Contacts of the helix formed by residues 518 - 527 (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 VAL 518 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L ARG* 5.8 0.7 - - - +
119L ASP* 3.8 29.4 - - + +
174L TYR* 3.8 21.7 - - + -
179L HIS* 4.1 9.6 - - + +
181L ALA* 3.9 28.5 - - + -
182L TYR* 3.4 33.0 - - + +
516L ARG 3.3 3.3 + - - +
517L PRO* 1.3 72.3 - - - +
519L GLU* 1.3 71.5 + - - +
520L ILE 3.1 0.7 - - - -
521L LEU* 3.1 5.1 + - + -
522L ARG* 2.9 30.1 + - - +
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Residues in contact with GLU 519 (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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179L HIS* 4.7 1.5 - - - -
181L ALA* 4.0 12.9 - - + +
271L TRP* 3.6 34.0 - - + -
509L THR* 3.6 16.4 - - + +
510L PRO* 3.3 27.5 - - + +
511L ILE* 3.6 8.6 - - + +
512L ALA* 2.7 41.3 + - - +
513L ASP 4.7 0.3 - - - +
516L ARG 4.4 1.9 - - - +
517L PRO* 3.8 8.5 - - - +
518L VAL* 1.3 100.8 + - + +
520L ILE* 1.3 59.9 + - - +
522L ARG* 3.6 1.0 + - - +
523L THR* 3.6 14.2 + - - -
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Residues in contact with ILE 520 (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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9L ILE* 4.0 18.2 - - + +
11L VAL* 4.2 12.3 - - + -
14L ILE* 4.6 7.2 - - + -
23L ILE* 4.0 18.8 - - + -
25L VAL* 3.8 33.4 - - + -
32L ILE* 3.7 22.0 - - + -
506L LEU* 4.3 9.2 - - + -
511L ILE* 3.8 12.1 - - + +
517L PRO* 3.2 12.0 + - + +
518L VAL 3.1 1.0 - - - -
519L GLU* 1.3 79.9 - - - +
521L LEU* 1.3 58.4 + - + +
523L THR* 3.4 3.3 + - - -
524L VAL* 2.9 41.4 + - + +
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Residues in contact with LEU 521 (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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11L VAL* 4.3 14.4 - - + -
14L ILE* 4.6 11.4 - - + -
15L THR* 4.7 0.7 - - - +
16L ARG* 3.4 28.3 - - - +
119L ASP* 3.6 12.6 - - - +
174L TYR* 4.1 23.1 - - + +
517L PRO 3.6 15.5 - - - +
518L VAL* 3.1 10.2 + - + +
520L ILE* 1.3 77.8 - - + +
522L ARG* 1.3 62.4 + - - +
524L VAL* 4.4 5.2 - - - +
525L HIS* 2.7 50.7 + - + +
50S ALA 4.5 0.4 - - - +
52S ALA* 3.9 27.4 - - + -
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Residues in contact with ARG 522 (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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116L HIS* 3.5 6.6 + - - -
119L ASP* 2.4 50.5 + - + +
120L TRP* 3.4 41.5 - - + +
181L ALA* 2.9 44.2 + - - +
182L TYR* 4.1 7.1 - - - +
268L TYR* 3.4 17.8 + - - -
271L TRP* 3.7 39.4 - - + +
407L THR* 3.6 4.7 - - - +
518L VAL* 2.9 27.3 + - - +
519L GLU 4.0 4.7 - - - +
520L ILE 3.3 0.4 - - - -
521L LEU* 1.3 77.4 - - - +
523L THR* 1.3 61.0 + - - +
526L SER* 3.2 23.2 + - - -
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Residues in contact with THR 523 (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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271L TRP* 4.0 10.0 - - - -
274L ILE* 4.5 1.7 - - - +
407L THR* 3.5 18.0 + - - +
502L VAL* 4.8 2.0 - - + +
505L ALA* 3.6 34.7 + - + +
506L LEU* 3.9 26.5 - - + -
509L THR* 4.0 10.0 + - - -
519L GLU 3.6 9.3 + - - -
520L ILE 3.4 3.6 + - - -
521L LEU 3.2 0.2 - - - -
522L ARG* 1.3 76.7 - - - +
524L VAL* 1.3 65.5 + - - +
526L SER* 2.7 23.7 + - - -
527L TYR* 3.5 10.5 - - + -
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Residues in contact with VAL 524 (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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14L ILE* 4.1 17.9 - - + -
17L ILE* 4.6 0.9 - - + -
21L LEU* 4.1 17.0 - - + -
23L ILE* 3.7 27.4 - - + -
490L LEU* 4.8 2.2 - - + -
502L VAL* 4.2 15.6 - - + +
506L LEU* 4.6 5.6 - - + -
520L ILE* 2.9 31.9 + - + +
521L LEU* 4.2 4.9 - - - +
523L THR* 1.3 77.6 - - - +
525L HIS* 1.3 63.8 + - + +
527L TYR* 3.3 8.8 + - - +
529L PRO* 3.2 33.7 - - + +
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Residues in contact with HIS 525 (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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14L ILE* 4.6 3.3 - - + +
15L THR 2.9 27.8 + - - -
16L ARG* 3.0 44.0 + - + +
17L ILE* 3.8 13.6 - - + +
111L HIS* 2.9 31.3 + - - +
115L LEU 4.1 6.7 - - - -
116L HIS* 3.5 19.3 - - + -
119L ASP* 2.8 17.6 + - - -
521L LEU* 2.7 46.0 + - + +
524L VAL* 1.3 69.1 - - + +
526L SER* 1.3 58.7 + - - +
527L TYR 3.0 2.9 - - - -
528L ASP 2.9 9.6 + - - -
529L PRO* 4.2 3.4 - - + -
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Residues in contact with SER 526 (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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116L HIS* 4.0 9.0 - - - -
407L THR* 3.7 16.6 - - - +
410L ARG* 3.3 36.8 + - - +
411L THR* 3.7 13.5 - - - -
414L ARG* 2.6 34.6 + - - +
522L ARG 3.2 17.0 + - - -
523L THR 2.7 19.1 + - - -
525L HIS* 1.3 76.7 - - - +
527L TYR* 1.3 50.8 + - - +
528L ASP 3.2 0.7 - - - -
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Residues in contact with TYR 527 (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* 3.3 3.6 - - - +
368L GLU* 3.1 41.4 + - + -
369L VAL 5.2 0.7 - - - -
410L ARG* 3.3 33.2 + - - +
414L ARG* 3.8 4.9 + - - +
463L ARG* 4.8 4.2 - - - +
486L SER* 5.2 0.7 + - - -
489L ASN* 3.6 39.6 + - + -
490L LEU* 4.6 9.6 - - + +
501L ALA* 3.1 29.2 + - + -
502L VAL* 4.1 17.7 - - + -
505L ALA* 3.5 14.0 - - + +
523L THR* 3.5 14.8 - - + -
524L VAL 3.3 9.1 + - - +
525L HIS 3.0 0.4 - - - -
526L SER* 1.3 78.3 + - - +
528L ASP* 1.3 71.9 + - - +
529L PRO* 3.3 7.1 - - + +
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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