Contacts of the helix formed by residues 518 - 527 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 5.8 0.4 - - - +
119B ASP* 3.8 29.6 - - + +
174B TYR* 3.8 21.0 - - + -
179B HIS* 4.1 10.3 - - + +
181B ALA* 3.9 27.6 - - + -
182B TYR* 3.4 32.1 - - + +
516B ARG 3.3 4.3 + - - +
517B PRO* 1.3 71.7 - - - +
519B GLU* 1.3 73.5 + - - +
520B ILE 3.1 0.9 - - - -
521B LEU* 3.1 5.5 + - + +
522B ARG* 2.9 30.2 + - - +
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Residues in contact with GLU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B HIS* 4.7 1.3 - - - -
181B ALA* 4.0 11.4 - - + +
271B TRP* 3.6 34.8 - - + -
509B THR* 3.6 16.7 - - + +
510B PRO* 3.3 26.5 - - + +
511B ILE* 3.6 7.7 - - + +
512B ALA* 2.7 41.4 + - - +
513B ASP 4.7 0.3 - - - +
516B ARG 4.4 2.4 - - - +
517B PRO* 3.8 8.8 - - - +
518B VAL* 1.3 98.8 + - + +
520B ILE* 1.3 60.3 + - - +
522B ARG* 3.6 1.0 + - - +
523B THR* 3.6 14.9 + - - -
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Residues in contact with ILE 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.0 18.6 - - + +
11B VAL* 4.2 11.9 - - + -
14B ILE* 4.6 7.4 - - + -
23B ILE* 4.0 18.8 - - + -
25B VAL* 3.8 33.4 - - + -
32B ILE* 3.7 22.0 - - + -
506B LEU* 4.3 9.4 - - + -
511B ILE* 3.8 11.6 - - + +
517B PRO* 3.2 11.3 + - + +
518B VAL 3.1 0.8 - - - -
519B GLU* 1.3 78.7 - - - +
521B LEU* 1.3 58.1 + - + +
523B THR* 3.4 3.1 + - - -
524B VAL* 2.9 41.8 + - + +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA 4.5 0.4 - - - +
52A ALA* 3.9 26.9 - - + -
11B VAL* 4.3 14.6 - - + -
14B ILE* 4.6 11.2 - - + -
15B THR* 4.7 1.3 - - - +
16B ARG* 3.4 29.2 - - - +
119B ASP* 3.6 11.9 - - - +
174B TYR* 4.1 22.4 - - + -
517B PRO 3.6 15.7 - - - +
518B VAL* 3.1 9.8 + - + +
520B ILE* 1.3 77.6 - - + +
522B ARG* 1.3 62.5 + - - +
524B VAL* 4.4 5.6 - - - +
525B HIS* 2.7 51.4 + - + +
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Residues in contact with ARG 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B HIS* 3.5 6.6 + - - -
119B ASP* 2.4 50.6 + - + +
120B TRP* 3.4 41.2 - - + +
181B ALA* 2.9 43.2 + - - +
182B TYR* 4.1 7.7 - - - +
268B TYR* 3.4 18.4 + - - -
271B TRP* 3.7 40.0 - - + +
407B THR* 3.6 5.4 - - - +
518B VAL* 2.9 27.1 + - - +
519B GLU 4.0 4.7 - - - +
520B ILE 3.3 0.2 - - - -
521B LEU* 1.3 77.2 - - - +
523B THR* 1.3 60.1 + - - +
526B SER* 3.2 23.2 + - - -
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Residues in contact with THR 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B TRP* 4.0 10.7 - - - -
274B ILE* 4.5 1.9 - - - +
407B THR* 3.5 18.4 + - - +
502B VAL* 4.8 2.0 - - + +
505B ALA* 3.6 32.6 + - + +
506B LEU* 3.9 26.9 - - + -
509B THR* 4.0 10.4 + - - -
519B GLU 3.6 9.4 + - - -
520B ILE 3.4 2.3 + - - -
521B LEU 3.2 0.2 - - - -
522B ARG* 1.3 76.0 - - - +
524B VAL* 1.3 67.3 - - - +
526B SER* 2.7 24.5 + - - -
527B TYR* 3.5 11.1 - - + -
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.2 18.4 - - + -
17B ILE* 4.6 1.1 - - + -
21B LEU* 4.1 16.4 - - + -
23B ILE* 3.7 27.8 - - + -
490B LEU* 4.8 2.5 - - + -
502B VAL* 4.2 15.7 - - + +
506B LEU* 4.6 5.8 - - + -
520B ILE* 2.9 30.6 + - + +
521B LEU* 4.2 4.7 - - - +
523B THR* 1.3 78.0 - - - +
525B HIS* 1.3 63.4 + - + +
527B TYR* 3.3 8.8 + - - +
529B PRO* 3.2 34.1 - - + +
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Residues in contact with HIS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.6 3.7 - - + +
15B THR 2.9 28.0 + - - -
16B ARG* 3.0 43.0 + - - +
17B ILE* 3.8 13.5 - - + +
111B HIS* 2.9 30.6 + - - +
115B LEU 4.1 7.0 - - - -
116B HIS* 3.5 20.2 - - + -
119B ASP* 2.8 17.9 + - - -
521B LEU* 2.7 43.5 + - + +
524B VAL* 1.3 70.4 - - + +
526B SER* 1.3 58.6 + - - +
527B TYR 3.0 2.9 - - - -
528B ASP 2.9 9.6 + - - -
529B PRO* 4.2 3.6 - - + -
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Residues in contact with SER 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B HIS* 4.0 9.4 + - - -
407B THR* 3.7 16.5 - - - +
410B ARG* 3.3 36.4 + - - +
411B THR* 3.7 13.2 - - - -
414B ARG* 2.6 34.5 + - - +
522B ARG 3.2 16.4 + - - -
523B THR 2.7 18.9 + - - -
525B HIS* 1.3 78.0 - - - +
527B TYR* 1.3 51.1 + - - +
528B ASP 3.2 0.7 - - - -
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Residues in contact with TYR 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B THR* 3.3 4.5 - - - +
368B GLU* 3.1 38.6 + - + -
369B VAL 5.2 0.9 - - - -
410B ARG* 3.3 34.9 + - - +
414B ARG* 3.8 4.7 + - - +
463B ARG* 4.8 4.7 - - - +
486B SER* 5.2 0.7 + - - -
489B ASN* 3.6 39.0 + - + -
490B LEU* 4.6 9.4 - - + +
501B ALA* 3.1 28.8 + - + -
502B VAL* 4.1 18.4 - - + -
505B ALA* 3.5 13.7 - - + +
523B THR 3.5 15.5 - - - -
524B VAL 3.3 8.6 + - - +
525B HIS 3.0 1.0 - - - -
526B SER* 1.3 78.5 + - - +
528B ASP* 1.3 72.2 - - - +
529B PRO* 3.3 7.0 - - + +
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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