Contacts of the helix formed by residues 485 - 490 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369F VAL* 3.5 12.9 - - + +
463F ARG* 3.2 30.3 - - + +
464F GLY* 3.5 22.0 - - - +
465F MET 3.5 16.6 - - - +
466F LEU* 4.0 2.9 - - + -
484F VAL* 1.3 93.1 - - + +
486F SER* 1.3 60.5 + - - +
488F TRP* 3.0 15.2 + - + +
489F ASN* 3.1 13.5 + - - -
537F FCO 3.2 35.0 - - - +
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Residues in contact with SER 486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F MET* 3.6 7.2 - - - +
463F ARG* 4.3 2.6 - - - +
484F VAL* 3.3 0.8 - - - +
485F PRO* 1.3 74.5 - - - +
487F THR* 1.3 56.3 + - - +
489F ASN* 4.5 5.1 + - - +
490F LEU* 3.0 41.6 + - - +
527F TYR 5.2 0.5 + - - -
528F ASP 4.0 3.6 + - - -
529F PRO* 3.9 4.3 - - - +
530F CYS* 3.1 42.0 + - - +
534F GLY* 4.2 4.9 - - - -
537F FCO 2.8 25.8 + - - -
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Residues in contact with THR 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321F GLU* 4.1 9.6 - - - +
357F MET* 4.0 8.3 - - + -
358F LYS* 3.3 34.3 - - + +
360F PRO* 3.2 31.1 - - + +
361F ARG* 5.6 0.2 + - - -
484F VAL* 2.8 27.8 + - - +
486F SER* 1.3 77.5 - - - +
488F TRP* 1.3 63.3 + - - +
491F GLY* 3.3 17.5 + - - -
534F GLY* 2.8 31.2 + - - +
536F HIS* 4.0 5.0 - - + -
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Residues in contact with TRP 488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F LEU* 4.4 11.9 - - + -
319F ILE* 4.1 29.2 - - + -
360F PRO* 3.5 41.8 - - + +
361F ARG* 3.9 22.9 + - - -
362F TYR* 3.7 29.6 - - + -
367F PHE* 3.9 37.0 - - + +
369F VAL* 3.6 25.2 - - + +
465F MET* 4.0 24.0 + - - -
483F VAL* 3.8 14.9 + - + +
484F VAL 3.3 21.9 + - - -
485F PRO* 3.0 9.7 + - + +
487F THR* 1.3 80.7 - - - +
489F ASN* 1.3 61.4 + - - +
490F LEU 3.7 0.2 + - - -
491F GLY 4.1 2.1 + - - -
500F SER* 4.2 9.9 - - - -
501F ALA 4.4 0.7 + - - -
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Residues in contact with ASN 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F GLU* 3.6 11.4 - - - +
369F VAL* 3.2 42.6 + - - +
463F ARG* 3.8 10.3 + - - +
485F PRO 3.1 15.9 + - - +
486F SER* 4.6 2.8 + - - +
488F TRP* 1.3 75.2 - - - +
490F LEU* 1.3 68.5 + - + +
500F SER* 3.7 1.0 + - - -
501F ALA* 3.6 9.5 + - - -
502F VAL* 2.9 30.5 + - - +
527F TYR* 3.6 36.4 + - + -
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Residues in contact with LEU 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU* 3.8 30.1 - - + -
23F ILE* 5.4 0.4 - - + -
37F SER* 2.8 31.4 + - - +
39F SER* 4.3 2.8 + - - +
355F SER* 5.0 0.2 + - - -
357F MET* 3.8 19.1 - - + +
486F SER* 3.0 27.8 + - - +
489F ASN* 1.3 86.8 - - + +
491F GLY* 1.3 62.0 - - - +
492F PRO* 4.7 0.2 - - - +
500F SER* 4.3 0.2 - - - -
502F VAL* 3.9 24.0 - - + -
524F VAL* 4.8 0.4 - - + -
527F TYR* 4.6 6.5 - - + +
529F PRO* 3.3 41.5 - - + -
531F 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