Contacts of the strand formed by residues 359 - 362 (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 ALA 359 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321D GLU* 4.2 0.7 - - - -
322D HIS* 2.8 47.5 + - + +
326D SER* 5.1 0.2 - - - +
358D LYS* 1.3 73.3 - - - +
360D PRO* 1.3 65.6 - - - +
361D ARG* 3.4 12.6 + - - +
487D THR 4.8 1.1 - - - -
491D GLY* 5.0 0.2 - - - -
492D PRO* 3.7 18.8 - - + +
493D ARG 3.7 25.1 - - - +
494D CYS* 4.2 1.1 - - - -
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Residues in contact with PRO 360 (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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319D ILE* 5.3 0.7 - - + -
320D GLU 3.5 7.6 - - - +
321D GLU* 3.8 12.6 - - + +
358D LYS 3.3 4.9 - - - +
359D ALA* 1.3 82.4 - - - +
361D ARG* 1.3 76.9 + - - +
365D GLU 4.8 0.2 - - - +
366D ALA* 5.0 1.4 - - - -
367D PHE 5.1 0.2 + - - -
483D VAL* 3.8 20.4 - - + -
487D THR* 3.2 44.4 - - + +
488D TRP* 3.5 43.3 - - + +
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Residues in contact with ARG 361 (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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318D LEU 3.7 1.7 - - - +
319D ILE* 3.7 2.9 - - - -
320D GLU* 2.8 32.4 + - + +
322D HIS* 3.6 31.9 - - + +
359D ALA* 3.4 17.8 + - - +
360D PRO* 1.3 89.1 + - - +
362D TYR* 1.3 60.2 + - - +
363D LYS 4.0 0.4 + - - -
364D GLY* 4.1 19.2 + - - +
365D GLU 3.4 15.7 - - - +
366D ALA* 3.9 16.8 - - - +
367D PHE 5.6 0.4 - - - +
487D THR 5.6 0.2 + - - -
488D TRP* 3.8 8.8 + - - -
491D GLY 5.6 0.4 - - - -
492D PRO 3.4 17.8 + - - -
494D CYS* 3.5 29.3 - - + +
498D LYS* 2.9 30.9 + - - +
499D LEU 3.9 0.8 - - - -
500D SER* 3.8 16.4 - - - +
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Residues in contact with TYR 362 (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* 3.7 18.6 - - + -
302D VAL* 3.9 20.2 - - + +
304D TRP* 3.9 17.0 - + - -
313D ASP 3.7 8.5 + - - -
314D PHE* 3.8 7.6 - + - -
315D ASN* 2.9 54.0 + - - +
318D LEU* 3.5 26.6 - - + +
319D ILE* 4.2 12.3 - - + -
361D ARG* 1.3 69.7 - - - +
363D LYS* 1.3 71.7 + - + +
365D GLU* 2.7 28.7 + - - +
367D PHE* 3.4 33.6 - + + -
488D TRP* 3.7 10.8 - + + -
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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