Contacts of the strand formed by residues 732 - 738 (chain B) in PDB entry 3FBY
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 732 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561B VAL* 3.0 23.6 - - - +
562B GLN* 3.1 15.1 + - - +
586B PHE* 3.9 17.7 - - + -
587B HIS 3.7 3.4 - - - +
588B VAL* 4.4 6.7 - - + +
596B TYR 4.5 2.0 - - - +
597B ALA* 3.7 24.7 - - + -
726B CYS* 4.5 3.4 - - + -
729B GLN* 3.3 49.4 - - + +
730B GLU 4.6 0.2 - - - +
731B ASN* 1.3 73.6 - - - +
733B ILE* 1.3 62.9 + - - +
734B TRP* 3.3 45.5 - - + -
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Residues in contact with ILE 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B VAL* 3.9 15.9 - - + -
296B PRO* 3.9 32.1 - - + +
554B LEU* 6.4 0.4 - - + -
559B GLU* 4.2 9.2 - - + +
560B ILE 3.6 6.7 - - - +
561B VAL* 4.4 14.1 - - + -
585B THR 3.4 2.3 - - - +
586B PHE* 3.8 1.2 - - - -
587B HIS* 2.7 43.9 + - - +
589B ASN* 3.7 30.3 - - + +
731B ASN* 4.3 0.9 - - + +
732B ILE* 1.3 78.9 - - - +
734B TRP* 1.3 66.3 + - - +
735B ALA* 3.8 22.9 - - + -
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Residues in contact with TRP 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B TRP* 3.6 28.5 - + - -
559B GLU* 3.4 1.2 - - - +
560B ILE* 2.7 69.5 + - + +
561B VAL 4.2 0.4 - - - -
562B GLN* 3.7 17.7 - - + -
585B THR 3.4 5.8 - - - -
586B PHE* 5.1 5.7 - - + -
597B ALA* 4.7 0.7 - - + -
598B GLY 2.7 24.0 + - - +
684B TRP* 3.6 22.4 - + + -
724B VAL* 3.2 30.7 - - + +
725B PHE 3.1 26.5 - - - -
726B CYS* 4.4 1.1 - - + -
732B ILE* 3.3 44.8 - - + +
733B ILE* 1.3 75.6 - - - +
735B ALA* 1.3 58.6 + - - +
737B LEU* 3.4 20.5 - - + +
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Residues in contact with ALA 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ASP* 5.0 1.3 - - + -
296B PRO* 3.8 21.1 - - + -
298B SER* 4.3 2.7 - - - +
559B GLU* 3.0 26.9 - - - +
585B THR* 2.9 39.1 + - - +
733B ILE* 3.8 13.2 - - + -
734B TRP* 1.3 73.5 - - - +
736B ASN* 1.3 68.8 + - + +
737B LEU* 3.3 2.5 - - - -
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Residues in contact with ASN 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU 3.9 15.3 + - - +
273B ASP* 4.3 14.6 - - - +
274B GLY* 4.4 6.7 - - - +
298B SER* 3.2 22.4 + - - -
558B ARG* 2.8 45.2 + - - +
683B ARG* 2.9 49.1 + - - +
735B ALA* 1.3 75.9 - - - +
737B LEU* 1.3 65.3 + - - +
738B ARG* 3.4 13.2 + - - +
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Residues in contact with LEU 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B THR* 3.6 8.7 - - + +
531B PHE* 4.4 17.9 - - + -
558B ARG* 2.7 66.4 + - - +
559B GLU* 3.6 4.3 - - - +
560B ILE* 3.8 17.3 - - + +
582B PHE* 4.4 5.6 - - + -
583B GLU 3.5 2.9 - - - +
584B GLY* 3.8 6.5 - - - -
684B TRP* 3.5 37.9 - - + -
724B VAL* 5.3 2.2 - - + -
734B TRP* 3.4 33.2 - - + +
735B ALA 3.3 1.4 - - - -
736B ASN* 1.3 77.6 - - - +
738B ARG* 1.3 60.0 + - - +
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Residues in contact with ARG 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B VAL* 6.2 0.2 - - + -
529B THR* 3.4 10.7 - - - +
558B ARG* 3.2 25.6 - - - +
581B ASP 3.9 0.4 - - - +
582B PHE* 3.3 5.4 - - - -
583B GLU* 2.6 60.9 + - + +
683B ARG* 4.5 4.2 - - - +
736B ASN* 3.4 22.5 + - - +
737B LEU* 1.3 77.6 - - - +
739B TYR* 1.3 62.2 + - - +
740B ARG* 4.3 15.9 - - - +
1002B SO4 2.8 36.6 + - - -
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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