALA* 3.6 8.1 - - + +
414L ARG* 3.6 61.2 - - + +
417L GLN* 3.5 33.0 - - - +
462L PRO 3.6 13.9 - - - +
463L ARG* 4.6 2.5 - - - -
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Residues in contact with LEU 372 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277L THR* 4.5 4.0 - - - +
280L PHE* 3.7 25.4 - - + -
368L GLU* 3.7 18.2 - - - +
370L GLY 3.3 0.6 - - - -
371L PRO* 1.3 78.3 - - - +
373L ALA* 1.3 58.3 + - - +
375L VAL* 3.8 1.7 - - + -
376L LEU* 2.8 54.7 + - + +
404L LEU* 3.5 36.6 - - + +
405L PHE* 4.6 2.5 - - - -
406L SER 4.6 1.8 - - - +
409L GLY 3.7 15.7 - - - +
410L ARG* 4.2 24.7 + - + +
413L ALA* 3.6 13.9 - - + +
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Residues in contact with ALA 373 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280L PHE* 3.7 24.0 - - + +
281L LEU 3.6 15.9 - - - +
282L THR* 4.7 1.8 - - - -
368L GLU* 3.4 27.8 + - + +
369L VAL* 3.8 1.5 - - - -
370L GLY 3.0 14.8 + - - +
372L LEU* 1.3 79.3 - - - +
374L SER* 1.3 61.3 + - - +
376L LEU* 3.9 2.0 - - - +
377L VAL* 3.1 30.7 + - - +
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Residues in contact with SER 374 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282L THR* 3.6 20.8 + - - +
298L THR* 6.0 5.1 - - - -
299L PRO 5.0 1.9 - - - +
370L GLY 2.8 23.1 + - - -
371L PRO 3.6 3.1 - - - -
373L ALA* 1.3 77.4 - - - +
375L VAL* 1.3 58.7 + - - +
377L VAL* 3.4 3.5 + - - +
378L ALA* 3.0 29.3 + - - +
417L GLN* 3.7 14.9 + - - -
460L ASN* 3.1 24.6 + - - -
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Residues in contact with VAL 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371L PRO 2.8 25.8 + - - +
372L LEU* 3.9 3.4 - - + +
374L SER* 1.3 70.9 - - - +
376L LEU* 1.3 67.7 + - + +
378L ALA* 4.5 4.9 - - - -
379L TYR* 3.0 28.1 + - - +
386L THR* 3.8 5.9 - - + +
390L VAL* 3.9 26.2 - - + -
404L LEU* 5.7 4.9 - - + -
413L ALA* 3.7 28.5 - - + +
416L ILE* 4.0 26.7 - - + -
417L GLN* 4.1 12.6 - - + +
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Residues in contact with LEU 376 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280L PHE* 4.0 18.2 - - + -
303L ILE* 3.7 14.1 - - + +
308L LEU* 3.6 29.0 - - + +
372L LEU* 2.8 39.8 + - + +
373L ALA* 3.9 4.3 - - - +
375L VAL* 1.3 79.8 - - + +
377L VAL* 1.3 55.4 + - - +
379L TYR* 4.0 4.1 - - + +
380L ALA* 2.9 32.1 + - - +
404L LEU* 4.2 26.5 - - + -
405L PHE* 3.3 36.3 - - + -
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Residues in contact with VAL 377 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280L PHE 4.9 5.8 - - - +
281L LEU* 5.0 0.2 - - - -
282L THR* 3.5 24.7 - - + +
299L PRO* 3.9 5.6 - - + +
300L GLN 3.7 29.4 - - - +
301L GLY* 3.8 20.2 - - - +
303L ILE* 4.2 20.6 - - + -
311L VAL* 4.1 3.8 - - + -
373L ALA 3.1 15.9 + - - +
374L SER 3.8 1.1 - - - +
376L LEU* 1.3 73.8 - - - +
378L ALA* 1.3 65.7 + - - +
380L ALA* 3.3 3.1 + - - +
381L LYS* 2.9 34.2 + - + +
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Residues in contact with ALA 378 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298L THR* 5.5 3.8 - - + -
299L PRO* 3.4 25.5 - - + +
374L SER 3.0 16.8 + - - +
375L VAL* 4.1 1.6 - - - +
377L VAL* 1.3 76.3 - - - +
379L TYR* 1.3 54.6 + - - +
381L LYS* 3.2 2.4 + - - +
382L LYS 2.9 10.2 + - - -
383L HIS* 2.7 40.0 + - + +
386L THR* 3.5 26.7 - - + +
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Residues in contact with TYR 379 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308L LEU* 4.2 25.4 - - + -
375L VAL* 3.0 19.9 + - + +
376L LEU* 4.0 4.0 - - + +
378L ALA* 1.3 74.4 - - - +
380L ALA* 1.3 62.6 + - - +
382L LYS* 2.9 22.2 + - - +
386L THR* 3.7 11.4 - - + +
387L VAL* 3.8 38.4 - - + +
390L VAL* 3.4 35.3 - - + +
391L ASP* 4.0 16.3 + - - -
394L LEU* 4.7 1.4 - - - +
401L PRO* 4.1 24.4 - - + +
404L LEU* 5.1 5.4 - - + -
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Residues in contact with ALA 380 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303L ILE* 4.3 1.3 - - + -
308L LEU* 3.1 37.1 - - + +
311L VAL* 3.3 23.4 - - + +
376L LEU 2.9 19.4 + - - +
377L VAL 3.7 0.2 - - - +
379L TYR* 1.3 79.6 - - - +
381L LYS* 1.3 57.7 + - - +
382L LYS* 3.0 15.0 + - - +
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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