Contacts of the strand formed by residues 319 - 322 (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 ILE 319 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314H PHE* 4.2 17.5 - - + -
316H PRO* 3.6 34.5 - - + +
317H ASP 3.3 1.5 - - - +
318H LEU* 1.3 78.8 - - - +
320H GLU* 1.3 72.2 - - - +
321H GLU* 4.9 1.6 - - + +
335H HIS* 3.2 26.9 - - - -
336H PRO* 3.7 24.2 - - + -
360H PRO* 5.3 0.2 - - + -
361H ARG 3.7 4.7 - - - -
362H TYR* 4.2 10.1 - - + -
465H MET* 5.0 7.0 - - + -
467H SER* 5.3 2.0 - - - +
469H TRP* 4.2 11.2 - - + -
483H VAL* 4.9 10.3 - - + -
488H TRP* 4.1 29.8 - - + -
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Residues in contact with GLU 320 (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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317H ASP 5.9 1.1 - - - +
318H LEU 3.9 3.6 + - - +
319H ILE* 1.3 79.0 - - - +
321H GLU* 1.3 59.6 + - - +
322H HIS* 4.6 5.6 - - - +
333H ALA* 2.5 53.0 - - + +
334H HIS* 2.6 11.2 + - - -
335H HIS* 3.5 15.3 + - + +
360H PRO* 3.5 0.9 - - - +
361H ARG* 2.8 39.6 + - + +
364H GLY 6.3 0.9 - - - +
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Residues in contact with GLU 321 (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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319H ILE* 5.0 3.8 - - + -
320H GLU* 1.3 73.4 - - - +
322H HIS* 1.3 64.0 + - - +
323H VAL* 4.7 2.8 - - - +
332H GLY 3.8 2.1 - - - +
333H ALA* 3.0 18.6 - - - -
334H HIS* 3.2 18.4 + - + +
336H PRO* 4.9 5.3 - - + +
358H LYS* 4.0 31.3 + - + +
359H ALA 3.7 4.3 - - - -
360H PRO* 3.8 20.8 - - + +
481H GLN* 3.9 18.9 + - - -
482H LEU 4.0 5.2 - - - +
483H VAL* 3.3 43.2 - - + +
487H THR* 4.1 5.7 - - - +
540H MG 4.0 7.3 - - - -
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Residues in contact with HIS 322 (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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320H GLU* 4.2 5.6 - - - +
321H GLU* 1.3 73.4 - - - +
323H VAL* 1.3 73.8 + - - +
324H LYS 3.6 1.8 - - - +
326H SER* 3.9 1.2 + - - -
331H ALA 5.1 1.4 + - - -
333H ALA* 3.4 27.5 + - + +
358H LYS* 3.6 5.0 - - - +
359H ALA* 2.8 52.5 + - + +
361H ARG* 3.6 28.5 - - + +
364H GLY* 5.7 2.6 - - - -
493H ARG 5.8 0.2 - - - -
494H CYS* 3.6 14.6 - - + -
495H ALA* 3.3 36.1 + - + +
496H GLU* 5.0 8.9 + - - -
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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