Contacts of the helix formed by residues 485 - 490 (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 PRO 485 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369L VAL* 3.5 13.1 - - + +
463L ARG* 3.2 31.2 - - + +
464L GLY* 3.5 21.5 - - - +
465L MET 3.5 16.5 - - - +
466L LEU* 4.0 3.1 - - + -
484L VAL* 1.3 93.9 - - + +
486L SER* 1.3 59.2 + - - -
488L TRP* 3.0 16.0 + - + +
489L ASN* 3.1 13.6 + - - -
537L FCO 3.2 34.5 - - - +
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Residues in contact with SER 486 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357L MET* 3.6 7.0 - - - +
463L ARG* 4.3 2.5 + - - +
484L VAL* 3.3 1.0 - - - +
485L PRO* 1.3 74.0 - - - +
487L THR* 1.3 56.5 + - - +
489L ASN* 4.5 5.1 + - - +
490L LEU* 3.0 41.4 + - - +
527L TYR 5.2 0.5 + - - -
528L ASP 4.0 3.8 + - - -
529L PRO* 3.9 4.7 - - - +
530L CYS* 3.1 42.3 + - - +
534L GLY* 4.2 4.7 - - - -
537L FCO 2.8 25.2 + - - -
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Residues in contact with THR 487 (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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321L GLU* 4.1 10.1 - - - +
357L MET* 4.0 8.5 - - + -
358L LYS* 3.3 34.8 - - + +
360L PRO* 3.2 30.6 - - + +
361L ARG* 5.6 0.2 + - - -
484L VAL* 2.8 28.9 + - - +
486L SER* 1.3 77.3 - - - +
488L TRP* 1.3 62.9 + - - +
491L GLY* 3.3 17.0 + - - -
534L GLY* 2.8 31.3 + - - +
536L HIS* 4.0 4.0 - - + -
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Residues in contact with TRP 488 (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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281L LEU* 4.4 11.4 - - + -
319L ILE* 4.1 29.4 - - + -
360L PRO* 3.5 42.5 - - + +
361L ARG* 3.9 22.7 + - - -
362L TYR* 3.7 28.3 - - + -
367L PHE* 3.9 39.6 + - + +
369L VAL* 3.6 25.5 - - + +
465L MET* 4.0 24.0 + - - -
483L VAL* 3.8 14.2 + - + +
484L VAL 3.3 23.1 + - - -
485L PRO* 3.0 9.3 + - + +
487L THR* 1.3 80.7 - - - +
489L ASN* 1.3 61.7 + - - +
491L GLY* 4.1 2.3 + - - -
500L SER* 4.2 10.0 - - - -
501L ALA 4.4 1.0 + - - -
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Residues in contact with ASN 489 (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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368L GLU* 3.6 11.6 - - - +
369L VAL* 3.2 42.5 + - - +
463L ARG* 3.8 10.5 + - - +
485L PRO 3.1 15.7 + - - +
486L SER* 4.6 3.2 + - - +
488L TRP* 1.3 74.1 - - - +
490L LEU* 1.3 68.8 + - + +
491L GLY 3.7 0.2 - - - -
500L SER* 3.7 1.6 + - - -
501L ALA* 3.6 10.4 + - - +
502L VAL* 2.9 30.7 + - - +
527L TYR* 3.6 35.7 + - + -
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Residues in contact with LEU 490 (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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21L LEU* 3.8 30.1 - - + -
23L ILE* 5.4 0.2 - - + -
37L SER* 2.8 31.7 + - - +
39L SER* 4.3 2.6 + - - +
355L SER* 5.0 0.2 + - - -
357L MET* 3.8 18.9 - - + +
486L SER* 3.0 27.2 + - - +
489L ASN* 1.3 86.1 - - + +
491L GLY* 1.3 62.8 - - - +
492L PRO* 4.7 0.2 - - - +
500L SER* 4.3 0.2 - - - -
502L VAL* 3.9 23.8 - - + -
524L VAL* 4.8 0.7 - - + -
527L TYR* 4.6 6.5 - - + +
529L PRO* 3.3 42.4 - - + -
531L ILE* 4.5 3.1 - - + -
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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