Contacts of the helix formed by residues 518 - 527 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16J ARG* 5.8 0.2 - - - +
119J ASP* 3.8 30.1 - - + +
174J TYR* 3.8 22.0 - - + -
179J HIS* 4.1 10.5 - - + +
181J ALA* 3.9 28.3 - - + -
182J TYR* 3.4 31.9 - - + +
516J ARG 3.3 3.5 + - - +
517J PRO* 1.3 72.9 - - - +
519J GLU* 1.3 71.1 + - - +
520J ILE 3.1 0.9 - - - -
521J LEU* 3.1 5.6 + - + +
522J ARG* 2.9 30.7 + - - +
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Residues in contact with GLU 519 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179J HIS* 4.7 1.1 - - - -
181J ALA* 4.0 11.3 - - + +
271J TRP* 3.6 35.0 - - + -
509J THR* 3.6 17.1 - - + +
510J PRO* 3.3 26.1 - - + +
511J ILE* 3.6 7.9 - - + +
512J ALA* 2.7 40.9 + - - +
513J ASP 4.7 0.3 - - - +
516J ARG 4.4 2.3 - - - +
517J PRO* 3.1 9.4 - - - +
518J VAL* 1.3 98.9 + - + +
520J ILE* 1.3 60.9 + - - +
522J ARG* 3.6 0.8 + - - +
523J THR* 3.6 14.9 + - - -
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Residues in contact with ILE 520 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ILE* 4.0 19.1 - - + +
11J VAL* 4.2 12.1 - - + -
14J ILE* 4.6 7.4 - - + -
23J ILE* 4.0 19.7 - - + -
25J VAL* 3.8 32.8 - - + -
32J ILE* 3.7 21.3 - - + -
506J LEU* 4.3 9.6 - - + +
511J ILE* 3.8 11.0 - - + +
517J PRO* 3.2 12.1 + - + +
518J VAL 3.1 0.6 - - - -
519J GLU* 1.3 79.2 - - - +
521J LEU* 1.3 57.7 + - + +
523J THR* 3.4 2.8 + - - -
524J VAL* 2.9 40.8 + - + +
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Residues in contact with LEU 521 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ALA 4.5 0.2 - - - +
52I ALA* 3.9 26.9 - - + -
11J VAL* 4.3 14.6 - - + -
14J ILE* 4.6 11.2 - - + -
15J THR* 4.7 1.1 - - - +
16J ARG* 3.4 28.9 - - - +
119J ASP* 3.6 13.0 - - - +
174J TYR* 4.1 23.6 - - + +
517J PRO 3.6 15.5 - - - +
518J VAL 3.1 8.9 + - - +
520J ILE* 1.3 77.9 - - + +
522J ARG* 1.3 62.4 + - - +
524J VAL* 4.4 5.4 - - - +
525J HIS* 2.7 50.6 + - + +
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Residues in contact with ARG 522 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J HIS* 3.5 6.2 + - - -
119J ASP* 2.4 49.1 + - + +
120J TRP* 3.4 41.2 - - + +
181J ALA* 2.9 43.4 + - - +
182J TYR* 4.1 7.1 - - - +
268J TYR* 3.4 18.4 + - - -
271J TRP* 3.7 39.0 - - + +
407J THR* 3.6 4.4 - - - +
518J VAL* 2.9 26.9 + - - +
519J GLU* 4.0 5.1 - - - +
520J ILE 3.3 0.4 - - - -
521J LEU* 1.3 77.0 - - - +
523J THR* 1.3 60.8 + - - +
526J SER* 3.2 23.7 + - - -
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Residues in contact with THR 523 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271J TRP* 4.0 10.4 - - - -
274J ILE* 4.5 1.9 - - - +
407J THR* 3.5 18.4 + - - +
502J VAL* 4.8 2.0 - - + +
505J ALA* 3.6 33.8 + - + +
506J LEU* 3.9 26.7 - - + -
509J THR* 4.0 10.2 + - - -
519J GLU 3.6 8.9 + - - -
520J ILE 3.4 2.1 + - - -
521J LEU 3.2 0.4 - - - -
522J ARG* 1.3 76.4 - - - +
524J VAL* 1.3 66.1 + - - +
526J SER* 2.7 23.8 + - - -
527J TYR* 3.5 10.8 - - + -
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Residues in contact with VAL 524 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ILE* 4.1 17.7 - - + -
17J ILE* 4.6 0.7 - - + -
21J LEU* 4.1 16.4 - - + -
23J ILE* 3.7 27.6 - - + -
490J LEU* 4.8 2.0 - - + -
502J VAL* 4.2 15.9 - - + +
506J LEU* 4.6 5.6 - - + -
520J ILE* 2.9 31.7 + - + +
521J LEU* 4.2 5.4 - - - +
523J THR* 1.3 76.6 - - - +
525J HIS* 1.3 64.2 + - + +
527J TYR* 3.3 8.8 + - - +
529J PRO* 3.2 34.3 - - + +
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Residues in contact with HIS 525 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ILE* 4.6 4.0 - - + +
15J THR 2.9 27.9 + - - -
16J ARG* 3.0 43.6 + - + +
17J ILE* 3.8 13.5 - - + +
111J HIS* 2.9 31.0 + - - +
115J LEU 4.1 7.0 - - - -
116J HIS* 3.5 19.3 - - + -
119J ASP* 2.8 17.8 + - - -
521J LEU* 2.7 44.5 + - + +
524J VAL* 1.3 70.8 - - + +
526J SER* 1.3 59.5 + - - +
527J TYR 3.0 2.7 - - - -
528J ASP 2.9 9.1 + - - -
529J PRO* 4.2 3.6 - - + -
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Residues in contact with SER 526 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J HIS* 4.0 9.4 - - - -
407J THR* 3.7 16.6 - - - +
410J ARG* 3.3 36.1 + - - +
411J THR* 3.7 13.2 - - - -
414J ARG* 2.6 34.0 + - - +
522J ARG 3.2 16.8 + - - -
523J THR 2.7 19.3 + - - -
525J HIS* 1.3 76.9 - - - +
527J TYR* 1.3 51.0 + - - +
528J ASP 3.2 0.4 - - - -
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Residues in contact with TYR 527 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277J THR* 3.3 4.7 - - - +
368J GLU* 3.1 39.3 + - + -
369J VAL 5.2 0.9 - - - -
410J ARG* 3.3 36.2 + - - +
414J ARG* 3.8 4.5 + - - +
463J ARG* 4.8 4.5 - - - +
486J SER* 5.2 0.5 + - - -
489J ASN* 3.6 38.8 + - + +
490J LEU* 4.6 9.0 - - + +
501J ALA* 3.1 28.1 + - + -
502J VAL* 4.1 18.6 - - + -
505J ALA* 3.5 13.7 - - + +
523J THR 3.5 15.3 - - - -
524J VAL 3.3 8.9 + - - +
525J HIS 3.0 0.8 - - - -
526J SER* 1.3 78.3 + - - +
528J ASP* 1.3 72.2 - - - +
529J PRO* 4.2 7.3 - - + +
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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