Contacts of the helix formed by residues 485 - 490 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369H VAL* 3.5 13.4 - - + +
463H ARG* 3.2 31.6 - - + +
464H GLY* 3.5 22.4 - - - +
465H MET 3.5 16.8 - - - +
466H LEU* 4.0 3.1 - - + -
484H VAL* 1.3 95.4 - - + +
486H SER* 1.3 60.1 + - - +
488H TRP* 3.0 16.1 + - + +
489H ASN* 3.1 13.5 + - - -
537H FCO 3.2 34.1 - - - +
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Residues in contact with SER 486 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H MET* 3.6 7.3 - - - +
463H ARG* 4.3 2.3 + - - +
484H VAL* 3.3 0.8 - - - +
485H PRO* 1.3 74.5 - - - +
487H THR* 1.3 56.4 + - - +
488H TRP 3.2 0.2 - - - -
489H ASN* 4.5 5.1 + - - +
490H LEU* 3.0 43.0 + - - +
527H TYR 5.2 0.7 + - - -
528H ASP 4.0 3.3 + - - -
529H PRO* 3.9 4.9 - - - +
530H CYS* 3.1 41.1 + - - +
534H GLY* 4.2 4.9 - - - -
537H FCO 2.8 26.6 + - - -
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Residues in contact with THR 487 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321H GLU* 4.1 9.6 - - - +
357H MET* 4.0 8.7 - - + -
358H LYS* 3.3 32.8 - - + +
360H PRO* 3.2 31.1 - - + +
484H VAL* 2.8 28.9 + - - +
486H SER* 1.3 77.5 - - - +
488H TRP* 1.3 63.0 + - - +
491H GLY* 3.3 17.0 + - - -
534H GLY* 2.8 31.2 + - - +
536H HIS* 4.0 4.8 - - + -
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Residues in contact with TRP 488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H LEU* 4.4 11.4 - - + -
319H ILE* 4.1 29.8 - - + -
360H PRO* 3.5 42.7 - - + +
361H ARG* 3.9 22.2 + - - -
362H TYR* 3.7 28.7 - - + -
367H PHE* 3.9 38.6 + - + +
369H VAL* 3.6 25.9 - - + +
465H MET* 4.0 24.3 + - - -
483H VAL* 3.8 14.1 + - + +
484H VAL 3.3 23.6 + - - -
485H PRO* 3.0 9.3 + - + +
487H THR* 1.3 79.9 - - - +
489H ASN* 1.3 61.8 + - - +
490H LEU 3.7 0.2 + - - -
491H GLY 4.1 2.4 + - - -
500H SER* 4.2 10.4 - - - -
501H ALA 4.4 0.9 + - - -
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Residues in contact with ASN 489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368H GLU* 3.6 11.1 - - - +
369H VAL* 3.2 42.9 + - - +
463H ARG* 3.8 10.1 + - - +
485H PRO 3.1 15.5 + - - +
486H SER* 4.5 3.6 + - - +
488H TRP* 1.3 75.4 - - - +
490H LEU* 1.3 68.6 + - + +
500H SER* 3.7 1.4 + - - -
501H ALA* 3.6 9.6 + - - -
502H VAL* 2.9 30.7 + - - +
527H TYR* 3.6 36.3 + - + -
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Residues in contact with LEU 490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H LEU* 3.8 29.6 - - + -
23H ILE* 5.4 0.4 - - + -
37H SER* 2.8 31.8 + - - +
39H SER* 4.3 2.8 + - - +
355H SER* 5.0 0.2 + - - -
357H MET* 3.8 18.7 - - + +
486H SER* 3.0 27.4 + - - +
489H ASN* 1.3 86.3 - - + +
491H GLY* 1.3 61.8 + - - +
492H PRO* 4.7 0.2 - - - +
500H SER* 4.3 0.4 - - - -
502H VAL* 3.9 24.7 - - + -
524H VAL* 4.8 0.7 - - + -
527H TYR* 4.6 6.5 - - + +
529H PRO* 3.3 41.7 - - + -
531H 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