Contacts of the strand formed by residues 608 - 615 (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 SER 608 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B GLY 3.4 2.3 - - - +
604B GLN* 3.0 30.0 + - - -
605B ASP* 2.7 32.1 + - - +
606B SER 3.7 0.2 - - - -
607B SER* 1.3 79.8 - - - +
609B PHE* 1.3 61.7 + - - +
640B VAL 3.1 5.8 - - - -
641B LYS* 2.7 39.1 + - - -
717B MET* 3.5 12.2 - - - +
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Residues in contact with PHE 609 (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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539B LEU* 4.1 18.8 - - + -
570B LEU* 4.1 13.2 - - + -
600B ILE* 4.1 14.4 - - + -
601B PHE 4.0 1.8 - - - +
602B GLY 3.4 8.7 - - - -
603B TYR* 3.6 30.3 - + + -
605B ASP 3.4 16.6 - - - -
606B SER 3.5 24.2 - - - -
608B SER* 1.3 72.4 - - - +
610B TYR* 1.3 59.7 + - - +
611B VAL* 3.3 31.4 - - + -
640B VAL* 2.6 66.4 + - + +
650B LEU* 5.2 0.9 - - + -
654B LEU* 4.6 7.2 - - + -
717B MET* 3.5 10.4 - - - +
725B PHE* 5.9 0.7 - + - -
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Residues in contact with TYR 610 (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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600B ILE* 3.3 11.4 - - - +
601B PHE* 2.7 74.4 + + + +
602B GLY* 4.4 2.0 - - - -
609B PHE* 1.3 74.5 - - - +
611B VAL* 1.3 61.1 + - - +
637B LEU* 4.7 1.1 - - + -
638B LYS 3.4 4.0 - - - +
639B ALA* 3.4 28.3 - - + -
667B LEU* 4.0 4.9 - - + -
688B HIS* 4.5 3.8 - - - -
695B ILE* 3.7 24.2 - - + -
714B ASP* 2.6 32.2 + - - -
715B THR 3.6 4.5 + - - -
716B THR* 2.8 18.9 + - - -
717B MET* 2.9 44.2 + - + -
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Residues in contact with VAL 611 (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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599B PHE 3.4 9.4 - - - +
600B ILE* 4.0 3.4 - - + -
601B PHE* 5.1 1.1 - - - -
609B PHE* 3.3 35.4 - - + -
610B TYR* 1.3 74.9 - - - +
612B VAL* 1.3 79.0 + - - +
613B MET* 3.9 13.6 + - + +
636B GLN 3.7 0.3 - - - +
637B LEU* 3.6 5.1 - - - +
638B LYS* 2.8 37.3 + - + +
640B VAL* 3.7 13.9 - - + -
654B LEU* 4.5 7.2 - - + -
725B PHE* 3.8 29.4 - - + -
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Residues in contact with VAL 612 (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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598B GLY* 2.8 27.0 - - - -
599B PHE* 2.9 48.6 + - + +
601B PHE* 4.4 2.2 - - + -
611B VAL* 1.3 77.9 - - - +
613B MET* 1.3 59.7 + - - +
614B TRP* 6.0 0.4 - - + -
635B ILE* 3.4 32.1 - - + -
636B GLN 3.2 4.7 - - - +
637B LEU* 3.3 28.0 - - + -
668B TRP* 5.6 0.2 - - + -
697B VAL* 4.4 7.0 - - + -
699B PHE* 3.6 17.7 - - + -
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Residues in contact with MET 613 (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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596B TYR* 3.6 17.9 - - + -
597B ALA 3.3 5.2 - - - -
598B GLY* 4.8 0.2 - - - -
611B VAL* 3.9 11.6 + - + -
612B VAL* 1.3 75.5 - - - +
614B TRP* 1.3 66.1 + - - +
635B ILE* 3.5 6.9 - - - +
636B GLN* 3.0 51.1 + - + +
638B LYS* 3.8 16.4 - - + -
654B LEU* 3.3 55.9 - - + +
725B PHE* 3.1 38.8 - - + -
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Residues in contact with TRP 614 (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* 3.2 31.2 - + + -
595B ASP 3.4 0.2 - - - +
596B TYR* 3.8 3.1 - - - -
597B ALA* 2.7 28.4 + - - +
612B VAL* 6.0 0.4 - - + -
613B MET* 1.3 78.0 - - - +
615B LYS* 1.3 77.4 + - - +
634B GLY* 3.4 15.6 - - - +
635B ILE* 3.4 37.7 - - + +
636B GLN* 5.6 0.4 - - - +
672B ARG* 4.6 11.7 - - - -
674B VAL* 2.7 29.8 + - + -
675B GLY* 3.5 7.2 - - - -
676B TRP* 2.8 38.9 + + + -
682B TYR* 3.5 52.3 - + + -
699B PHE* 4.7 11.2 - + + -
706B VAL* 5.6 2.2 - - + -
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Residues in contact with LYS 615 (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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594B ASP* 2.7 24.8 + - - +
595B ASP* 2.8 31.0 + - - -
596B TYR* 3.5 44.2 - - + -
614B TRP* 1.3 93.0 - - - +
616B GLN* 1.3 64.3 + - - +
617B MET 2.9 28.5 + - - +
619B GLN* 3.0 18.5 + - - -
631B ALA* 4.1 5.8 - - + -
632B GLU 3.9 13.7 + - - +
633B PRO* 3.7 5.6 - - - +
634B GLY 4.8 2.0 + - - +
636B GLN* 5.6 0.2 - - - +
655B TRP* 3.4 23.1 - - - -
675B GLY* 3.3 8.3 - - - -
676B TRP* 3.6 2.2 - - - -
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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