Contacts of the helix formed by residues 518 - 527 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ARG* 5.8 0.2 - - - +
119D ASP* 3.8 29.6 - - + +
174D TYR* 3.8 22.8 - - + -
179D HIS* 4.1 10.5 - - + +
181D ALA* 3.9 27.8 - - + -
182D TYR* 3.4 31.6 - - + +
516D ARG 3.3 2.9 + - - +
517D PRO* 1.3 71.6 - - - +
519D GLU* 1.3 72.3 + - - +
520D ILE 3.1 0.7 - - - -
521D LEU* 3.1 5.5 + - + +
522D ARG* 2.9 30.5 + - - +
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Residues in contact with GLU 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D HIS* 4.7 1.1 - - - -
181D ALA* 4.0 10.3 - - + +
271D TRP* 3.6 33.9 - - + -
509D THR* 3.6 16.8 - - + +
510D PRO* 3.3 25.4 - - + +
511D ILE* 3.6 7.3 - - + +
512D ALA* 2.7 41.4 + - - +
513D ASP 4.7 0.2 - - - +
516D ARG 4.4 2.3 - - - +
517D PRO* 3.1 9.2 - - - +
518D VAL* 1.3 100.6 + - + +
520D ILE* 1.3 60.9 + - - +
522D ARG* 3.6 1.9 + - - +
523D THR* 3.6 14.7 + - - -
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Residues in contact with ILE 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 4.0 18.4 - - + +
11D VAL* 4.2 12.1 - - + -
14D ILE* 4.6 7.2 - - + -
23D ILE* 4.0 20.4 - - + -
25D VAL* 3.8 34.1 - - + -
32D ILE* 3.7 21.5 - - + -
506D LEU* 4.3 9.8 - - + +
511D ILE* 3.8 12.1 - - + +
517D PRO* 3.2 12.4 + - + +
518D VAL 3.1 0.6 - - - -
519D GLU* 1.3 78.6 - - - +
521D LEU* 1.3 58.5 + - + +
523D THR* 3.4 3.1 + - - -
524D VAL* 2.9 40.9 + - + +
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Residues in contact with LEU 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA 4.5 0.4 - - - +
52C ALA* 3.9 28.7 - - + -
11D VAL* 4.3 14.4 - - + -
14D ILE* 4.6 11.7 - - + -
15D THR* 4.7 1.3 - - - +
16D ARG* 3.4 29.2 - - - +
119D ASP* 3.6 13.2 - - - +
174D TYR* 4.1 21.5 - - + -
517D PRO 3.6 15.7 - - - +
518D VAL* 3.5 9.6 - - + +
520D ILE* 1.3 79.1 - - + +
522D ARG* 1.3 61.5 + - - +
524D VAL* 4.4 5.4 - - - +
525D HIS* 2.7 49.4 + - + +
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Residues in contact with ARG 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D HIS* 3.5 6.6 + - - -
119D ASP* 2.4 49.3 + - + -
120D TRP* 3.4 40.3 - - + +
181D ALA* 2.9 43.8 + - - +
182D TYR* 4.1 7.1 - - - +
268D TYR* 3.4 18.4 + - - -
271D TRP* 3.7 39.2 - - + +
407D THR* 3.6 5.0 - - - +
518D VAL* 2.9 28.0 + - - +
519D GLU* 4.0 4.9 - - - +
520D ILE 3.3 0.2 - - - -
521D LEU* 1.3 76.0 - - - +
523D THR* 1.3 61.2 - - - +
526D SER* 3.2 23.6 + - - -
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Residues in contact with THR 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D TRP* 4.0 10.0 - - - -
274D ILE* 4.5 1.7 - - - +
407D THR* 3.5 18.8 + - - +
502D VAL* 4.8 2.0 - - + +
505D ALA* 3.6 33.8 + - + +
506D LEU* 3.9 26.0 - - + -
509D THR* 4.0 10.7 + - - -
519D GLU 3.6 8.9 + - - -
520D ILE 3.4 3.0 + - - -
521D LEU 3.2 0.2 - - - -
522D ARG* 1.3 75.8 - - - +
524D VAL* 1.3 67.2 + - - +
526D SER* 2.7 24.4 + - - -
527D TYR* 3.5 10.8 - - + -
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Residues in contact with VAL 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 4.2 18.2 - - + -
17D ILE* 4.6 1.3 - - + -
21D LEU* 4.1 16.2 - - + -
23D ILE* 3.7 26.9 - - + -
490D LEU* 4.8 2.0 - - + -
502D VAL* 4.2 15.4 - - + +
506D LEU* 4.6 5.6 - - + -
520D ILE* 2.9 32.3 + - + +
521D LEU* 4.2 4.7 - - - +
523D THR* 1.3 78.1 - - - +
525D HIS* 1.3 65.2 + - + +
527D TYR* 3.3 9.0 + - - +
529D PRO* 3.2 33.8 - - + +
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Residues in contact with HIS 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 4.6 3.5 - - + +
15D THR 2.9 28.7 + - - -
16D ARG* 3.0 43.9 + - + +
17D ILE* 3.8 13.3 - - + +
111D HIS* 2.9 24.4 + - - +
115D LEU 4.1 6.7 - - - -
116D HIS* 3.5 20.0 - - + -
119D ASP* 2.8 18.4 + - - -
521D LEU* 2.7 44.6 + - + +
524D VAL* 1.3 71.2 - - + +
526D SER* 1.3 58.5 + - - +
527D TYR 3.0 2.5 - - - -
528D ASP 2.9 16.2 + - - -
529D PRO* 4.2 3.6 - - + -
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Residues in contact with SER 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D HIS* 4.0 8.9 + - - -
407D THR* 3.7 16.1 - - - +
410D ARG* 3.3 35.7 + - - +
411D THR* 3.7 13.9 - - - -
414D ARG* 2.6 34.6 + - - +
522D ARG 3.2 16.5 + - - -
523D THR 2.7 20.0 + - - -
525D HIS* 1.3 75.8 - - - +
527D TYR* 1.3 51.5 + - - +
528D ASP 3.2 0.7 - - - -
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Residues in contact with TYR 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D THR* 3.3 4.2 - - - +
368D GLU* 3.1 39.4 + - + -
369D VAL 5.2 0.9 - - - -
410D ARG* 3.3 35.5 + - - +
414D ARG* 3.8 4.5 + - - +
463D ARG* 4.8 4.2 - - - +
486D SER* 5.2 0.7 + - - -
489D ASN* 3.6 38.9 + - + -
490D LEU* 4.6 8.8 - - + +
501D ALA* 3.1 28.1 + - + -
502D VAL* 4.1 18.6 - - + -
505D ALA* 3.5 13.7 - - + +
523D THR 3.5 15.3 - - - -
524D VAL 3.3 8.7 + - - +
525D HIS 3.0 0.8 - - - -
526D SER* 1.3 79.4 + - - +
528D ASP* 1.3 72.4 - - - +
529D 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