Contacts of the helix formed by residues 485 - 490 (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 PRO 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369D VAL* 3.5 14.4 - - + +
463D ARG* 3.2 30.5 - - + +
464D GLY* 3.5 22.4 - - - +
465D MET 3.5 17.4 - - - +
466D LEU* 4.0 3.1 - - + -
484D VAL* 1.3 93.9 - - + +
486D SER* 1.3 59.9 + - - +
488D TRP* 3.0 16.0 + - + +
489D ASN* 3.1 13.6 + - - -
537D FCO 3.2 35.0 - - - +
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Residues in contact with SER 486 (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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357D MET* 3.6 7.0 - - - +
463D ARG* 4.3 2.6 - - - +
484D VAL 3.3 0.6 - - - -
485D PRO* 1.3 74.5 - - - +
487D THR* 1.3 56.6 + - - +
489D ASN* 4.5 5.1 + - - +
490D LEU* 3.0 43.1 + - - +
527D TYR 5.2 0.5 + - - -
528D ASP 4.0 3.8 + - - -
529D PRO* 3.9 5.0 - - - +
530D CYS* 3.1 42.7 + - - +
534D GLY* 4.2 4.7 - - - -
537D FCO 2.8 24.8 + - - -
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Residues in contact with THR 487 (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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321D GLU* 4.1 9.9 - - - +
357D MET* 4.0 8.5 - - + -
358D LYS* 3.3 33.9 - - + +
360D PRO* 3.2 29.9 - - + +
484D VAL* 2.8 29.0 + - - +
486D SER* 1.3 78.0 - - - +
488D TRP* 1.3 63.6 + - - +
491D GLY* 3.3 17.7 + - - -
534D GLY* 2.8 30.7 + - - +
536D HIS* 4.0 4.7 - - + +
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Residues in contact with TRP 488 (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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281D LEU* 4.4 11.0 - - + -
319D ILE* 4.1 28.7 - - + -
360D PRO* 3.5 42.0 - - + +
361D ARG* 3.9 22.2 + - - -
362D TYR* 3.7 28.9 - - + -
367D PHE* 3.9 39.0 + - + +
369D VAL* 3.6 26.1 - - + +
465D MET* 4.0 24.4 + - - -
483D VAL* 3.8 14.1 - - + +
484D VAL 3.3 23.3 + - - -
485D PRO* 3.0 9.3 + - + +
487D THR* 1.3 80.8 - - - +
489D ASN* 1.3 63.0 + - - +
491D GLY 4.1 2.3 + - - -
500D SER* 4.2 10.4 - - - -
501D ALA 4.4 1.2 + - - -
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Residues in contact with ASN 489 (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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368D GLU* 3.6 12.0 - - - +
369D VAL* 3.2 41.8 + - - +
463D ARG* 3.8 10.7 + - - +
485D PRO 3.1 16.5 + - - +
486D SER* 4.6 2.8 + - - +
488D TRP* 1.3 75.2 - - - +
490D LEU* 1.3 70.0 + - + +
491D GLY 3.7 0.2 - - - -
500D SER* 3.7 1.2 + - - -
501D ALA* 3.6 9.9 + - - -
502D VAL* 2.9 31.0 + - - +
527D TYR* 3.6 35.3 + - + -
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Residues in contact with LEU 490 (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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21D LEU* 3.8 28.9 - - + -
23D ILE* 5.4 0.7 - - + -
37D SER* 2.8 32.0 + - - +
39D SER* 4.3 3.4 + - - +
355D SER* 5.0 0.2 + - - -
357D MET* 3.8 18.2 - - + +
486D SER* 3.0 26.3 + - - +
489D ASN* 1.3 87.1 - - + +
491D GLY* 1.3 63.0 + - - +
492D PRO* 4.7 0.2 - - - +
502D VAL* 3.9 23.1 - - + -
524D VAL* 4.8 1.1 - - + -
527D TYR* 4.6 6.3 - - + +
529D PRO* 3.3 42.2 - - + -
530D CYS 4.6 0.2 - - - +
531D ILE* 4.5 2.9 - - + -
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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