Contacts of the helix formed by residues 518 - 527 (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 VAL 518 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F ARG* 5.8 0.2 - - - +
119F ASP* 3.8 29.8 - - + +
174F TYR* 3.8 22.8 - - + -
179F HIS* 4.1 11.0 - - + +
181F ALA* 3.9 27.4 - - + -
182F TYR* 3.4 31.9 - - + +
516F ARG 3.3 2.5 + - - +
517F PRO* 1.3 72.5 - - - +
519F GLU* 1.3 73.3 + - - +
520F ILE 3.1 0.9 - - - -
521F LEU* 3.1 5.3 + - + -
522F ARG* 2.9 30.7 + - - +
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Residues in contact with GLU 519 (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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179F HIS* 4.7 1.8 - - - -
181F ALA* 4.0 12.0 - - + +
271F TRP* 3.6 33.9 - - + -
509F THR* 3.6 17.7 - - + +
510F PRO* 3.3 26.6 - - + +
511F ILE* 3.6 7.0 - - + +
512F ALA* 2.7 40.9 + - - +
513F ASP 4.7 0.5 - - - +
516F ARG 4.4 2.1 - - - +
517F PRO* 3.1 9.6 - - - +
518F VAL* 1.3 99.8 + - + +
520F ILE* 1.3 60.6 + - - +
522F ARG* 3.6 1.2 + - - +
523F THR* 3.6 14.4 + - - -
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Residues in contact with ILE 520 (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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9F ILE* 4.0 18.6 - - + +
11F VAL* 4.2 12.3 - - + -
14F ILE* 4.6 7.4 - - + -
23F ILE* 4.0 18.8 - - + -
25F VAL* 3.8 33.2 - - + -
32F ILE* 3.7 21.8 - - + -
506F LEU* 4.3 9.4 - - + -
511F ILE* 3.8 12.3 - - + +
517F PRO* 3.2 12.2 + - + +
518F VAL 3.1 0.8 - - - -
519F GLU* 1.3 79.1 - - - +
521F LEU* 1.3 58.7 + - + +
523F THR* 3.4 3.3 + - - -
524F VAL* 2.9 41.0 + - + +
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Residues in contact with LEU 521 (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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50E ALA 4.5 0.4 - - - +
52E ALA* 3.9 26.9 - - + -
11F VAL* 4.3 14.4 - - + -
14F ILE* 4.6 11.7 - - + -
15F THR* 4.7 1.1 - - - +
16F ARG* 3.4 29.2 - - - +
119F ASP* 3.6 12.8 - - - +
174F TYR* 4.1 22.0 - - + +
517F PRO 3.6 15.9 - - - +
518F VAL* 3.1 9.8 + - + +
520F ILE* 1.3 77.6 - - + +
522F ARG* 1.3 61.5 + - - +
524F VAL* 4.4 5.2 - - - +
525F HIS* 2.7 50.0 + - + +
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Residues in contact with ARG 522 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F HIS* 3.5 6.8 + - - -
119F ASP* 2.4 49.8 + - + -
120F TRP* 3.4 42.3 - - + +
181F ALA* 2.9 43.8 + - - +
182F TYR* 4.1 7.5 - - - +
268F TYR* 3.4 18.0 + - - -
271F TRP* 3.7 39.5 - - + +
407F THR* 3.6 4.7 - - - +
518F VAL* 2.9 28.2 + - - +
519F GLU* 4.0 4.5 - - - +
520F ILE 3.3 0.4 - - - -
521F LEU* 1.3 77.2 - - - +
523F THR* 1.3 61.2 + - - +
526F SER* 3.2 22.9 + - - -
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Residues in contact with THR 523 (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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271F TRP* 4.0 10.6 - - - -
274F ILE* 4.5 1.7 - - - +
407F THR* 3.5 19.7 + - - +
502F VAL* 4.8 2.5 - - + +
505F ALA* 3.6 34.3 + - + +
506F LEU* 3.9 25.4 - - + -
509F THR* 4.0 10.4 + - - -
519F GLU 3.6 9.2 + - - -
520F ILE 3.4 3.4 + - - -
522F ARG* 1.3 76.0 - - - +
524F VAL* 1.3 67.4 + - - +
526F SER* 2.7 23.7 + - - -
527F TYR* 3.5 11.1 - - + -
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Residues in contact with VAL 524 (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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14F ILE* 4.2 18.4 - - + -
17F ILE* 4.6 1.3 - - + -
21F LEU* 4.1 16.2 - - + -
23F ILE* 3.7 27.1 - - + -
490F LEU* 4.8 2.5 - - + -
502F VAL* 4.2 15.7 - - + +
506F LEU* 4.6 5.8 - - + -
520F ILE* 2.9 31.7 + - + +
521F LEU* 4.2 4.9 - - - +
523F THR* 1.3 76.9 - - - +
525F HIS* 1.3 64.3 + - + +
527F TYR* 3.3 9.2 + - - +
529F PRO* 3.2 33.7 - - + +
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Residues in contact with HIS 525 (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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14F ILE* 4.6 3.7 - - + +
15F THR 2.9 27.6 + - - -
16F ARG* 3.0 44.0 + - + +
17F ILE* 3.8 13.8 - - + +
111F HIS* 2.9 30.3 + - - +
115F LEU 4.1 7.9 - - - -
116F HIS* 3.5 19.1 - - + -
119F ASP* 2.8 18.1 + - - -
521F LEU* 2.7 45.0 + - + +
524F VAL* 1.3 70.4 - - - +
526F SER* 1.3 58.8 + - - +
527F TYR 3.0 2.9 - - - -
528F ASP 2.9 9.1 + - - -
529F PRO* 4.2 4.0 - - + -
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Residues in contact with SER 526 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F HIS* 4.0 9.6 + - - -
407F THR* 3.7 15.8 - - - +
410F ARG* 3.3 36.9 + - - +
411F THR* 3.7 13.5 - - - -
414F ARG* 2.6 34.5 + - - +
522F ARG 3.2 16.0 + - - -
523F THR 2.7 19.3 + - - -
525F HIS* 1.3 75.8 - - - +
527F TYR* 1.3 51.5 + - - +
528F ASP 3.2 0.7 - - - -
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Residues in contact with TYR 527 (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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277F THR* 3.3 4.0 - - - +
368F GLU* 3.1 40.9 + - + -
369F VAL 5.2 0.7 - - - -
410F ARG* 3.3 34.6 + - - +
414F ARG* 3.8 4.7 + - - +
463F ARG* 4.8 4.3 - - - +
486F SER* 5.2 0.7 + - - -
489F ASN* 3.6 39.7 + - + -
490F LEU* 4.6 9.0 - - + +
501F ALA* 3.1 28.9 + - + -
502F VAL* 4.1 17.3 - - + -
505F ALA* 3.5 13.1 - - + +
523F THR 3.5 15.5 - - - -
524F VAL 3.3 8.4 + - - +
525F HIS 3.0 0.6 - - - -
526F SER* 1.3 78.8 + - - +
528F ASP* 1.3 71.4 + - - +
529F PRO* 3.3 6.9 - - + +
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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