Contacts of the strand formed by residues 720 - 727 (chain C) 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 GLY 720 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454C SER* 3.2 11.0 + - - -
576C ALA* 3.7 2.9 - - - -
577C PHE* 3.1 36.1 + - - +
580C VAL* 5.6 1.7 - - - +
602C GLY* 3.7 7.4 + - - -
603C TYR 3.3 13.5 - - - -
604C GLN* 4.7 2.0 - - - -
688C HIS* 5.6 0.7 - - - -
719C GLY* 1.3 74.2 - - - -
721C ARG* 1.3 66.1 + - - -
722C LEU* 5.2 0.5 - - - +
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Residues in contact with ARG 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425C PHE* 5.1 7.7 - - - -
535C GLN* 2.6 30.5 + - - +
572C VAL* 3.4 29.2 + - + +
573C GLY 2.9 31.4 + - - +
574C TYR* 3.3 33.0 - - - +
575C THR 3.4 13.5 - - - +
576C ALA* 3.6 15.0 - - + -
577C PHE* 4.7 0.2 - - - -
600C ILE 3.8 0.3 - - - +
601C PHE* 3.5 2.4 - - - -
602C GLY 3.2 9.4 + - - -
603C TYR* 2.8 59.2 + - - +
604C GLN 5.3 2.2 + - - -
720C GLY* 1.3 73.9 - - - -
722C LEU* 1.3 64.0 + - - +
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Residues in contact with LEU 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C PHE* 3.3 17.1 - - + -
572C VAL* 3.5 5.6 - - - +
573C GLY* 2.8 25.1 + - - -
575C THR 4.0 4.4 + - - +
577C PHE* 3.6 24.5 - - + -
580C VAL* 4.0 15.7 - - + -
582C PHE* 3.5 36.1 - - + -
600C ILE* 3.2 1.6 - - - +
601C PHE* 3.6 25.6 - - + -
602C GLY 4.9 0.4 - - - +
686C LEU* 4.7 0.2 - - + -
720C GLY 5.5 0.4 - - - +
721C ARG* 1.3 78.9 - - - +
723C GLY* 1.3 59.4 + - - +
739C TYR* 3.5 37.7 - - + -
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Residues in contact with GLY 723 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C PHE* 4.3 10.0 - - - -
560C ILE* 6.0 0.2 - - - -
571C ALA 3.1 13.5 - - - -
572C VAL* 4.0 2.9 - - - -
582C PHE* 4.0 5.2 - - - -
599C PHE* 3.4 5.9 - - - +
600C ILE* 2.7 43.1 + - - +
722C LEU* 1.3 77.0 - - - +
724C VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 724 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C PHE* 6.3 0.7 - - + -
551C TRP* 3.8 24.0 - - + -
560C ILE* 3.8 28.9 - - + -
569C GLY 3.8 0.2 - - - +
570C LEU* 3.2 10.2 - - - +
571C ALA* 2.9 35.2 + - + +
582C PHE* 5.4 3.6 - - + -
598C GLY 3.6 4.3 - - - +
599C PHE* 4.1 3.6 - - + +
600C ILE* 4.1 2.5 - - - -
684C TRP* 4.9 4.3 - - + -
723C GLY* 1.3 79.9 - - - +
725C PHE* 1.3 61.5 + - - +
734C TRP* 3.4 45.1 - - + -
737C LEU* 5.7 1.6 - - + -
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Residues in contact with PHE 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C LEU* 3.8 16.2 - - + -
551C TRP* 4.7 0.4 - - - -
568C PRO* 4.8 1.1 - - + -
569C GLY 3.4 5.2 - - - -
570C LEU* 3.5 25.6 - - + -
596C TYR* 4.3 9.2 - - + -
597C ALA* 3.4 1.0 - - - -
598C GLY 2.7 43.4 + - - +
600C ILE* 3.9 12.3 - - + -
609C PHE* 5.5 1.6 - + - -
611C VAL* 3.9 15.7 - - + -
613C MET* 3.7 45.1 - - + -
654C LEU* 4.0 15.9 - - + -
724C VAL* 1.3 75.1 - - - +
726C CYS* 1.3 81.9 + - - +
727C PHE* 3.7 23.3 - + + -
734C TRP* 3.6 6.4 - - - -
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Residues in contact with CYS 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549C PRO* 4.5 1.6 - - - -
551C TRP* 3.7 26.7 - - - -
562C GLN* 3.9 23.3 - - - -
566C SER* 4.1 13.5 - - - -
568C PRO* 3.4 1.0 - - - +
569C GLY 3.1 29.1 + - - -
596C TYR 3.5 6.5 - - - +
725C PHE* 1.3 85.0 - - - +
727C PHE* 1.3 64.8 + - - +
729C GLN 4.6 2.9 - - - +
732C ILE* 3.5 26.0 - - + -
734C TRP* 4.6 1.1 - - + -
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Residues in contact with PHE 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C SER 4.8 1.6 - - - -
567C ASP* 4.8 1.8 - - - -
568C PRO* 3.5 41.7 - - + -
595C ASP* 3.5 1.2 - - - +
596C TYR* 3.2 36.1 + + + +
621C TYR* 3.9 23.6 - + - -
622C TRP* 5.6 0.9 - + - -
651C ARG* 3.5 37.0 - - + -
654C LEU* 4.7 2.7 - - + -
655C TRP* 3.6 45.4 - + + -
725C PHE* 3.7 19.5 - + + -
726C CYS* 1.3 80.3 - - - +
728C SER* 1.3 76.4 - - - +
729C GLN 3.3 0.4 - - - -
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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