Contacts of the strand formed by residues 596 - 605 (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 TYR 596 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595B ASP* 1.3 78.1 - - - +
597B ALA* 1.3 60.9 + - - +
613B MET* 3.6 25.4 - - + -
614B TRP 3.7 1.1 - - - -
615B LYS* 3.5 42.0 - - + -
631B ALA* 2.9 18.9 - - + +
632B GLU 4.2 2.5 + - - -
636B GLN* 3.5 32.9 + - - -
655B TRP* 2.8 55.9 + + - -
657B THR* 4.2 0.5 + - - -
725B PHE* 4.1 6.7 - + + -
726B CYS* 3.5 3.9 - - - +
727B PHE* 3.1 46.2 + + + +
729B GLN* 3.6 10.6 - - - +
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Residues in contact with ALA 597 (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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586B PHE* 3.5 34.1 - - + -
588B VAL* 5.5 0.4 - - + -
595B ASP 3.9 0.4 + - - -
596B TYR* 1.3 74.8 - - - +
598B GLY* 1.3 58.5 + - - +
613B MET* 3.3 1.4 - - - -
614B TRP* 2.7 42.5 + - - +
676B TRP* 5.0 2.0 - - - +
725B PHE* 3.7 13.0 - - - +
726B CYS* 4.4 0.4 - - - +
729B GLN* 5.4 0.4 - - + -
732B ILE* 3.7 26.0 - - + -
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Residues in contact with GLY 598 (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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586B PHE* 5.6 2.0 - - - -
597B ALA* 1.3 77.2 - - - +
599B PHE* 1.3 63.7 + - - -
612B VAL* 2.8 17.5 - - - -
613B MET 4.8 0.2 - - - -
684B TRP* 6.0 0.4 - - - -
725B PHE* 3.0 26.3 + - - -
734B TRP* 2.7 30.5 + - - +
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Residues in contact with PHE 599 (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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582B PHE* 3.8 20.9 - + + -
598B GLY* 1.3 76.5 - - - +
600B ILE* 1.3 67.9 + - - +
601B PHE* 4.1 13.5 - + - -
611B VAL* 3.4 4.5 - - - +
612B VAL* 2.9 67.5 + - + +
684B TRP* 3.3 62.6 - + + -
686B LEU* 3.9 26.2 - - + -
697B VAL* 4.8 4.9 - - + -
699B PHE* 4.2 5.8 - + - -
723B GLY 3.4 12.8 - - - +
724B VAL* 4.0 4.3 - - + +
725B PHE 4.1 0.2 - - - +
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Residues in contact with ILE 600 (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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570B LEU* 2.8 46.0 - - + -
572B VAL* 4.6 4.9 - - + -
582B PHE* 4.3 2.8 - - - -
599B PHE* 1.3 80.7 - - - +
601B PHE* 1.3 66.9 + - - +
603B TYR* 4.0 30.3 - - + -
609B PHE* 4.1 13.2 - - + -
610B TYR 3.3 15.9 - - - +
611B VAL* 4.0 6.7 - - + -
722B LEU* 3.2 7.6 - - - +
723B GLY* 2.7 46.3 + - - +
724B VAL 4.4 2.5 - - - +
725B PHE* 3.7 13.7 - - + -
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Residues in contact with PHE 601 (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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580B VAL* 5.3 0.9 - - + -
599B PHE* 4.1 12.3 - + - -
600B ILE* 1.3 78.3 - - - +
602B GLY* 1.3 60.3 + - - +
603B TYR 3.2 2.5 + - - -
609B PHE* 4.0 0.3 - - - +
610B TYR* 2.7 65.7 + + + +
612B VAL* 4.4 2.2 - - + -
637B LEU* 4.0 18.2 - - + -
686B LEU* 3.3 39.3 - - + -
688B HIS* 3.5 29.2 - + - +
695B ILE* 3.6 42.6 - - + -
721B ARG 3.5 5.8 - - - -
722B LEU* 3.5 17.9 - - + -
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Residues in contact with GLY 602 (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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601B PHE* 1.3 76.5 - - - +
603B TYR* 1.3 64.7 + - - +
604B GLN* 3.2 0.9 + - - +
608B SER 3.4 2.6 - - - +
609B PHE* 3.4 2.4 - - - -
610B TYR* 4.4 9.0 - - - -
688B HIS* 4.6 7.7 + - - -
717B MET* 3.2 29.0 - - - +
719B GLY 3.6 20.2 - - - -
720B GLY* 3.8 10.3 + - - -
721B ARG 3.2 5.1 + - - -
722B LEU* 5.0 0.4 - - - +
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Residues in contact with TYR 603 (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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535B GLN* 4.3 6.3 + - - -
537B VAL* 3.1 24.9 - - + +
570B LEU* 3.7 20.0 - - + -
572B VAL* 3.7 22.2 - - + -
600B ILE* 4.0 12.1 - - + -
601B PHE 3.2 0.8 - - - -
602B GLY* 1.3 75.8 - - - +
604B GLN* 1.3 60.8 - - - +
605B ASP* 3.2 29.7 - - - -
606B SER* 2.9 19.5 + - - -
609B PHE* 3.6 30.7 - + + -
720B GLY* 3.3 5.0 - - - -
721B ARG* 2.8 71.2 + - - +
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Residues in contact with GLN 604 (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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424B ASP 5.4 1.6 - - - +
435B ASP* 5.2 0.5 - - - +
438B GLY 3.3 12.6 + - - +
439B ASP 3.1 23.8 + - - +
440B GLY* 3.5 30.3 + - - +
602B GLY 3.8 2.7 - - - +
603B TYR* 1.3 82.2 - - - +
605B ASP* 1.3 72.7 + - - +
608B SER* 3.0 14.8 + - - +
641B LYS* 4.2 7.4 + - - -
716B THR 4.4 1.0 - - - +
717B MET* 3.3 20.6 - - - +
718B ARG 3.5 8.9 - - - +
719B GLY 3.0 28.0 + - - +
720B GLY* 4.5 1.3 - - - -
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Residues in contact with ASP 605 (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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422B ASP 5.7 1.3 - - - +
423B HIS 4.8 1.8 - - - +
424B ASP* 4.5 28.9 - - + +
603B TYR* 3.2 23.2 - - - -
604B GLN* 1.3 82.4 - - - +
606B SER* 1.3 55.4 + - - +
607B SER* 2.7 44.2 + - - -
608B SER* 2.7 44.5 + - - +
609B PHE* 3.4 1.0 - - - -
641B LYS* 4.4 2.4 + - - -
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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